@article {164791, title = {Emerging strategies for computational identification of protein-protein interaction hotspots.}, journal = {Curr Opin Struct Biol}, volume = {98}, year = {2026}, month = {2026 Mar 10}, pages = {103241}, abstract = {

A small number of residues at protein-protein interfaces, commonly referred to as hotspots, dominate binding free energy and play a decisive role in stabilizing protein complexes. Identifying these residues is central to understanding the energetic architecture of protein-protein interactions and to developing strategies for therapeutic intervention. Although experimental approaches such as alanine scanning have provided critical insights, they are often impractical for large or dynamic systems. This has positioned computational approaches at the forefront of hotspot analysis. This review highlights recent developments in molecular dynamics simulations and machine-learning-based predictors for hotspot identification, discusses current challenges, and outlines emerging directions in the field. Finally, we suggest that combining these complementary approaches could offer a powerful framework for capturing the dynamic and energetic complexity of protein interfaces, making hotspot predictions more robust and interpretable.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2026.103241}, url = {https://www.sciencedirect.com/science/article/pii/S0959440X26000230?via\%3Dihub}, author = {Pathak, Aditi and Tiwari, Vikas and Sowdhamini, Ramanathan} } @article {152899, title = {The alteration of structural network upon transient association between proteins studied using graph theory.}, journal = {Proteins}, volume = {93}, year = {2025}, month = {2025 Jan}, pages = {217-225}, abstract = {

Proteins such as enzymes perform their function by predominant non-covalent bond interactions between transiently interacting units. There is an impact on the overall structural topology of the protein, albeit transient nature of such interactions, that enable proteins to deactivate or activate. This aspect of the alteration of the structural topology is studied by employing protein structural networks, which are node-edge representative models of protein structure, reported as a robust tool for capturing interactions between residues. Several methods have been optimized to collect meaningful, functionally relevant information by studying alteration of structural networks. In this article, different methods of comparing protein structural networks are employed, along with spectral decomposition of graphs to study the subtle impact of protein-protein interactions. A detailed analysis of the structural network of interacting partners is performed across a dataset of around 900 pairs of bound complexes and corresponding unbound protein structures. The variation in network parameters at, around, and far away from the interface are analyzed. Finally, we present interesting case studies, where an allosteric mechanism of structural impact is understood from communication-path detection methods. The results of this analysis are beneficial in understanding protein stability, for future engineering, and docking studies.

}, keywords = {Algorithms, Allosteric Regulation, Databases, Protein, Models, Molecular, Protein Binding, Protein Conformation, Protein Interaction Mapping, Protein Interaction Maps, Proteins}, issn = {1097-0134}, doi = {10.1002/prot.26606}, author = {Prabantu, Vasam Manjveekar and Tandon, Himani and Sandhya, Sankaran and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {152167, title = {Comparative analysis of permanent and transient domain-domain interactions in multi-domain proteins.}, journal = {Proteins}, volume = {93}, year = {2025}, month = {2025 Jan}, pages = {197-208}, abstract = {

Protein domains are structural, functional, and evolutionary units. These domains bring out the diversity of functionality by means of interactions with other co-existing domains and provide stability. Hence, it is important to study intra-protein inter-domain interactions from the perspective of types of interactions. Domains within a chain could interact over short timeframes or permanently, rather like protein-protein interactions (PPIs). However, no systematic study has been carried out between two classes, namely permanent and transient domain-domain interactions. In this work, we studied 263 two-domain proteins, belonging to either of these classes and their interfaces on the basis of several factors, such as interface area and details of interactions (number, strength, and types of interactions). We also characterized them based on residue conservation at the interface, correlation of residue motions across domains, its involvement in repeat formation, and their involvement in particular molecular processes. Finally, we could analyze the interactions arising from domains in two-domain monomeric proteins, and we observed significant differences between these two classes of domain interactions and a few similarities. This study will help to obtain a better understanding of structure-function and folding principles of multi-domain proteins.

}, keywords = {Binding Sites, Databases, Protein, Humans, Models, Molecular, Protein Binding, Protein Domains, Protein Folding, Protein Interaction Domains and Motifs, Protein Interaction Mapping, Proteins}, issn = {1097-0134}, doi = {10.1002/prot.26581}, author = {Sidhanta, Swayam Prakash Das and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {162679, title = {Computational Analyses of Bifurcated Inter-Protein Interactions in Protein-Protein Assemblies Reveal Their Pivotal Role in Conferring Stability.}, journal = {Proteins}, year = {2025}, month = {2025 Nov 28}, abstract = {

Majority of the proteome is constituted by oligomers and their function is governed by underlying protein-protein interactions. Interfacial residues, namely residues right at the interface of two protein chains, are known to confer stability and specificity in dimers. However, other interactions play a significant role in the formation and maintenance of oligomers in protein assemblies as well. Inter-protein bifurcated interactions are those where one residue simultaneously interacts with two residues belonging to two neighboring protein chains. The characteristic features of such higher-order interactions remain largely unexplored and unknown. In this study, we focused on residues specifically involved in bifurcated interactions (referred as RBI). We examine the bifurcated inter-protein interactions by assembling a dataset of protein assemblies of known 3D structures. We have characterized the type of interactions and the residues involved in the interactions using parameters like energy contributions and conservation scores. We find that the residues participating in bifurcated inter-protein interactions contribute more to the stability of the complex than other interfacial residues. Furthermore, we have presented examples where mutation of a residue involved in a bifurcated interaction results in detrimental outcomes. This study highlights the significance of inter-protein bifurcated interactions that contribute to the stability of multiple interfaces in protein oligomers and hence contribute to the expansion of the understanding of protein assemblies.

}, issn = {1097-0134}, doi = {10.1002/prot.70090}, author = {Bheemireddy, Sneha and Menon, Revathy and Chavali, Sreenivas and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {153398, title = {Computational analysis of the effect of a binding protein (RbpA) on the dynamics of Mycobacterium tuberculosis RNA polymerase assembly.}, journal = {PLoS One}, volume = {20}, year = {2025}, month = {2025}, pages = {e0317187}, abstract = {

BACKGROUND: RNA polymerase-binding protein A (RbpA) is an actinomycetes-specific protein crucial for the growth and survival of the pathogen Mycobacterium tuberculosis. Its role is essential and influences the transcription and antibiotic responses. However, the regulatory mechanisms underlying RbpA-mediated transcription remain unknown. In this study, we employed various computational techniques to investigate the role of RbpA in the formation and dynamics of the RNA polymerase complex.

RESULTS: Our analysis reveals significant structural rearrangements in RNA polymerase happen upon interaction with RbpA. Hotspot residues, crucial amino acids in the RbpA-mediated transcriptional regulation, were identified through our examination. The study elucidates the dynamic behavior within the complex, providing insights into the flexibility and functional dynamics of the RbpA-RNA polymerase interaction. Notably, potential allosteric mechanisms, involving the interface of subunits α1 and α2 were uncovered, shedding light on how RbpA modulates transcriptional activity.

CONCLUSIONS: Finally, potential ligands meant for the α1-α2 binding site were identified through virtual screening. The outcomes of our computational study serve as a foundation for experimental investigations into inhibitors targeting the RbpA-regulated dynamics in RNA polymerase. Overall, this research contributes valuable information for understanding the intricate regulatory networks of RbpA in the context of transcription and suggests potential avenues for the development of RbpA-targeted therapeutics.

}, keywords = {Bacterial Proteins, Binding Sites, DNA-Directed RNA Polymerases, Molecular Dynamics Simulation, Mycobacterium tuberculosis, Protein Binding, Transcription, Genetic}, issn = {1932-6203}, doi = {10.1371/journal.pone.0317187}, url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0317187}, author = {Bheemireddy, Sneha and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {161125, title = {Computational structural analysis sheds light on the molecular grammar of gap junction proteins.}, journal = {Biochimie}, year = {2025}, month = {2025 Oct 06}, abstract = {

Gap junctions are multimeric intercellular channels that permit ions and small molecules to pass directly from one cell to another. Despite being fundamental to multicellular life, these channels are formed by distantly related protein families: innexins in invertebrates and connexins in vertebrates. Vertebrates also express pannexins, distant homologues of primordial innexins, which only form hemichannels. While these families have diverse sequences and different oligomeric states, their monomeric structures are highly similar. We generated structure-guided sequence alignments to establish equivalent residues across innexins, connexins, and pannexins. Further, computational approaches for determining protein-protein interaction hotspots, residue conservation, accessible surface area and local conformations of residues, provide insights into the relationships between residue positions and channel properties. We find that exposed transmembrane residues of TM1 and TM2 are more conserved than those in TM3 and TM4, especially in connexins and pannexins. Moreover, we see that residues in the extracellular extended hairpins of pannexins show more conformational flexibility, in variable protein blocks, than equivalent residues in connexins. This hints that the rigidity of this element could be a prerequisite for hemichannel docking. Finally, we identify inter- and intra-hemichannel interface hotspots that are positionally conserved across the families, implying their role in hemichannel and, ultimately, gap junction formation. Such analyses reveal a molecular grammar that underlies gap junction design and offer a basis for targeted perturbation of channel properties.

}, issn = {1638-6183}, doi = {10.1016/j.biochi.2025.10.001}, author = {Pathak, Aditi and Sowdhamini, Ramanathan} } @article {160476, title = {Exploration of structural space of Cus17 lectin with glycans using molecular docking and simulation studies.}, journal = {Comput Struct Biotechnol J}, volume = {27}, year = {2025}, month = {2025}, pages = {3319-3327}, abstract = {

The Cus17 phloem protein, in the case of species, plays an important role in the phloem-based defense of the plant. Cus17 can bind to various carbohydrates present on insect exoskeletons or fungal cells. The recent experimental structure of chitotriose bound Cus17 elucidates the carbohydrate interacting residues of Cus17. Higher chito-oligosaccharides are also known to interact with Cus17, but the lack of experimental structure impedes our understanding of their interaction. In this study, we have employed methods to explore the binding interactions of higher chito-oligosaccharides with Cus17. Chitoheptaose forms stable interactions with canonical binding site residues Trp48 and Asp50. Smaller chito-oligosaccharides were observed to be relatively unstable at the canonical binding site of Cus17. Further, the chito-oligosaccharides were inspected for interactions with predicted ligand binding sites. We also generated different tetramers of Cus17 and docked the chito-oligosaccharides to the tetrameric Cus17. All chito-oligosaccharides were found to make persistent interactions with Cus17 tetramer. Interestingly, chitotriose shows the best binding affinity and maintains stable interactions with Cus17 tetramer upon extended simulations with the canonical site.

}, keywords = {Non-canonical binding; Oligosaccharides; Protein-ligand interactions}, issn = {2001-0370}, doi = {10.1016/j.csbj.2025.07.028}, author = {Tiwari, Vikas and Pathak, Aditi and Poojary, Tejaswini and Sowdhamini, Ramanathan and Surolia, Avadhesha} } @article {157482, title = {GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database.}, journal = {Database (Oxford)}, volume = {2025}, year = {2025}, month = {2025 May 09}, abstract = {

Despite the vast amount of sequence data available, a significant disparity exists between the number of protein sequences identified and the relatively few structures that have been resolved. This disparity highlights the challenge in structural biology to bridge the gap between sequence information and 3D structural data, and the necessity for robust databases capable of linking distant homologs to known structures. Studies have indicated that there are a limited number of structural folds, despite the vast diversity of proteins. Hence, computational tools can enhance our ability to classify protein sequences, much before their structures are determined or their functions are characterized, thereby bridging the gap between sequence and structural data. GenDiS (Genomic Distribution of Superfamilies) is a repository with information on the genomic distribution of protein domain superfamilies, involving a one-time computational exercise to search for trusted homologs of protein domains of known structures against the vast sequence database. We have updated this database employing advanced bioinformatics tools, including DELTA-BLAST (domain enhanced lookup time accelerated BLAST) for initial detection of hits and HMMSCAN for validation, significantly improving the accuracy of domain identification. Using these tools, over 151 million sequence homologs for 2060 superfamilies [SCOPe (Structural Classification of Proteins extended)] were identified and 116 million out of them were validated as true positives. Through a case study on glycolysis-related enzymes, variations in domain architectures of these enzymes are explored, revealing evolutionary changes and functional diversity among these essential proteins. We present another case, LOG gene, where one can tune in and find significant mutations across the evolutionary lineage. The GenDiS database, GenDiS3, and the associated tools made available at https://caps.ncbs.res.in/gendis3/ offer a powerful resource for researchers in functional annotation and evolutionary studies. Database URL: https://caps.ncbs.res.in/gendis3/.

}, keywords = {Computational Biology, Databases, Protein, Protein Domains, Proteins}, issn = {1758-0463}, doi = {10.1093/database/baaf035}, url = {https://academic.oup.com/database/article/doi/10.1093/database/baaf035/8127847?login=true}, author = {Joshi, Sarthak and Mohapatra, Shailendu and Kumar, Dhwani and Joshi, Adwait and Iyer, Meenakshi and Sowdhamini, Ramanathan} } @article {159715, title = {Using protein blocks to build custom fragment libraries from protein structures.}, journal = {Biochimie}, year = {2025}, month = {2025 Aug 13}, abstract = {

The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous proteins but also in the recurrence of supersecondary motifs across unrelated proteins, underscoring the abundance and robustness of these structural units. Here, we present a novel pipeline for generating customized protein fragment libraries using protein blocks (PBs)-a structural alphabet that encodes local backbone conformations. Our method efficiently extracts structurally similar fragments from a curated, non-redundant protein structure database by converting three-dimensional structures into one-dimensional PB sequences. By integrating predicted PB sequences with the PB-ALIGN and PB-kPRED tools, our approach identifies relevant fragments independently of sequence homology. Fragment quality is further assessed using a new scoring function that combines secondary structure similarity and PB alignment metrics. The resulting libraries contain fragments of at least seven PBs (11 amino acid residues), covering over 70 \% of the local backbone structure. Our results demonstrate that PBs enable efficient mining of high-quality structural fragments from diverse protein spaces, including proteins with disordered regions. The pipeline is accessible as an online tool (PB-Frag, http://pbpred-us2b.univ-nantes.fr/pbfrag).

}, issn = {1638-6183}, doi = {10.1016/j.biochi.2025.08.011}, author = {Dhingra, Surbhi and T{\'e}letch{\'e}a, St{\'e}phane and Sowdhamini, Ramanathan and Sanejouand, Yves-Henri and de Brevern, Alexandre G and Cadet, Fr{\'e}d{\'e}ric and Offmann, Bernard} } @article {149369, title = {Computational analysis of human gut microbial prolyl oligopeptidases (POPs) reveal candidate genes as therapeutics for celiac disease.}, journal = {Sci Rep}, volume = {14}, year = {2024}, month = {2024 Aug 23}, pages = {19641}, abstract = {

Celiac disease (CD) is a common autoimmune disorder in which the patients are unable to digest gluten, which is present in foods made up of wheat, barley and rye. Whilst diagnosis happens late in 80\% of the cases, avoidance of such foods appears to be the common solution. Alternative management strategies are required for the patients and their families since CD is also genetically carried over. Probiotic therapeutics and the consumption of appropriate enzymes, such as prolyloligopeptidases (POPs), from gut-friendly bacteria could reduce the disease burden and provide a better lifestyle for CD patients. We have examined around 5000 gut bacterial genomes and identified nearly 4000 non-redundant putative POPs. A select set of 10 gut bacterial POP sequences were subject to three-dimensional modelling, ligand docking and molecular dynamics simulations where stable interactions were observed between the POPs and gluten peptides. Our study provides sequence and structural analysis of potential POP enzymes in gut bacterial genomes, which form a strong basis to offer probiotic solutions to CD patients. In particular, these enzymes could be lead future therapeutics for this disease.

}, keywords = {Bacteria, Celiac Disease, Computational Biology, Gastrointestinal Microbiome, Glutens, Humans, Molecular Docking Simulation, Molecular Dynamics Simulation, Probiotics, Prolyl Oligopeptidases, Serine Endopeptidases}, issn = {2045-2322}, doi = {10.1038/s41598-024-70079-1}, author = {Nayak, Soumya and Regati, Dheemanth Reddy and Sowdhamini, Ramanathan} } @article {147302, title = {Computational Analysis of the Accumulation of Mutations in Therapeutically Important RNA Viral Proteins During Pandemics with Special Emphasis on SARS-CoV-2.}, journal = {J Mol Biol}, volume = {436}, year = {2024}, month = {2024 Jul 22}, pages = {168716}, abstract = {

Single stranded RNA viruses are primary causative agents for pandemics, causing extensive morbidity and mortality worldwide. A pivotal question in pandemic preparedness and therapeutic intervention is what are the specific mutations which are more likely to emerge during such global health crises? This study aims to identify markers for mutations with the highest probability of emergence in these pandemics, focusing on the SARS-CoV-2 spike protein, an essential and therapeutically significant viral protein, starting from sequence information from the onset of the pandemic until July 2022. Quite consistently, we observed that emerged mutations tended to demonstrate a high genetic score, which reflects high similarity of the type of codon required for translation between an amino acid and to the mutated one. Further, this pattern is also observed in therapeutically significant proteins of other ssRNA pandemic viruses, including influenza (HA, NA), spike proteins of Ebola, envelope of Dengue and Chikungunya. We propose that the genetic score serves as an initial indicator, preceding the actual impact of the mutation on viral fitness. Finally, we developed a comprehensive computational pipeline to further explore and predict the subsequent effects of mutations on viral fitness. We believe that our pipeline can narrow down and predict future mutations in therapeutically important viral proteins during a pandemic.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2024.168716}, author = {Sharma, Abhishek and Chandrashekar, C R and Krishna, Sudhir and Sowdhamini, Ramanathan} } @article {136530, title = {Interfacial residues in protein-protein complexes are in the eyes of the beholder.}, journal = {Proteins}, year = {2024}, month = {2023 Nov 19}, abstract = {

Interactions between proteins are vital in almost all biological processes. The characterization of protein-protein interactions helps us understand the mechanistic basis of biological processes, thereby enabling the manipulation of proteins for biotechnological and clinical purposes. The interface residues of a protein-protein complex are assumed to have the following two properties: (a) they always interact with a residue of a partner protein, which forms the basis for distance-based interface residue identification methods, and (b) they are solvent-exposed in the isolated form of the protein and become buried in the complex form, which forms the basis for Accessible Surface Area (ASA)-based methods. The study interrogates this popular assumption by recognizing interface residues in protein-protein complexes through these two methods. The results show that a few residues are identified uniquely by each method, and the extent of conservation, propensities, and their contribution to the stability of protein-protein interaction varies substantially between these residues. The case study analyses showed that interface residues, unique to distance, participate in crucial interactions that hold the proteins together, whereas the interface residues unique to the ASA method have a potential role in the recognition, dynamics, and specificity of the complex and can also be a hotspot. Overall, the study recommends applying both distance and ASA methods so that some interface residues missed by either method but crucial to the stability, recognition, dynamics, and function of protein-protein complexes are identified in a complementary manner.

}, issn = {1097-0134}, doi = {10.1002/prot.26628}, author = {Parvathy, Jayadevan and Yazhini, Arangasamy and Srinivasan, Narayanaswamy and Sowdhamini, Ramanathan} } @article {144804, title = {Normal Mode Analysis Elicits Conformational Shifts in Proteins at Both Proximal and Distal Regions to the Phosphosite Stemming from Single-Site Phosphorylation.}, journal = {ACS Omega}, volume = {9}, year = {2024}, month = {2024 Jun 11}, pages = {24520-24537}, abstract = {

Phosphorylation, a fundamental biochemical switch, intricately regulates protein function and signaling pathways. Our study employs extensive computational structural analyses on a curated data set of phosphorylated and unphosphorylated protein pairs to explore the multifaceted impact of phosphorylation on protein conformation. Using normal mode analysis (NMA), we investigated changes in protein flexibility post-phosphorylation, highlighting an enhanced level of structural dynamism. Our findings reveal that phosphorylation induces not only local changes at the phosphorylation site but also extensive alterations in distant regions, showcasing its far-reaching influence on protein structure-dynamics. Through in-depth case studies on polyubiquitin B and glycogen synthase kinase-3 beta, we elucidate how phosphorylation at distinct sites leads to variable structural and dynamic modifications, potentially dictating functional outcomes. While phosphorylation largely preserves the residue motion correlation, it significantly disrupts low-frequency global modes, presenting a dualistic impact on protein dynamics. We also explored alterations in the total accessible surface area (ASA), emphasizing region-specific changes around phosphorylation sites. This study sheds light on phosphorylation-induced conformational changes, dynamic modulation, and surface accessibility alterations, leveraging an integrated computational approach with RMSD, NMA, and ASA, thereby contributing to a comprehensive understanding of cellular regulation and suggesting promising avenues for therapeutic interventions.

}, issn = {2470-1343}, doi = {10.1021/acsomega.4c00523}, author = {Subhadarshini, Seemadri and Tandon, Himani and Srinivasan, Narayanaswamy and Sowdhamini, Ramanathan} } @article {149371, title = {Sensing volatiles throughout the body: geographic- and tissue-specific olfactory receptor expression in the fig wasp.}, journal = {Insect Sci}, year = {2024}, month = {2024 Aug 25}, abstract = {

An essential adaptive strategy in insects is the evolution of olfactory receptors (ORs) to recognize important volatile environmental chemical cues. Our model species, Ceratosolen fusciceps, a specialist wasp pollinator of Ficus racemosa, likely possesses an OR repertoire that allows it to distinguish fig-specific volatiles in highly variable environments. Using a newly assembled genome-guided transcriptome, we annotated 63 ORs in the species and reconstructed the phylogeny of Ceratosolen ORs in conjunction with other hymenopteran species. Expression analysis showed that though ORs were mainly expressed in the female antennae, 20\% were also expressed in nonantennal tissues such as the head, thorax, abdomen, legs, wings, and ovipositor. Specific upregulated expression was observed in OR30C in the head and OR60C in the wings. We identified OR expression from all major body parts of female C. fusciceps, suggesting novel roles of ORs throughout the body. Further examination of the OR expression of C. fusciceps in widely separated geographical locations, that is, South (urban) and Northeast (rural) India, revealed distinct OR expression levels in different locations. This discrepancy likely parallels the observed variation in fig volatiles between these regions and provides new insights into the evolution of insect ORs and their expression across geographical locations and tissues.

}, issn = {1744-7917}, doi = {10.1111/1744-7917.13441}, author = {Krishnan, Sushma and Karpe, Snehal Dilip and Kumar, Hithesh and Nongbri, Lucy B and Venkateswaran, Vignesh and Sowdhamini, Ramanathan and Grosse-Wilde, Ewald and Hansson, Bill S and Borges, Renee M} } @article {144788, title = {Structural insights into the role of deleterious mutations at the dimeric interface of Toll-like receptor interferon-β related adaptor protein.}, journal = {Proteins}, year = {2024}, month = {2024 May 30}, abstract = {

Toll-like receptors (TLRs) are major players in the innate immune system-recognizing pathogens and differentiating self/non-self components of immunity. These proteins are present either on the plasma membrane or endosome and recognize pathogens at their extracellular domains. They are characterized by a single transmembrane helix and an intracellular toll-interleukin-1 receptor (TIR) domain. Few TIRs directly invoke downstream signaling, while others require other TIR domains of adaptors like TIR domain-containing adaptor-inducing interferon-β (TRIF) and TRIF-related adaptor molecule (TRAM). On recognizing pathogenic lipopolysaccharides, TLR4 dimerises and interacts with the intracellular TRAM dimer through the TIR domain to recruit a downstream signaling adaptor (TRIF). We have performed an in-depth study of the structural effect of two mutations (P116H and C117H) at the dimeric interface of the adaptor TRAM, which are known to abrogate downstream signaling. We modeled the structure and performed molecular dynamics studies in order to decipher the structural basis of this effect. We observed that these mutations led to an increased radius of gyration of the complex and resulted in several changes to the interaction energy values when compared against the wild type (WT) and positive control mutants. We identified highly interacting residues as hubs in the WT dimer, and a few such hubs that were lost in the mutant dimers. Changes in the protein residue path, hampering the information flow between the crucial A86/E87/D88/D89 and T155/S156 sites, were observed for the mutants. Overall, we show that such residue changes can have subtle but long-distance effects, impacting the signaling path allosterically.

}, issn = {1097-0134}, doi = {10.1002/prot.26707}, author = {Verma, Shailya and Menon, Revathy and Sowdhamini, Ramanathan} } @article {153395, title = {Toll-like receptor 4 pathway evolutionary trajectory and functional emergence.}, journal = {Frontiers in Immunology}, volume = {15}, year = {2024}, month = {2024}, pages = {1494017}, abstract = {

INTRODUCTION: Toll-like receptors 4 (TLR4) recognize lipopolysaccharides (LPS) from bacteria as their conventional ligands and undergo downstream signaling to produce cytokines. They mediate the signaling either by the TIRAP-MyD88 complex or by the TRAM-TRIF complex. The MyD88 pathway is common to all other TLRs, whereas the TRAM-TRIF complex is largely exclusive to TLR4. Here we study the TIR domain of TRAM and TRIF ortholog proteins that are crucial for downstream signaling. Our previous work on pan-genome-wide survey, indicates to be the ancestral organism with both TRAM and TRIF proteins.

METHODS: To gain a deeper insight into the protein function and to compare them with adaptor proteins, we modeled the docking of the TRAM-TRIF complex of representative organisms across various taxa. These modeling experiments provide insights to ascertain a possible interaction surface and calculate the energetics and electrostatic potential of the complex. Furthermore, this enables us to employ normal mode analysis (NMA) to examine fluctuating, interacting, and other specific residue clusters that could have a role in protein functioning in both and . We also performed molecular dynamics simulations of these complexes and cross-validated the functionally important residues using network parameters.

RESULTS: We compared the stoichiometry of TRAM-TRIF complexes and found that the tetrameric models (TRAM and TRIF dimer) were more stable than the trimeric model (TRAM dimer and TRIF monomer). While the critical residues of TIRAP, TRIF, and MyD88 were preserved, we also found that the important residues of TRAM signaling were not conserved in .

DISCUSSION: This suggests the presence of functional TIRAP-MyD88-mediated TLR4 signaling and TRIF-mediated TLR3 signaling in the ancestral species. The overall biological function of this signaling domain appears to be gradually acquired through the orchestration of several motifs through an evolutionary scale.

}, keywords = {Adaptor Proteins, Vesicular Transport, Animals, Evolution, Molecular, Humans, Membrane Glycoproteins, Molecular Docking Simulation, Myeloid Differentiation Factor 88, Protein Binding, Receptors, Interleukin-1, Signal Transduction, Toll-Like Receptor 4}, issn = {1664-3224}, doi = {10.3389/fimmu.2024.1494017}, url = {https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1494017/full}, author = {Verma, Shailya and Sowdhamini, Ramanathan} } @article {149387, title = {Transcriptional regulation of hormone signalling genes in black pepper in response to Phytophthora capsici.}, journal = {BMC Genomics}, volume = {25}, year = {2024}, month = {2024 Sep 30}, pages = {910}, abstract = {

INTRODUCTION: Black pepper (Piper nigrum L.) is a non-model spice crop of significant agricultural and biological importance. The {\textquoteright}quick wilt{\textquoteright} disease caused by the oomycete Phytophthora capsici is a major threat, leading to substantial crop loss. The molecular mechanisms governing the plant immune responses to this pathogen remain unclear. This study employs RNA sequencing and transcriptome analysis to explore the defense mechanisms of P. nigrum against P. capsici.

RESULTS: Two-month-old P. nigrum plantlets were subjected to infection with P. capsici, and leaf samples were collected at 6- and 12-hours post-inoculation. RNA was extracted, sequenced, and the resulting data were processed and assembled. Differential gene expression analysis was conducted to identify genes responding to the infection. Additionally, the study investigated the involvement of Salicylic acid (SA), Jasmonic acid (JA), and Ethylene (ET) signalling pathways. Our transcriptome assembly comprised 64,667 transcripts with 96.7\% completeness, providing valuable insights into the P. nigrum transcriptome. Annotation of these transcripts identified functional categories and domains, provided details on molecular processes. Gene expression analysis identified 4,714 transcripts at 6\ h post-infection (hpi) and 9,416 at 12 hpi as differentially expressed, revealing dynamic regulation of immune-related genes. Furthermore, the study investigated key genes involved in biosynthesis pathways of Salicylic acid, Jasmonic acid, and Ethylene signalling. Notably, we found differential regulation of critical genes associated with these pathways while comparing data before and after infection, thereby shedding light on their roles in defense mechanism in P. nigrum defense.

CONCLUSIONS: This comprehensive transcriptome analysis of P. nigrum response to P. capsici attack provides valuable insights into the plant defense mechanisms. The dynamic regulation of innate immunity and the involvement of key signalling pathways highlight the complexity of the plant-pathogen interaction. This study contributes to our understanding of plant immunity and offers potential strategies for enhancing P. nigrum resistance to this harmful pathogen.

}, keywords = {Cyclopentanes, Disease Resistance, Gene Expression Profiling, Gene Expression Regulation, Plant, Oxylipins, Phytophthora, Piper nigrum, Plant Diseases, Plant Growth Regulators, Signal Transduction, Transcriptome}, issn = {1471-2164}, doi = {10.1186/s12864-024-10802-4}, author = {Mahadevan, Chidambareswaren and Shafi, K Mohamed and Nagarathnam, B and Sakuntala, Manjula and Sowdhamini, Ramanathan} } @article {124446, title = {Bioinformatics analysis of mutations sheds light on the evolution of Dengue NS1 protein with implications in the identification of potential functional and druggable sites.}, journal = {Mol Biol Evol}, year = {2023}, month = {2023 Feb 16}, abstract = {

Non-structural protein (NS1) is a 350 amino acid long conserved protein in the dengue virus. Conservation of NS1 is expected due to its importance in dengue pathogenesis. The protein is known to exist in dimeric and hexameric states. The dimeric state is involved in its interaction with host proteins and viral replication, whereas the hexameric state is involved in viral invasion. In this work, we performed extensive structure and sequence analysis of NS1 protein, and uncovered the role of NS1 quaternary states in its evolution. A three-dimensional modeling of unresolved loop regions in NS1 structure is performed. {\textquoteright}Conserved{\textquoteright} and {\textquoteright}Variable{\textquoteright} regions within NS1 protein were identified from sequences obtained from patient samples and the role of compensatory mutations in selecting destabilizing mutations was identified. Molecular dynamics (MD) simulations were performed to extensively study the effect of a few mutations on NS1 structure stability and study compensatory mutations. Virtual saturation mutagenesis, predicting the effect of every individual amino acid substitution on NS1 stability sequentially, revealed virtual-conserved and variable sites. The increase in number of observed and virtual conserved regions across NS1 quaternary states suggests the role of higher order structure formation in its evolutionary conservation. Our sequence and structure analysis could enable in identifying possible protein-protein interfaces and druggable sites. Virtual screening of nearly 10,000 small molecules, including FDA-approved drugs, permitted us to recognize six drug-like molecules targeting the dimeric sites. These molecules could be promising due to their stable interactions with NS1 throughout the simulation.

}, issn = {1537-1719}, doi = {10.1093/molbev/msad033}, author = {Sharma, Abhishek and Krishna, Sudhir and Sowdhamini, Ramanathan} } @article {129154, title = {A census of actin-associated proteins in humans.}, journal = {Front Cell Dev Biol}, volume = {11}, year = {2023}, month = {2023}, pages = {1168050}, abstract = {

Actin filaments help in maintaining the cell structure and coordinating cellular movements and cargo transport within the cell. Actin participates in the interaction with several proteins and also with itself to form the helical filamentous actin (F-actin). Actin-binding proteins (ABPs) and actin-associated proteins (AAPs) coordinate the actin filament assembly and processing, regulate the flux between globular G-actin and F-actin in the cell, and help maintain the cellular structure and integrity. We have used protein-protein interaction data available through multiple sources (STRING, BioGRID, mentha, and a few others), functional annotation, and classical actin-binding domains to identify actin-binding and actin-associated proteins in the human proteome. Here, we report 2482 AAPs and present an analysis of their structural and sequential domains, functions, evolutionary conservation, cellular localization, abundance, and tissue-specific expression patterns. This analysis provides a base for the characterization of proteins involved in actin dynamics and turnover in the cell.

}, issn = {2296-634X}, doi = {10.3389/fcell.2023.1168050}, author = {Meenakshi S, Iyer and Rao, Madan and Mayor, Satyajit and Sowdhamini, Ramanathan} } @article {130540, title = {Influence of pH on indole-dependent heterodimeric interactions between Anopheles gambiae odorant-binding proteins OBP1 and OBP4.}, journal = {Int J Biol Macromol}, year = {2023}, month = {2023 Jun 15}, pages = {125422}, abstract = {

Insect Odorant Binding Proteins (OBPs) constitute important components of their olfactory apparatus, as they are essential for odor recognition. OBPs undergo conformational changes upon pH change, altering their interactions with odorants. Moreover, they can form heterodimers with novel binding characteristics. Anopheles gambiae OBP1 and OBP4 were found capable of forming heterodimers possibly involved in the specific perception of the attractant indole. In order to understand how these OBPs interact in the presence of indole and to investigate the likelihood of a pH-dependent heterodimerization mechanism, the crystal structures of OBP4 at pH 4.6 and 8.5 were determined. Structural comparison to each other and with the OBP4-indole complex (3Q8I, pH 6.85) revealed a flexible N-terminus and conformational changes in the α4-loop-α5 region at acidic pH. Fluorescence competition assays showed a weak binding of indole to OBP4 that become further impaired at acidic pH. Additional Molecular Dynamic and Differential Scanning Calorimetry studies displayed that the influence of pH on OBP4 stability is significant compared to the modest effect of indole. Furthermore, OBP1-OBP4 heterodimeric models were generated at pH 4.5, 6.5, and 8.5, and compared concerning their interface energy and cross-correlated motions in the absence and presence of indole. The results indicate that the increase in pH may induce the stabilization of OBP4 by increasing its helicity, thereby enabling indole binding at neutral pH that further stabilizes the protein and possibly promotes the creation of a binding site for OBP1. A decrease in interface stability and loss of correlated motions upon transition to acidic pH may provoke the heterodimeric dissociation allowing indole release. Finally, we propose a potential OBP1-OBP4 heterodimer formation/disruption mechanism induced by pH change and indole binding.

}, issn = {1879-0003}, doi = {10.1016/j.ijbiomac.2023.125422}, author = {Mam, Bhavika and Tsitsanou, Katerina E and Liggri, Panagiota G V and Saitta, Francesca and Stamati, Evgenia C V and Mahita, Jarjapu and Leonis, George and Drakou, Christina E and Papadopoulos, Manthos and Arnaud, Philippe and Offmann, Bernard and Fessas, Dimitrios and Sowdhamini, Ramanathan and Zographos, Spyros E} } @article {125197, title = {Minus-C subfamily has diverged from Classic odorant-binding proteins in honeybees}, journal = {APIDOLOGIE }, volume = {54}, year = {2023}, month = {02/2023}, pages = {12}, abstract = {

Odorant-binding proteins (OBPs) in insects bind to volatile chemical cues that are important in regulating insect behavior. It is hypothesized that OBPs bind with specificity to certain volatiles and may help in transport and delivery to odorant receptors (ORs), and may help in buffering the olfactory response and aid the insect in various behaviors. Honeybees are eusocial insects that perceive olfactory cues and strongly rely on them to perform complex olfactory behaviors. Here, we have identified and annotated odorant-binding proteins and few chemosensory proteins from the genome of the dwarf honey bee, Apis florea, using an exhaustive homology-based bioinformatic pipeline and analyzed the evolutionary relationships between the OBP subfamilies. Our study confirms that the Minus-C subfamily in honey bees has diverged from the Classic subfamily of odorant-binding proteins.

}, doi = {10.1007/s13592-022-00988-5}, author = {Mam, Bhavika and Karpe, Snehal D. and Sowdhamini, Ramanathan} } @article {128079, title = {Structural rationale to understand the effect of disease-associated mutations on Myotubularin.}, journal = {Curr Res Struct Biol}, volume = {5}, year = {2023}, month = {2023}, pages = {100100}, abstract = {

Myotubularin or MTM1 is a lipid phosphatase that regulates vesicular trafficking in the cell. The gene is mutated in a severe form of muscular disease, X-linked myotubular myopathy or XLMTM, affecting 1 in 50,000 newborn males worldwide. There have been several studies on the disease pathology of XLMTM, but the structural effects of missense mutations of MTM1 are underexplored due to the unavailability of a crystal structure. MTM1 consists of three domains-a lipid-binding N-terminal GRAM domain, the phosphatase domain and a coiled-coil domain which aids dimerisation of Myotubularin homologs. While most mutations reported to date map to the phosphatase domain of MTM1, the other two domains on the sequence are also frequently mutated in XLMTM. To understand the overall structural and functional effects of missense mutations on MTM1, we curated several missense mutations and performed and studies. Apart from significantly impaired binding to substrate, abrogation of phosphatase activity was observed for a few mutants. Possible long-range effects of mutations from non-catalytic domains on phosphatase activity were observed as well. Coiled-coil domain mutants have been characterised here for the first time in XLMTM literature.

}, issn = {2665-928X}, doi = {10.1016/j.crstbi.2023.100100}, author = {Bhattacharyya, Teerna and Ghosh, Avishek and Verma, Shailya and Raghu, Padinjat and Sowdhamini, Ramanathan} } @article {129503, title = {Transcriptome data analysis of primary cardiomyopathies reveals perturbations in arachidonic acid metabolism.}, journal = {Front Cardiovasc Med}, volume = {10}, year = {2023}, month = {2023}, pages = {1110119}, abstract = {

INTRODUCTION: Cardiomyopathies are complex heart diseases with significant prevalence around the world. Among these, primary forms are the major contributors to heart failure and sudden cardiac death. As a high-energy demanding engine, the heart utilizes fatty acids, glucose, amino acid, lactate and ketone bodies for energy to meet its requirement. However, continuous myocardial stress and cardiomyopathies drive towards metabolic impairment that advances heart failure (HF) pathogenesis. So far, metabolic profile correlation across different cardiomyopathies remains poorly understood.

METHODS: In this study, we systematically explore metabolic differences amongst primary cardiomyopathies. By assessing the metabolic gene expression of all primary cardiomyopathies, we highlight the significantly shared and distinct metabolic pathways that may represent specialized adaptations to unique cellular demands. We utilized publicly available RNA-seq datasets to profile global changes in the above diseases (|| >= 0.28 and BH\  0.1) and performed gene set analysis (GSA) using the PAGE statistics on KEGG pathways.

RESULTS: Our analysis demonstrates that genes in arachidonic acid metabolism (AA) are significantly perturbed across cardiomyopathies. In particular, the arachidonic acid metabolism gene interacts with fibroblast marker genes and can potentially influence fibrosis during cardiomyopathy.

CONCLUSION: The profound significance of AA metabolism within the cardiovascular system renders it a key player in modulating the phenotypes of cardiomyopathies.

}, issn = {2297-055X}, doi = {10.3389/fcvm.2023.1110119}, author = {Chauhan, Pankaj Kumar and Sowdhamini, Ramanathan} } @article {115027, title = {Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members.}, journal = {BMC Genomics}, volume = {23}, year = {2022}, month = {2022 Jul 16}, pages = {516}, abstract = {

BACKGROUND: Plant species from Rosaceae family are economically important. One of the major environmental factors impacting those species is cold stress. Although several Rosaceae plant genomes have recently been sequenced, there have been very few research conducted on cold upregulated genes and their promoter binding sites. In this study, we used computational approaches to identify and analyse potential cold stress response genes across ten Rosaceae family members.

RESULTS: Cold stress upregulated gene data from apple and strawberry were used to identify syntelogs in other Rosaceae species. Gene duplication analysis was carried out to better understand the distribution of these syntelog genes in different Rosaceae members. A total of 11,145 popular abiotic stress transcription factor-binding sites were identified in the upstream region of these potential cold-responsive genes, which were subsequently categorised into distinct transcription factor (TF) classes. MYB classes of transcription factor binding site (TFBS) were abundant, followed by bHLH, WRKY, and AP2/ERF. TFBS patterns in the promoter regions were compared among these species and gene families, found to be quite different even amongst functionally related syntelogs. A case study on important cold stress responsive transcription factor family, AP2/ERF showed less conservation in TFBS patterns in the promoter regions. This indicates that syntelogs from the same group may be comparable at the gene level but not at the level of cis-regulatory elements. Therefore, for such genes from the same family, different repertoire of TFs could be recruited for regulation and expression. Duplication events must have played a significant role in the similarity of TFBS patterns amongst few syntelogs of closely related species.

CONCLUSIONS: Our study overall suggests that, despite being from the same gene family, different combinations of TFs may play a role in their regulation and expression. The findings of this study will provide information about potential genes involved in the cold stress response, which will aid future functional research of these gene families involved in many important biological processes.

}, keywords = {Cold-Shock Response, Gene Expression Regulation, Plant, Multigene Family, Phylogeny, Plant Proteins, Rosaceae, Stress, Physiological, Transcription Factors}, issn = {1471-2164}, doi = {10.1186/s12864-022-08751-x}, author = {Shafi, K Mohamed and Sowdhamini, Ramanathan} } @article {118723, title = {Computational tools to study RNA-protein complexes.}, journal = {Front Mol Biosci}, volume = {9}, year = {2022}, month = {2022}, pages = {954926}, abstract = {

RNA is the key player in many cellular processes such as signal transduction, replication, transport, cell division, transcription, and translation. These diverse functions are accomplished through interactions of RNA with proteins. However, protein-RNA interactions are still poorly derstood in contrast to protein-protein and protein-DNA interactions. This knowledge gap can be attributed to the limited availability of protein-RNA structures along with the experimental difficulties in studying these complexes. Recent progress in computational resources has expanded the number of tools available for studying protein-RNA interactions at various molecular levels. These include tools for predicting interacting residues from primary sequences, modelling of protein-RNA complexes, predicting hotspots in these complexes and insights into derstanding in the dynamics of their interactions. Each of these tools has its strengths and limitations, which makes it significant to select an optimal approach for the question of interest. Here we present a mini review of computational tools to study different aspects of protein-RNA interactions, with focus on overall application, development of the field and the future perspectives.

}, issn = {2296-889X}, doi = {10.3389/fmolb.2022.954926}, author = {Bheemireddy, Sneha and Sandhya, Sankaran and Srinivasan, Narayanaswamy and Sowdhamini, Ramanathan} } @article {110447, title = {DDX24 is required for muscle fiber organization and the suppression of wound-induced Wnt activity necessary for pole re-establishment during planarian regeneration.}, journal = {Dev Biol}, year = {2022}, month = {2022 May 03}, abstract = {

Planarians have a remarkable ability to undergo whole-body regeneration. Successful regeneration outcome is determined by processes like polarity establishment at the wound site, which is followed by pole (organizer) specification. Interestingly, these determinants are almost exclusively expressed by muscles in these animals. However, the molecular toolkit that enables the functional versatility of planarian muscles remains poorly understood. Here we report that SMED_DDX24, a D-E-A-D Box RNA helicase, is necessary for planarian survival and regeneration. We found that DDX24 is enriched in muscles and its knockdown disrupts muscle fiber organization. This leads to defective pole specification, which in turn results in misregulation of many positional control genes specifically during regeneration. ddx24 RNAi also upregulates wound-induced Wnt signalling. Suppressing this ectopic Wnt activity rescues the knockdown phenotype by enabling better anterior pole regeneration. To summarize, our work highlights the role of an RNA helicase in muscle fiber organization, and modulating amputation-induced wnt levels, both of which seem critical for pole re-organization, thereby regulating whole-body regeneration.

}, issn = {1095-564X}, doi = {10.1016/j.ydbio.2022.04.011}, author = {Sarkar, Souradeep R and Dubey, Vinay Kumar and Jahagirdar, Anusha and Lakshmanan, Vairavan and Haroon, Mohamed Mohamed and Sowndarya, Sai and Sowdhamini, Ramanathan and Palakodeti, Dasaradhi} } @article {109309, title = {Development of candidate gene-based markers and map-based cloning of a dominant rust resistance gene in cultivated groundnut (Arachis hypogaea L.).}, journal = {Gene}, volume = {827}, year = {2022}, month = {2022 Apr 04}, pages = {146474}, abstract = {

A dominant rust resistance gene, VG 9514-Rgene was isolated through map-based cloning. Sequence analysis revealed non-synonymous mutations in the TIR, NBS and LRR region of the R-protein. Candidate gene-based markers from these SNPs revealed complete co-segregation of the isolated VG 9514-Rgene with rust resistance in a RIL population and confirmed their map position in between FRS 72 and SSR_GO340445 markers in arahy03 chromosome. Blastp search of VG 9514-Rprotein detected Arahy.T6DCA5 with \>80.0\% identity that localized at 142,544,745.0.142,549,184 in arahy03 chromosome. K/K calculation revealed that VG 9514-Rgene had undergone positive selection compared to four homologous genes in the groundnut genome. Homology based structure modelling of this R-protein revealed a typical consensus three-dimensional folding of TIR-NBS-LRR protein. Non-synonymous mutations in susceptible version of R-protein were mapped and found E268Q mutation in hhGRExE motif, Y309F in RNBS-A motif and I579T in MHD motif of NB-ARC domain are probable candidates for loss of function.

}, issn = {1879-0038}, doi = {10.1016/j.gene.2022.146474}, author = {Mondal, Suvendu and Mohamed Shafi, K and Raizada, Avi and Song, Hui and Badigannavar, Anand M and Sowdhamini, Ramanathan} } @article {131287, title = {Draft genome sequence of an invasive plant .}, journal = {Bioinformation}, volume = {18}, year = {2022}, month = {2022}, pages = {739-741}, abstract = {

L. is an invasive species of global concern. An ornamental plant originating from central America, it has now spread across natural and human-dominated habitats across tropical and subtropical regions globally. Understanding the population and evolutionary genetics of this species could help gain deeper insights into invasion biology, and provide tools for more effective management. Such investigation would require a relatively good quality genome assembly. While there have been reports of a transcriptome, it has been challenging to construct the genome assembly because of the large genome size. We present here the first draft genome assembly of L. which has an N50 value of 62 Kb, genome completeness of 99.3\% and genome coverage of 74.3\%. We hope that such an assembly will help researchers study colonization history, the genetic basis of adaptation and invasiveness, and help design strategies to contain the invasiveness of this plant, allowing biodiversity recovery in several parts of the globe.

}, issn = {0973-2063}, doi = {10.6026/97320630018739}, author = {Joshi, Adwait G and Praveen, P and Ramakrishnan, Uma and Sowdhamini, Ramanathan} } @article {108045, title = {DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins.}, journal = {Database (Oxford)}, volume = {2022}, year = {2022}, month = {2022 Mar 01}, abstract = {

Disulphide bonds are stabilizing crosslinks in proteins and serve to enhance their thermal stability. In proteins that are small and rich in disulphide bonds, they could be the major determining factor for the choice of conformational state since their constraints on appropriate backbone conformation can be substantial. Such crosslinks and their positional conservation could itself enable protein family and functional association. Despite the importance of the field, there is no comprehensive database on disulphide crosslinks that is available to the public. Herein we provide information on disulphides in DSDBASE2.0, an updated and significantly expanded database that is freely available, fully annotated and manually curated database on native and modelled disulphides. The web interface also provides several useful computational tools that have been specifically developed for proteins containing disulphide crosslinks. The modelling of disulphide crosslinks is performed using stereochemical criteria, coded within our Modelling of Disulphides in Proteins (MODIP) algorithm. The inclusion of modelled disulphides potentially enhances the loop database substantially, thereby permitting the recognition of compatible polypeptide segments that could serve as templates for immediate modelling. The DSDBASE2.0 database has been updated to include 153,944 PDB entries, 216,096 native and 20,153,850 modelled disulphide bond segments from PDB January 2021 release. The current database also provides a resource to user-friendly search for multiple disulphide bond containing loops, along with annotation of their function using GO and subcellular localization of the query. Furthermore, it is possible to obtain the three-dimensional models of disulphide-rich small proteins using an independent algorithm, RANMOD, that generates and examines random, but allowed backbone conformations of the polypeptide. DSDBASE2.0 still remains the largest open-access repository that organizes all disulphide bonds of proteins on a single platform. The database can be accessed from http://caps.ncbs.res.in/dsdbase2.

}, issn = {1758-0463}, doi = {10.1093/database/baac005}, author = {Kalmankar, Neha V and Pavalam, Murugavel and Indrakumar, Sowmya and Srinivasan, Narayanaswamy and Sowdhamini, Ramanathan} } @article {106549, title = {Editorial: Advances in Molecular Docking and Structure-Based Modelling.}, journal = {Front Mol Biosci}, volume = {9}, year = {2022}, month = {2022}, pages = {839826}, issn = {2296-889X}, doi = {10.3389/fmolb.2022.839826}, author = {Rebehmed, Joseph and de Brevern, Alexandre G and Sowdhamini, Ramanathan and Joseph, Agnel Praveen} } @article {118434, title = {Effects of a plant cyclotide on conformational dynamics and destabilization of β-amyloid fibrils through molecular dynamics simulations.}, journal = {Front Mol Biosci}, volume = {9}, year = {2022}, month = {2022}, pages = {986704}, abstract = {

Aggregation of β-amyloid (Aβ) peptide is one of the hallmarks of Alzheimer{\textquoteright}s disease (AD) which results in chronic and progressive neurodegeneration of the brain. A recent study by our group have shown the ability of cyclic disulfide-rich peptides ("cyclotides") isolated from a medicinal plant, , to inhibit the aggregation of Aβ peptides and reduce oxidative stress caused by reactive oxygen species using models of transgenic . In the present study, through extensive computational docking and multi-ns molecular dynamics (MD) simulation, we evaluated if cyclotides can stably bind to Aβ molecules and/or destabilize the Aβ fibril by preventing conformational changes from α-helical to β-sheet rich structures. We demonstrate that cyclotides bind effectively and stably to different forms of Aβ structures hydrogen bonding and hydrophobic interactions. One of the conserved hydrophobic interface residues, Tyr10 was mutated to Ala and the impact of this virtual mutation was estimated by additional MD simulations for the wild-type (WT) and mutant protein-peptide complexes. A detailed MD simulation analyses revealed that cyclotides form hydrogen bonds with the toxic amyloid assemblies thereby weakening the inter-strand hydrogen bonds between the Aβ peptide. The φ-ѱ distribution map of residues in the cyclotide binding pocket that ideally adopt β-sheet conformation show deviation towards right-handed ɑ-helical (ɑ) conformation. This effect was similar to that observed for the Tyr10Ala mutant and doubly so, for the cyclotide bound form. It is therefore possible to hypothesise that the opening up of amyloid β-sheet is due to an unfolding process occurring in the Aβ caused by cyclotide binding and inhibition. Our current findings provide novel structural insights on the mode of interaction between cyclotides and Aβ fibrils and describe their anti-amyloid aggregation potential. This sheds light on the future of cyclotide-based drug design against protein aggregation, a hallmark event in many neurodegenerative diseases.

}, issn = {2296-889X}, doi = {10.3389/fmolb.2022.986704}, author = {Kalmankar, Neha V and Gehi, Bhuvaneshwari Rajendrakumar and Sowdhamini, Ramanathan} } @article {115259, title = {Exploring the medicinally important secondary metabolites landscape through the lens of transcriptome data in fenugreek (Trigonella foenum graecum L.).}, journal = {Sci Rep}, volume = {12}, year = {2022}, month = {2022 Aug 08}, pages = {13534}, abstract = {

Fenugreek (Trigonella foenum-graecum L.) is a self-pollinated leguminous crop belonging to the Fabaceae family. It is a multipurpose crop used as herb, spice, vegetable and forage. It is a traditional medicinal plant in India attributed with several nutritional and medicinal properties including antidiabetic and anticancer. We have performed a combined transcriptome assembly from RNA sequencing data derived from leaf, stem and root tissues. Around 209,831 transcripts were deciphered from the assembly of 92\% completeness and an N50 of 1382 bases. Whilst secondary metabolites of medicinal value, such as trigonelline, diosgenin, 4-hydroxyisoleucine and quercetin, are distributed in several tissues, we report transcripts that bear sequence signatures of enzymes involved in the biosynthesis of such metabolites and are highly expressed in leaves, stem and roots. One of the antidiabetic alkaloid, trigonelline and its biosynthesising enzyme, is highly abundant in leaves. These findings are of value to nutritional and the pharmaceutical industry.

}, keywords = {Diosgenin, Hypoglycemic Agents, Plant Extracts, Plants, Medicinal, Transcriptome, Trigonella}, issn = {2045-2322}, doi = {10.1038/s41598-022-17779-8}, author = {Naika, Mahantesha B N and Sathyanarayanan, Nitish and Sajeevan, Radha Sivarajan and Bhattacharyya, Teerna and Ghosh, Pritha and Iyer, Meenakshi S and Jarjapu, Mahita and Joshi, Adwait G and Harini, K and Shafi, K Mohamed and Kalmankar, Neha and Karpe, Snehal D and Mam, Bhavika and Pasha, Shaik Naseer and Sowdhamini, Ramanathan} } @article {116716, title = {A genome-wide search of Toll/Interleukin-1 receptor (TIR) domain-containing adapter molecule (TICAM) and their evolutionary divergence from other TIR domain containing proteins.}, journal = {Biol Direct}, volume = {17}, year = {2022}, month = {2022 Sep 02}, pages = {24}, abstract = {

Toll/Interleukin-1 receptor (TIR) domains are cytoplasmic domain that mediates receptor signalling. These domains are present in proteins like Toll-like receptors (TLR), its signaling adaptors and Interleukins, that form a major part of the immune system. These TIR domain containing signaling adaptors binds to the TLRs and interacts with their TIR domains for downstream signaling. We have examined the evolutionary divergence across the tree of life of two of these TIR domain containing adaptor molecules (TICAM) i.e., TIR domain-containing adapter-inducing interferon-β (TRIF/TICAM1) and TIR domain containing adaptor molecule2 (TRAM/TICAM2), by using computational approaches. We studied their orthologs, domain architecture, conserved motifs, and amino acid variations. Our study also adds a timeframe to infer the duplication of TICAM protein from Leptocardii and later divergence into TICAM1/TRIF and TICAM2/TRAM. More evidence of TRIF proteins was seen, but the absence of conserved co-existing domains such as TRIF-NTD, TIR, and RHIM domains in distant relatives hints on diversification and adaptation to different biological functions. TRAM was lost in Actinopteri and has conserved domain architecture of TIR across species except in Aves. An additional isoform of TRAM, TAG (TRAM adaptor with the GOLD domain), could be identified in species in the Mesozoic era. Finally, the Hypothesis based Likelihood ratio test was applied to look for selection pressure amongst orthologues of TRIF and TRAM to search for positively selected sites. These residues were mostly seen in the non-structural region of the proteins. Overall, this study unravels evolutionary information on the adaptors TRAM and TRIF and how well they had duplicated to perform diverse functions by changes in their domain architecture across lineages.

}, keywords = {Adaptor Proteins, Vesicular Transport, Receptors, Interleukin-1, Signal Transduction, Toll-Like Receptors}, issn = {1745-6150}, doi = {10.1186/s13062-022-00335-9}, author = {Verma, Shailya and Sowdhamini, Ramanathan} } @article {105164, title = {Immune profile and responses of a novel Dengue DNA vaccine encoding EDIII-NS1 consensus design based on Indo-African sequences.}, journal = {Mol Ther}, year = {2022}, month = {2022 Jan 06}, abstract = {

The ongoing COVID-19 pandemic highlights the need to tackle viral variants, expand the number of antigens and assess diverse delivery systems for vaccines against emerging viruses. In the present study, a DNA vaccine candidate was generated by combining in tandem envelope protein domain III (EDIII) of dengue virus serotypes 1-4 and a DENV-2 NS1 protein coding region. Each domain was designed as a serotype-specific consensus coding sequence derived from different genotypes based on whole genome sequencing of clinical isolates in India and complemented with data from Africa. This sequence was further optimized for protein expression. In silico structural analysis of the EDIII consensus sequence revealed that epitopes are structurally conserved and immunogenic. Vaccination of mice with this construct induced pan-serotype neutralizing antibodies and antigen-specific T cell responses. Assaying of intracellular IFN-γ staining, immunoglobulin IgG2(a/c)/IgG1 ratios and immune gene profiling suggest a strong Th1-dominant immune response. Finally, passive transfer of immune sera protected AG129 mice challenged with a virulent, non-mouse adapted DENV-2 strain. Our findings collectively suggest an alternative strategy for dengue vaccine design; offering a novel vaccine candidate with a possible broad spectrum protection and successful clinical translation either as a stand-alone or in a mix and match strategy.

}, issn = {1525-0024}, doi = {10.1016/j.ymthe.2022.01.013}, author = {Sankaradoss, Arun and Jagtap, Suraj and Nazir, Junaid and Moula, Shefta-E and Modak, Ayan and Fialho, Joshuah and Iyer, Meenakshi and Shastri, Jayanthi S and Dias, Mary and Gadepalli, Ravisekhar and Aggarwal, Alisha and Vedpathak, Manoj and Agrawal, Sachee and Pandit, Awadhesh and Nisheetha, Amul and Kumar, Anuj and Bordoloi, Mahasweta and Shafi, Mohamed and Shelar, Bhagyashree and Balachandra, Swathi S and Damodar, Tina and Masika, Moses Muia and Mwaura, Patrick and Anzala, Omu and Muthumani, Kar and Sowdhamini, Ramanathan and Medigeshi, Guruprasad R and Roy, Rahul and Pattabiraman, Chitra and Krishna, Sudhir and Sreekumar, Easwaran} } @article {120168, title = {Integrative network analysis interweaves the missing links in cardiomyopathy diseasome.}, journal = {Sci Rep}, volume = {12}, year = {2022}, month = {2022 Nov 16}, pages = {19670}, abstract = {

Cardiomyopathies are progressive disease conditions that give rise to an abnormal heart phenotype and are a leading cause of heart failures in the general population. These are complex diseases that show co-morbidity with other diseases. The molecular interaction network in the localised disease neighbourhood is an important step toward deciphering molecular mechanisms underlying these complex conditions. In this pursuit, we employed network medicine techniques to systematically investigate cardiomyopathy{\textquoteright}s genetic interplay with other diseases and uncover the molecular players underlying these associations. We predicted a set of candidate genes in cardiomyopathy by exploring the DIAMOnD algorithm on the human interactome. We next revealed how these candidate genes form association across different diseases and highlighted the predominant association with brain, cancer and metabolic diseases. Through integrative systems analysis of molecular pathways, heart-specific mouse knockout data and disease tissue-specific transcriptomic data, we screened and ascertained prominent candidates that show abnormal heart phenotype, including NOS3, MMP2 and SIRT1. Our computational analysis broadens the understanding of the genetic associations of cardiomyopathies with other diseases and holds great potential in cardiomyopathy research.

}, keywords = {Algorithms, Animals, Cardiomyopathies, Heart, Humans, Mice, Phenotype}, issn = {2045-2322}, doi = {10.1038/s41598-022-24246-x}, author = {Chauhan, Pankaj Kumar and Sowdhamini, Ramanathan} } @article {108049, title = {LIM domain-wide comprehensive virtual mutagenesis provides structural rationale for cardiomyopathy mutations in CSRP3.}, journal = {Sci Rep}, volume = {12}, year = {2022}, month = {2022 Mar 03}, pages = {3562}, abstract = {

Cardiomyopathies are a severe and chronic cardiovascular burden worldwide, affecting a large cohort in the general population. Cysteine and glycine-rich protein 3 (CSRP3) is one of key proteins implicated in dominant dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM). In this study, we device a rapid in silico screening protocol that creates a mutational landscape map for all possible allowed and disallowed substitutions in the protein of interest. This map provides the structural and functional insights on the stability of LIM domains of CSRP3. Further, the sequence analysis delineates the eukaryotic CSRP3 protein orthologs which complements the mutational map, but provide limited information of amino acid exchanges. Next, we also evaluated the effect of HCM/DCM mutations on these domains. One of highly destabilising mutations-L44P (also disease causing) and a neutral mutation-L44M were further subjected to molecular dynamics (MD) simulations. The results establish that L44P substitution affects the LIM domain structure by altering secondary structure and due to loss of hydrophobic interaction with Phenylananine 35. The present study provides a useful perspective to our understanding of the role of mutations in the CSRP3 LIM domains and their evolution. This study provides a novel computational screening method for quick identification of key mutation sites for specific protein structures that can reduce the burden on experimental research.

}, issn = {2045-2322}, doi = {10.1038/s41598-022-07553-1}, author = {Chauhan, Pankaj Kumar and Sowdhamini, Ramanathan} } @article {109312, title = {PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe.}, journal = {Database (Oxford)}, volume = {2022}, year = {2022}, month = {2022 Apr 12}, abstract = {

Sequence alignments are models that capture the structural, functional and evolutionary relationships between proteins. Structure-guided sequence alignments are helpful in the case of distantly related proteins with poor sequence identity, thus rendering routine sequence alignment methods ineffective. Protein Alignment organized as Structural Superfamilies or PASS2 database provides such sequence alignments of protein domains within a superfamily as per the Structural Classification of Proteins extended (SCOPe) database. The current update of PASS2 (i.e. PASS2.7) is following the latest release of SCOPe (2.07) and we provide data for 14 323 protein domains that are \<40\% identical and are organized into 2024 superfamilies. Several useful features derived from the alignments, such as conserved secondary structural motifs, HMMs and residues conserved across the superfamily, are also reported. Protein domains that are deviant from the rest of the members of a superfamily may compromise the quality of the alignment, and we found this to be the case in \~{}7\% of the total superfamilies we considered. To improve the alignment by objectively identifying such {\textquoteright}outliers{\textquoteright}, in this update, we have used a k-means-based unsupervised machine learning method for clustering superfamily members, where features provided were length of domains aligned, Cα-RMSD derived from the rigid-body superposition of all members and gaps contributed to the alignment by each domain. In a few cases, we have split the superfamily as per the clusters predicted and provided complete data for each cluster. A new feature included in this update is absolutely conserved interactions (ACIs) between residue backbones and side chains, which are obtained by aligning protein structure networks using structure-guided sequence alignments of superfamilies. ACIs provide valuable information about functionally important residues and the structure-function relationships of proteins. The ACIs and the corresponding conserved networks for backbone and sidechain have been marked on the superimposed structure separately.

DATABASE URL: The updated version of the PASS2 database is available at http://caps.ncbs.res.in/pass2/.

}, keywords = {Databases, Protein, Protein Domains, Protein Structure, Tertiary, Proteins, Sequence Alignment}, issn = {1758-0463}, doi = {10.1093/database/baac025}, author = {Bhattacharyya, Teerna and Nayak, Soumya and Goswami, Smit and Gadiyaram, Vasundhara and Mathew, Oommen K and Sowdhamini, Ramanathan} } @article {117965, title = {Structures of distantly-related interacting protein homologues are less divergent than non-interacting homologues.}, journal = {FEBS Open Bio}, year = {2022}, month = {2022 Sep 23}, abstract = {

Homologous proteins can display high structural variation due to evolutionary divergence at low sequence identity. This classical inverse relationship between sequence identity and structural similarity, established many years ago, has remained true between homologous proteins of known structure over time. However, a large number of heteromeric proteins also exist in the structural data bank, where the interacting subunits belong to the same fold and maintain low sequence identity between themselves. It is not clear if there is any selection pressure to deviate from the inverse sequence-structure relationship for such interacting distant homologues, in comparison to pairs of homologues which are not known to interact. We examined 12,824 fold pairs of interacting homologues of known structure, which includes both heteromers and multi-domain proteins. These were compared with monomeric proteins, resulting in 26,082 fold pairs as a dataset of non-interacting homologous systems. Interacting homologues were found to retain higher structural similarity than non-interacting homologues at diminishing sequence identity in a statistically significant manner. Interacting homologues are more similar in their 3D structures than non-interacting homologues and have a preference towards symmetric association. There appears to be a structural constraint between remote homologues due to this commitment.

}, issn = {2211-5463}, doi = {10.1002/2211-5463.13492}, author = {Naveenkumar, Nagarajan and Prabantu, Vasam Manjveekar and Vishwanath, Sneha and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {121148, title = {Transcriptome profiling of two Moringa species and insights into their antihyperglycemic activity.}, journal = {BMC Plant Biol}, volume = {22}, year = {2022}, month = {2022 Dec 02}, pages = {561}, abstract = {

BACKGROUND: Moringa concanensis Nimmo (MC), a plant that resembles Moringa oleifera Lam. (MO), has less scientific information but has traditionally been used as a medicinal plant. Moringa species have long been known for their medicinal qualities, which include antioxidant, anti-inflammatory, anticancer, and antihyperglycemic effects. We investigated the antidiabetic potential of MC and MO species in this study by using transcriptome profiling, metabolite analysis, and in vitro assay studies.

RESULTS: Our transcriptome analysis revealed the expression of enzymes involved in the biosynthesis of quercetin, chlorogenic acid, and benzylamine, all of which have previously been shown to have antidiabetic activity. We compared the expression patterns of five different tissues from MC and MO and it was found that the key enzymes involved in the biosynthesis of these compounds were highly expressed in leaf tissue. The expression estimated by MC transcriptome data in different tissues was verified using RT-qPCR analysis. The amount of these compounds was further quantified in the crude leaf extract of both species and found that MC had a higher abundance of quercetin and chlorogenic acid than MO. The crude leaf extract from both MC and MO were further tested in vitro, and the results demonstrated strong inhibitory activity for α-glucosidase and DPP-IV enzymes. Our findings suggest that compounds in leaf tissue, such as quercetin, benzylamine, and chlorogenic acid, could play a significant role in this antidiabetic activity. In addition, when comparing MO plants, we found that MC had a slightly higher effect in expression, abundance, and inhibitory activity.

CONCLUSIONS: This study presents the first report of MC transcriptome data, as well as a comparison of its anti-diabetic activity to MO. Our analysis discussed the significance of leaf tissue in antidiabetic activity compared to other tissues of both species. Overall, this study not only provides transcriptome resources for Moringa species, but also sheds light on antidiabetic potential of both species.

}, keywords = {Benzylamines, Chlorogenic Acid, Gene Expression Profiling, Hypoglycemic Agents, Moringa, Plant Extracts, Quercetin}, issn = {1471-2229}, doi = {10.1186/s12870-022-03938-6}, author = {Shafi, K Mohamed and Sajeevan, Radha Sivarajan and Kouser, Sania and Vishnuprasad, Chethala N and Sowdhamini, Ramanathan} } @article {96657, title = {Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting}, journal = {Front. Microbiol}, year = {2021}, month = {07/2021}, abstract = {

Background: Africa has one of the highest incidences of gonorrhea. Neisseria gonorrhoeae is gaining resistance to most of the available antibiotics, compromising treatment across the world. Whole-genome sequencing (WGS) is an efficient way of predicting AMR determinants and their spread in the population. Recent advances in next-generation sequencing technologies like Oxford Nanopore Technology (ONT) have helped in the generation of longer reads of DNA in a shorter duration with lower cost. Increasing accuracy of base-calling algorithms, high throughput, error-correction strategies, and ease of using the mobile sequencer MinION in remote areas lead to its adoption for routine microbial genome sequencing. To investigate whether MinION-only sequencing is sufficient for WGS and downstream analysis in resource-limited settings, we sequenced the genomes of 14 suspected N. gonorrhoeae isolates from Nairobi, Kenya.

}, doi = {10.3389/fmicb.2021.647565}, author = {Juma, Meshack and Sankaradoss, Arun and Ndombi, Redcliff and Mwaura, Patrick and Damoda, Tina and Nazir, Junaid and Pandit, Awadhesh and Khurana, Rupsy and Masika, Moses and Chirchir, Ruth and Gachie, John and Krishna, Sudhir and Sowdhamini, Ramanathan and Anzala, Omu and Meenakshi, Iyer S.} } @article {96412, title = {DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity.}, journal = {Bioinform Biol Insights}, volume = {15}, year = {2021}, month = {2021}, pages = {11779322211030364}, abstract = {

Protein-ligand binding prediction has extensive biological significance. Binding affinity helps in understanding the degree of protein-ligand interactions and is a useful measure in drug design. Protein-ligand docking using virtual screening and molecular dynamic simulations are required to predict the binding affinity of a ligand to its cognate receptor. Performing such analyses to cover the entire chemical space of small molecules requires intense computational power. Recent developments using deep learning have enabled us to make sense of massive amounts of complex data sets where the ability of the model to "learn" intrinsic patterns in a complex plane of data is the strength of the approach. Here, we have incorporated convolutional neural networks to find spatial relationships among data to help us predict affinity of binding of proteins in whole superfamilies toward a diverse set of ligands without the need of a docked pose or complex as user input. The models were trained and validated using a stringent methodology for feature extraction. Our model performs better in comparison to some existing methods used widely and is suitable for predictions on high-resolution protein crystal (⩽2.5 {\r A}) and nonpeptide ligand as individual inputs. Our approach to network construction and training on protein-ligand data set prepared in-house has yielded significant insights. We have also tested DEELIG on few COVID-19 main protease-inhibitor complexes relevant to the current public health scenario. DEELIG-based predictions can be incorporated in existing databases including RSCB PDB, PDBMoad, and PDBbind in filling missing binding affinity data for protein-ligand complexes.

}, issn = {1177-9322}, doi = {10.1177/11779322211030364}, author = {Ahmed, Asad and Mam, Bhavika and Sowdhamini, Ramanathan} } @article {94157, title = {Disulfide-Rich Cyclic Peptides from Protect against β-Amyloid Toxicity and Oxidative Stress in Transgenic .}, journal = {J Med Chem}, year = {2021}, month = {2021 May 28}, abstract = {

Neurotoxic aggregation of β-amyloid (Aβ) peptides is a hallmark of Alzheimer{\textquoteright}s disease and increased reactive oxygen species (ROS) is an associated process. In the present study, we report the neuroprotective effects of disulfide-rich, circular peptides from () (butterfly pea) on Aβ-induced toxicity in transgenic . Cyclotides (\~{}30 amino acids long) are a special class of cyclic cysteine knot peptides. We show that cyclotide-rich fractions from different plant tissues delay Aβ-induced paralysis in the transgenic CL4176 strain expressing the human muscle-specific Aβ gene. They also improved Aβ-induced chemotaxis defects in CL2355 strain expressing Aβ in the neuronal cells. ROS assay suggests that this protection is likely mediated by the inhibition of Aβ oligomerization. Furthermore, Aβ deposits were reduced in the CL2006 strain treated with the fractions. The study shows that cyclotides from could be a source of a novel pharmacophore scaffold against neurodegenerative diseases.

}, issn = {1520-4804}, doi = {10.1021/acs.jmedchem.1c00033}, author = {Kalmankar, Neha V and Hari, Hrudya and Sowdhamini, Ramanathan and Venkatesan, Radhika} } @article {92223, title = {Genome-wide survey of tyrosine phosphatases in thirty mammalian genomes}, journal = {Cell Signal}, year = {2021}, month = {04/2021}, abstract = {

The age of genomics has given us a wealth of information and the tools to study whole genomes. This, in turn, has facilitated genome-wide studies among organisms that were relatively less studied in the pre-genomic era or are non-model organisms. This paves the way to the discovery of interesting evolutionary patterns, which are brought to light by genome-wide surveys of protein superfamilies. Phosphorylation is a post-translational modification that is utilised across all clades of life, and acts as an important signalling switch, regulating several cellular processes. Tyrosine phosphatases, which are found predominantly in eukaryotes, act on phosphorylated tyrosine residues and sometimes on other substrates. Extending on our previous effort to look for tyrosine phosphatases in the human genome, we have looked for sequences of the cysteine-based tyrosine phosphatase superfamily in thirty mammalian genomes from all across Mammalia and validated the sequences with the presence of the signature catalytic motif. Domain architecture annotation, followed by in-depth analysis, revealed interesting taxon-specific patterns such as subtle differences between the protein families in marsupials and early mammals versus placental mammals. Finally, we discuss an interesting case of loss of the tyrosine phosphatase domain from a gene product in the course of eutherian evolution

}, doi = {10.1016/j.cellsig.2021.110009}, author = {Bhattacharyya, Teerna and Sowdhamini, Ramanathan} } @article {102047, title = {Ligand Docking Methods to Recognize Allosteric Inhibitors for G-Protein-Coupled Receptors.}, journal = {Bioinform Biol Insights}, volume = {15}, year = {2021}, month = {2021}, pages = {11779322211037769}, abstract = {

G-protein-coupled receptors (GPCRs) are membrane proteins which play an important role in many cellular processes and are excellent drug targets. Despite the existence of several US Food and Drug Administration (FDA)-approved GPCR-targeting drugs, there is a continuing challenge of side effects owing to the nonspecific nature of drug binding. We have investigated the diversity of the ligand binding site for this class of proteins against their cognate ligands using computational docking, even if their structures are known already in the ligand-complexed form. The cognate ligand of some of these receptors dock at allosteric binding site with better score than the binding at the conservative site. Interestingly, amino acid residues at such allosteric binding site are not conserved across GPCR subfamilies. Such a computational approach can assist in the prediction of specific allosteric binders for GPCRs.

}, issn = {1177-9322}, doi = {10.1177/11779322211037769}, author = {Harini, K and Jayashree, S and Tiwari, Vikas and Vishwanath, Sneha and Sowdhamini, Ramanathan} } @article {79804, title = {Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products.}, journal = {J Biosci}, volume = {45}, year = {2020}, month = {2020}, abstract = {

The world is currently facing the COVID-19 pandemic, for which mild symptoms include fever and dry cough. In severe cases, it could lead to pneumonia and ultimately death in some instances. Moreover, the causative pathogen is highly contagious and there are no drugs or vaccines for it yet. The pathogen, SARS-CoV-2, is one of the human coronaviruses which was identified to infect humans first in December 2019. SARS-CoV-2 shares evolutionary relationship to other highly pathogenic viruses such as Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS). We have exploited this similarity to model a target non-structural protein, NSP1, since it is implicated in the regulation of host gene expression by the virus and hijacking of host machinery. We next interrogated the capacity to repurpose around 2300 FDA-approved drugs and more than 3,00,000 small molecules of natural origin towards drug identification through virtual screening and molecular dynamics. Interestingly, we observed simple molecules like lactose, previously known anti-virals and few secondary metabolites of plants as promising hits. These herbal plants are already practiced in Ayurveda over centuries to treat respiratory problems and inflammation. Disclaimer: we would not like to recommend uptake of these small molecules for suspect COVID patients until it is approved by competent national or international authorities.

}, issn = {0973-7138}, author = {Sharma, Abhishek and Tiwari, Vikas and Sowdhamini, Ramanathan} } @article {78096, title = {Dataset for the combined transcriptome assembly of and functional annotation.}, journal = {Data Brief}, volume = {30}, year = {2020}, month = {2020 Jun}, pages = {105416}, abstract = {

In this paper, we present the data acquired during transcriptome analysis of the Moringa oleifera [1] from five different tissues (root, stem, leaf, flower and seed) by RNA sequencing. A total of 271 million reads were assembled with an N50 of 2094 bp. The combined transcriptome was assessed for transcript abundance across five tissues. The protein coding genes identified from the transcripts were annotated and used for orthology analysis. Further, enzymes involved in the biosynthesis of select medicinally important secondary metabolites, vitamins and ion transporters were identified and their expression levels across tissues were examined. The data generated by RNA sequencing has been deposited to NCBI public repository under the accession number PRJNA394193 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA394193).

}, issn = {2352-3409}, doi = {10.1016/j.dib.2020.105416}, author = {Shafi, K Mohamed and Joshi, Adwait G and Meenakshi, Iyer and Pasha, Shaik Naseer and Harini, K and Mahita, Jarjapu and Sajeevan, Radha Sivarajan and Karpe, Snehal D and Ghosh, Pritha and Nitish, Sathyanarayanan and Gandhimathi, A and Mathew, Oommen K and Prasanna, Subramanian Hari and Malini, Manoharan and Mutt, Eshita and Naika, Mahantesha and Ravooru, Nithin and Rao, Rajas M and Shingate, Prashant N and Sukhwal, Anshul and Sunitha, Margaret S and Upadhyay, Atul K and Vinekar, Rithvik S and Sowdhamini, Ramanathan} } @article {77381, title = {Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species.}, journal = {Front Plant Sci}, volume = {11}, year = {2020}, month = {2020}, pages = {267}, abstract = {

The genome of Asian cultivated rice ( L.) shows the presence of six organelle-specific and one plasma membrane () NHX-type cation proton antiporters. Of these, vacuolar-localized is extensively characterized. The genus consists of 27 species and 11 genome-types, with cultivated rice, diploid , having an AA-type genome. orthologous regions (gene organization, 5{\textquoteright} upstream cis elements, amino acid residues/motifs) from closely related AA genomes cluster distinctly from regions from more ancestral BB, FF and KKLL genomes. These sequence-specific distinctions also extend to two separate intron retention (IR) events involving transcripts that occur at the 5{\textquoteright} and 3{\textquoteright} ends of the NHX1 transcripts. We demonstrate that the IR event involving the 5{\textquoteright} UTR is present only in more recently evolved AA genomes while the IR event governing retention of the 13th intron of (terminal intron) is more ancient in origin, also occurring in halophytic wild rice, (KKLL). We also report presence of a retro-copy of the cDNA in the genome of (). Preferential species and tissue specific up- or down-regulation of the correctly spliced transcript/5{\textquoteright} UTR/13th intron-retaining splice variants under salinity was observed. The implications of IR on mRNA stability and ORF diversity in spp. is discussed.

}, issn = {1664-462X}, doi = {10.3389/fpls.2020.00267}, author = {Sellamuthu, Gothandapani and Jegadeeson, Vidya and Sajeevan, Radha Sivarajan and Rajakani, Raja and Parthasarathy, Pavithra and Raju, Kalaimani and Shabala, Lana and Chen, Zhong-Hua and Zhou, Meixue and Sowdhamini, Ramanathan and Shabala, Sergey and Venkataraman, Gayatri} } @article {78104, title = {A glance into the evolution of template-free protein structure prediction methodologies.}, journal = {Biochimie}, volume = {175}, year = {2020}, month = {2020 May 15}, pages = {85-92}, abstract = {

Prediction of protein structures using computational approaches has been explored for over two decades, paving a way for more focused research and development of algorithms in comparative modelling, ab intio modelling and structure refinement protocols. A tremendous success has been witnessed in template-based modelling protocols, whereas strategies that involve template-free modelling still lag behind, specifically for larger proteins (\>150 a.a.). Various improvements have been observed in ab initio protein structure prediction methodologies overtime, with recent ones attributed to the usage of deep learning approaches to construct protein backbone structure from its amino acid sequence. This review highlights the major strategies undertaken for template-free modelling of protein structures while discussing few tools developed under each strategy. It will also briefly comment on the progress observed in the field of ab initio modelling of proteins over the course of time as seen through the evolution of CASP platform.

}, issn = {1638-6183}, doi = {10.1016/j.biochi.2020.04.026}, author = {Dhingra, Surbhi and Sowdhamini, Ramanathan and Cadet, Fr{\'e}d{\'e}ric and Offmann, Bernard} } @article {83641, title = {A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways.}, journal = {MethodsX}, volume = {7}, year = {2020}, month = {2020}, pages = {101053}, abstract = {

This protocol describes a stepwise process to identify proteins of interest from a query proteome derived from NGS data. We implemented this protocol on transcriptome to identify proteins involved in secondary metabolite and vitamin biosynthesis and ion transport. This knowledge-driven protocol identifies proteins using an integrated approach involving sensitive sequence search and evolutionary relationships. We make use of functionally important residues (FIR) specific for the query protein family identified through its homologous sequences and literature. We screen protein hits based on the clustering with true homologues through phylogenetic tree reconstruction complemented with the FIR mapping. The protocol was validated for the protein hits through qRT-PCR and transcriptome quantification. Our protocol demonstrated a higher specificity as compared to other methods, particularly in distinguishing cross-family hits. This protocol was effective in transcriptome data analysis of as described in Pasha et al.{\textbullet}Knowledge-driven protocol to identify secondary metabolite synthesizing protein in a highly specific manner.{\textbullet}Use of functionally important residues for screening of true hits.{\textbullet}Beneficial for metabolite pathway reconstruction in any (species, metagenomics) NGS data.

}, issn = {2215-0161}, doi = {10.1016/j.mex.2020.101053}, author = {Joshi, Adwait G and Harini, K and Meenakshi, Iyer and Shafi, K Mohamed and Pasha, Shaik Naseer and Mahita, Jarjapu and Sajeevan, Radha Sivarajan and Karpe, Snehal D and Ghosh, Pritha and Nitish, Sathyanarayanan and Gandhimathi, A and Mathew, Oommen K and Prasanna, Subramanian Hari and Malini, Manoharan and Mutt, Eshita and Naika, Mahantesha and Ravooru, Nithin and Rao, Rajas M and Shingate, Prashant N and Sukhwal, Anshul and Sunitha, Margaret S and Upadhyay, Atul K and Vinekar, Rithvik S and Sowdhamini, Ramanathan} } @article {57789, title = {The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera).}, journal = {Genomics}, volume = {112}, year = {2020}, month = {01/2020}, pages = {621-628}, abstract = {

Moringa oleifera is a plant well-known for its nutrition value, drought resistance and medicinal properties. cDNA libraries from five different tissues (leaf, root, stem, seed and flower) of M. oleifera cultivar Bhagya were generated and sequenced. We developed a bioinformatics pipeline to assemble transcriptome, along with the previously published M. oleifera genome, to predict 17,148 gene models. Few candidate genes related to biosynthesis of secondary metabolites, vitamins and ion transporters were identified. Expressions were further confirmed by real-time quantitative PCR experiments for few promising leads. Quantitative estimation of metabolites, as well as elemental analysis, was also carried out to support our observations. Enzymes in the biosynthesis of vitamins and metabolites like quercetin and kaempferol are highly expressed in leaves, flowers and seeds. The expression of iron transporters and calcium storage proteins were observed in root and leaves. In general, leaves retain the highest amount of small molecules of interest.

}, issn = {1089-8646}, doi = {10.1016/j.ygeno.2019.04.014}, author = {Pasha, Shaik Naseer and Shafi, K Mohamed and Joshi, Adwait G and Meenakshi, Iyer and Harini, K and Mahita, Jarjapu and Sajeevan, Radha Sivarajan and Karpe, Snehal D and Ghosh, Pritha and Nitish, Sathyanarayanan and Gandhimathi, A and Mathew, Oommen K and Prasanna, Subramanian Hari and Malini, Manoharan and Mutt, Eshita and Naika, Mahantesha and Ravooru, Nithin and Rao, Rajas M and Shingate, Prashant N and Sukhwal, Anshul and Sunitha, Margaret S and Upadhyay, Atul K and Vinekar, Rithvik S and Sowdhamini, Ramanathan} } @article {80094, title = {Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis.}, journal = {Sci Rep}, volume = {10}, year = {2020}, month = {2020 Jul 29}, pages = {12658}, abstract = {

Clitoria ternatea a perennial climber of the Fabaceae family, is well known for its agricultural and medical applications. It is also currently the only known member of the Fabaceae family that produces abundant amounts of the ultra-stable macrocyclic peptides, cyclotides, across all tissues. Cyclotides are a class of gene-encoded, disulphide-rich, macrocyclic peptides (26-37 residues) acting as defensive metabolites in several plant species. Previous transcriptomic studies have demonstrated the genetic origin of cyclotides from the Fabaceae plant family to be embedded in the albumin-1 genes, unlike its counterparts in other plant families. However, the complete mechanism of its biosynthesis and the repertoire of enzymes involved in cyclotide folding and processing remains to be understood. In this study, using RNA-Seq data and de novo transcriptome assembly of Clitoria ternatea, we have identified 71 precursor genes of cyclotides. Out of 71 unique cyclotide precursor genes obtained, 51 sequences display unique cyclotide domains, of which 26 are novel cyclotide sequences, arising from four individual tissues. MALDI-TOF mass spectrometry analysis of fractions from different tissue extracts, coupled with precursor protein sequences obtained from transcriptomic data, established the cyclotide diversity in this plant species. Special focus in this study has also been on identifying possible enzymes responsible for proper folding and processing of cyclotides in the cell. Transcriptomic mining for oxidative folding enzymes such as protein-disulphide isomerases (PDI), ER oxidoreductin-1 (ERO1) and peptidylprolyl cis-trans isomerases (PPIases)/cyclophilins, and their levels of expression are also reported. In particular, it was observed that the CtPDI genes formed plant-specific clusters among PDI genes as compared to those from other plant species. Collectively, this work provides insights into the biogenesis of the medicinally important cyclotides and establishes the expression of certain key enzymes participating in peptide biosynthesis. Also, several novel cyclotide sequences are reported and precursor sequences are analysed in detail. In the absence of a published reference genome, a comprehensive transcriptomics approach was adopted to provide an overview of diverse properties and constituents of C. ternatea.

}, issn = {2045-2322}, doi = {10.1038/s41598-020-69452-7}, author = {Kalmankar, Neha V and Venkatesan, Radhika and Balaram, Padmanabhan and Sowdhamini, Ramanathan} } @article {48884, title = {Decoding systems biology of plant stress for sustainable agriculture development and optimized food production.}, journal = {Prog Biophys Mol Biol}, volume = {145}, year = {2019}, month = {2018 Dec 15}, pages = {19-39}, abstract = {

Plants are essential facilitators of human life on planet earth. Plants play a critical functional role in mediating the quality of air, availability of food and the sustainability of agricultural resources. However, plants are in constant interaction with its environment and often hampered by various types of stresses like biotic and abiotic ones. Biotic stress is a significant reason for crop-loss and causes yield loss in the range of 31-42\%, post-harvest loss due to biotic stress is in the range of 6-20\%, and abiotic stress causes 6-20\% of the crop damage. Recognizing the molecular factors driving plant stress-related events, and developing molecular strategies to aid plants to tolerate, resist or adapt to biotic and abiotic stress are critical for sustainable agriculture practice. In this review, we discuss how recent advances in bioinformatics, plant genomics, and data science could help to improve our understanding of plant stress biology and improve the scale of global food production. We present various areas of scientific and technological advances, such as increased availability of genomics data through whole genome sequencing that require attention. We also discuss emerging techniques including CRISPR-Cas9 based genome engineering systems to develop plant varieties that can handle combinatorial stress signals. Growing trend of converging multiple omics technologies and availability of accurate, multi-scale models of plant stress through the study of orthologs and synteny studies, would improve our knowledge of how plants perceive, respond, and manage stress to thrive as resilient crop species and thus help to reduce global food crisis.

}, issn = {1873-1732}, doi = {10.1016/j.pbiomolbio.2018.12.002}, author = {Shameer, Khader and Naika, Mahantesha B N and Shafi, K Mohamed and Sowdhamini, Ramanathan} } @article {99943, title = {Fold combinations in multi-domain proteins.}, journal = {Bioinformation}, volume = {15}, year = {2019}, month = {2019}, pages = {342-350}, abstract = {

Domain-domain interactions in multi-domain proteins play an important role in the combined function of individual domains for the overall biological activity of the protein. The functions of the tethered domains are often coupled and hence, limited numbers of domain architectures with defined folds are known in nature. Therefore, it is of interest to document the available fold-fold combinations and their preference in multi-domain proteins. Hence, we analyzed all multi-domain proteins with known structures in the protein databank and observed that only about 860 fold-fold combinations are present among them. Analyses of multi-domain proteins represented in sequence database result in recognition of 29,860 fold-fold combinations and it accounts for only 2.8\% of the theoretically possible 1,036,080 (1439C2) fold-fold combinations. The observed preference for fold-fold combinations in multi-domain proteins is interesting in the context of multiple functions through structural adaptation by gene fusion.

}, issn = {0973-2063}, doi = {10.6026/97320630015342}, author = {Naveenkumar, Nagarajan and Kumar, Gayatri and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy and Vishwanath, Sneha} } @article {59715, title = {A Functional Agonist of Insect Olfactory Receptors: Behavior, Physiology and Structure.}, journal = {Front Cell Neurosci}, volume = {13}, year = {2019}, month = {2019}, pages = {134}, abstract = {

Chemical signaling is ubiquitous and employs a variety of receptor types to detect the cacophony of molecules relevant for each living organism. Insects, our most diverse taxon, have evolved unique olfactory receptors with as little as 10\% sequence identity between receptor types. We have identified a promiscuous volatile, 2-methyltetrahydro-3-furanone (coffee furanone), that elicits chemosensory and behavioral activity across multiple insect orders and receptors. and physiology showed that coffee furanone was detected by roughly 80\% of the recorded neurons expressing the insect-specific olfactory receptor complex in the antenna of , at concentrations similar to other known, and less promiscuous, ligands. Neurons expressing specialized receptors, other chemoreceptor types, or mutants lacking the complex entirely did not respond to this compound. This indicates that coffee furanone is a promiscuous ligand for the insect olfactory receptor complex itself and did not induce non-specific cellular responses. In addition, we present homology modeling and docking studies with selected olfactory receptors that suggest conserved interaction regions for both coffee furanone and known ligands. Apart from its physiological activity, this known food additive elicits a behavioral response for several insects, including mosquitoes, flies, and cockroaches. A broad-scale behaviorally active molecule non-toxic to humans thus has significant implications for health and agriculture. Coffee furanone serves as a unique tool to unlock molecular, physiological, and behavioral relationships across this diverse receptor family and animal taxa.

}, issn = {1662-5102}, doi = {10.3389/fncel.2019.00134}, author = {Batra, Srishti and Corcoran, Jacob and Zhang, Dan-Dan and Pal, Pramit and K P, Umesh and Kulkarni, Renuka and L{\"o}fstedt, Christer and Sowdhamini, Ramanathan and Olsson, Shannon B} } @article {55796, title = {GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies.}, journal = {Database (Oxford)}, volume = {2019}, year = {2019}, month = {2019 01 01}, abstract = {

Since proteins evolve by divergent evolution, proteins with distant homology to each other may or may not bear similar functions. Improved computational approaches are required to recognize distant homologues that are functionally similar. One of the methods of assigning function to sequences is to use profiles derived from sequences of known structure. We describe an update of the Genomic Distribution of protein structural domain Superfamilies (GenDiS) database, namely GenDiS+, which provides a projection of SCOP superfamily members on the sequence space (NR database, NCBI). The sequences are validated using structure-based sequence alignment profiles and domain and full-length sequence alignments. GenDiS+ is a {\textquoteleft}tour de force{\textquoteright} for detecting homologues within around 160 000 taxonomic identifiers, starting from nearly 11 000 domains of known structure. Features, like full-sequence alignment and phylogeny, domain sequence alignment and phylogeny, list of associated structural and sequence domains with strength of interactions, links to databases like Pfam, UniProt and ModBase and list of sequences with a PDB structure, are provided.

}, issn = {1758-0463}, doi = {10.1093/database/baz042}, author = {Iyer, Meenakshi S and Bhargava, Kartik and Pavalam, Murugavel and Sowdhamini, Ramanathan} } @article {50994, title = {Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: .}, journal = {Bioinform Biol Insights}, volume = {13}, year = {2019}, month = {2019}, pages = {1177932218821362}, abstract = {

Computational approaches to high-throughput data are gaining importance because of explosion of sequences in the post-genomic era. This explosion of sequence data creates a huge gap among the domains of sequence structure and function, since the experimental techniques to determine the structure and function are very expensive, time taking, and laborious in nature. Therefore, there is an urgent need to emphasize on the development of computational approaches in the field of biological systems. Engagement of proteins in quaternary arrangements, such as domain swapping, might be relevant for higher compatibility of such genes at stress conditions. In this study, the capacity to engage in domain swapping was predicted from mere sequence information in the whole genome of holy Basil (), which is well known to be an anti-stress agent. Approximately, one-fourth of the proteins of are predicted to undergo three-dimensional (3D)-domain swapping. Furthermore, function annotation was carried out on all the predicted domain-swap sequences from the and for their distribution in different Pfam protein families and gene ontology (GO) terms. These domain-swapped protein sequences are associated with many Pfam protein families with a wide range of GO annotation terms. A comparative analysis of domain-swap-predicted sequences in with gene products in reveals that around 26\% (2522 sequences) are close homologues across the 2 genomes. Functional annotation of predicted domain-swapped sequences infers that predicted domain-swap sequences are involved in diverse molecular functions, such as in gene regulation of abiotic stress conditions and adaptation to different environmental niches. Finally, the positively predicted sequences of and were also examined for their presence in stress regulome, as recorded in our STIFDB database, to check the involvement of these proteins in different abiotic stresses.

}, issn = {1177-9322}, doi = {10.1177/1177932218821362}, author = {Upadhyay, Atul Kumar and Sowdhamini, Ramanathan} } @article {56126, title = {Genome-Wide Search for Tyrosine Phosphatases in the Human Genome Through Computational Approaches Leads to the Discovery of Few New Domain Architectures.}, journal = {Evol Bioinform Online}, volume = {15}, year = {2019}, month = {2019}, pages = {1176934319840289}, abstract = {

Reversible phosphorylation maintained by protein kinases and phosphatases is an integral part of intracellular signalling, and phosphorylation on tyrosine is extensively utilised in higher eukaryotes. Tyrosine phosphatases are enzymes that not only scavenge phosphotyrosine but are also involved in wide range of signalling pathways. As a result, mutations in these enzymes have been implicated in the pathogenesis of several diseases like cancer, autoimmune disorders, and muscle-related diseases. The genes that harbour phosphatase domain also display diversity in co-existing domains suggesting the recruitment of the catalytic machinery in diverse pathways. We have examined the current draft of the human genome, using a combination of 3 sequence search methods and validations, and identified 101 genes encoding tyrosine phosphatase-containing gene products, agreeing with previous reports. Such gene products adopt 37 unique domain architectures (DAs), including few new ones and harbouring few co-existing domains that have not been reported before. This semi-automated computational approach for detection of gene products belonging to a particular superfamily can now be easily applied at whole genome level on other mammalian genomes and for other protein domains as well.

}, issn = {1176-9343}, doi = {10.1177/1176934319840289}, author = {Bhattacharyya, Teerna and Sowdhamini, Ramanathan} } @article {50998, title = {Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions.}, journal = {Biol Direct}, volume = {14}, year = {2019}, month = {2019 Jan 15}, pages = {1}, abstract = {

BACKGROUND: Protein-protein interactions are crucial for normal biological processes and to regulate cellular reactions that affect gene expression and function. Several previous studies have emphasized the roles of residues at the interface of protein-protein complexes in conferring stability and specificity to the complex. Interface residues in a protein are well known for their interactions with sidechain and main chain atoms with the interacting protein. However, the extent of intra-protein interactions involving interface residues in a protein-protein complex and their relative contribution in comparison to inter-protein interactions are not clearly understood. This paper probes this feature using a dataset of protein-protein complexes of known 3-D structure.

RESULTS: We have analysed a dataset of 45 transient protein-protein complex structures with at least one of the interacting proteins with a known structure available also in the unbound form. We observe that a large proportion of interface residues (1608 out of 2137 interface residues, 75\%) are involved in intra and inter-protein interactions simultaneously. The amino acid propensities of such interfacial residues involved in bifurcated interactions are found to be highly similar to the general propensities to occur at protein-protein interfaces. Finally, we observe that a majority (83\%) of intra-protein interactions of interface residues with bifurcated interactions, are also observed in the protein uncomplexed form.

CONCLUSIONS: We have shown, to the best of our knowledge for the first time, that a vast majority of the protein-protein interface residues are involved in extensive intra-protein interactions apart from inter-protein interactions. For a majority of such interface residues the microenvironment in the tertiary structure is pre-formed and retained upon complex formation with its cognate partner during transient interactions.

REVIEWERS: This article was reviewed by Arumay Pal and Mallur Madhusudhan.

}, issn = {1745-6150}, doi = {10.1186/s13062-019-0232-2}, author = {Jayashree, Srinivasan and Murugavel, Pavalam and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {64899, title = {Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.}, journal = {Nat Commun}, volume = {10}, year = {2019}, month = {2019 Sep 11}, pages = {4127}, abstract = {

Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.

}, issn = {2041-1723}, doi = {10.1038/s41467-019-11931-1}, author = {Sathyanarayanan, Nitish and Cannone, Giuseppe and Gakhar, Lokesh and Katagihallimath, Nainesh and Sowdhamini, Ramanathan and Ramaswamy, Subramanian and Vinothkumar, Kutti R} } @article {53182, title = {PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe.}, journal = {Database (Oxford)}, volume = {2019}, year = {2019}, month = {2019 Jan 01}, abstract = {

The number of protein structures is increasing due to the individual initiatives and rapid development of structure determination techniques. Structure-based sequence alignments of distantly related proteins enable the investigation of structural, evolutionary and functional relationships between proteins and their domains leading to their common evolutionary origin. Protein Alignments organized as Structural Superfamilies (PASS2) is a database that provides such alignments of members of protein domain superfamilies of known structure and with less than 40\% sequence identity. PASS2 has been continuously updated in accordance to Structural Classification of Proteins (SCOP), and now Structural Classification of Proteins - extended (SCOPe). The current update directly corresponds to SCOPe 2.06, dealing with 2006 domain superfamilies of known structure and about 14\ 000 domains. Alignments have been augmented by features such as hidden Markov models, highly conserved residues, structural motifs and gene ontology terms, which are available for download. In this update, we introduce the concepts of {\textquoteright}extreme structural outliers{\textquoteright} and {\textquoteright}split superfamilies{\textquoteright} as well.

}, issn = {1758-0463}, doi = {10.1093/database/baz028}, author = {Ghosh, Pritha and Bhattacharyya, Teerna and Mathew, Oommen K and Sowdhamini, Ramanathan} } @article {64330, title = {Specialized structural and functional roles of residues selectively conserved in subfamilies of the pleckstrin homology domain family.}, journal = {FEBS Open Bio}, year = {2019}, month = {2019 Aug 22}, abstract = {

Homologous domains embedded in multi-domain proteins of different domain architectures may exhibit subtle, but important, differences in their structure and function. Here we consider two multi-domain proteins, ARNO and GRK2, which have very different domain architectures but both contain pleckstrin homology (PH) domains. We analyzed the roles of residues selectively conserved in these sub-families of PH-domains from ARNO and GRK2 proteins. Domain architecture-specific residues in PH-domain are found to contribute to structural and functional specialization of ARNO and GRK2 in terms of (i) specific intra- and inter-protein interactions, (ii) specificity for phospholipids and (iii) participation in conformational excursions, leading to various functional forms. Our approach can also be applied to subfamilies of other protein families to identify subfamily-specific residues and their specialized roles.

}, issn = {2211-5463}, doi = {10.1002/2211-5463.12725}, author = {Naveenkumar, Nagarajan and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {60326, title = {Topology prediction of insect olfactory receptors.}, journal = {Curr Opin Struct Biol}, volume = {55}, year = {2019}, month = {2019 Jun 21}, pages = {194-203}, abstract = {

Olfactory receptors are important transmembrane proteins that enable organisms to perceive odours and react to them. Structural understanding of insect olfactory receptors is scarce. In this review, we discuss different transmembrane helix prediction methods, consensus methods, topology prediction methods which can enable topology prediction of these proteins. We discuss the current success rates by applying the algorithms on few G-protein coupled receptors of known structure and olfactory receptor sequences and outstanding challenges. Finally, we discuss the impact of topology prediction on biology and modeling of ORs.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2019.05.014}, author = {Tiwari, Vikas and Karpe, Snehal D and Sowdhamini, Ramanathan} } @article {43842, title = {Vaccination and immunization strategies to design Aedes aegypti salivary protein based subunit vaccine tackling Flavivirus infection.}, journal = {Int J Biol Macromol}, volume = {122}, year = {2019}, month = {2018 Sep 13}, pages = {1203-1211}, abstract = {

Flavivirus causes arthropod-borne severe diseases that sometimes lead to the death. The Flavivirus species including Dengue virus, Zika virus and yellow fever virus are transmitted by the bite of Aedes mosquitoes. All these viral species target the people living in their respective endemic zone causing a high mortality rate. Recent studies show that immune factors present in the Ae. aegypti saliva is the hidden culprit promoting blood meal collection, suppressing host immune molecules and promoting disease establishment. This study was designed to develop a subunit vaccine using Aedes mosquito salivary proteins targeting the aforementioned Flaviviruses. Subunit vaccine was designed very precisely by combining the immunogenic B-cell epitope with CTL and HTL epitopes and also suitable adjuvant and linkers. Immunogenicity, allergenicity and physiochemical characterization were also performed for scientific validation. Molecular docking and molecular dynamics simulations studies were carried out to confirm the stable affinity between the vaccine protein (3D) and TLR3 receptor. At last, in silico cloning was executed to get the subunit vaccine restriction clone into pET28a vectro to express it in microbial expression system. Additionally, this study warrants the experimental evaluation for the validation purposes.

}, issn = {1879-0003}, doi = {10.1016/j.ijbiomac.2018.09.071}, author = {Pandey, Rajan Kumar and Dahiya, Surbhi and Mahita, Jarjapu and Sowdhamini, Ramanathan and Prajapati, Vijay Kumar} } @article {38421, title = {Genome-wide survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural classes.}, journal = {Mol Omics}, year = {2018}, month = {2018 Jul 04}, abstract = {

Domains are the basic building blocks of proteins which can combine to give rise to different domain architectures. Annotation of domains in a sequence is the first step towards understanding the biological function. Since there are a limited number of folds and evolutionarily related proteins have a similar structure, function can be inferred through remote homology. Computational sequence searches were performed for remote homologues on genomes of around \~{}160 000 different organisms, starting from nearly 11 000 superfamily queries of known structure. Case studies revealed that most of the associated domains are involved in the same biological process. Using all the proteins predicted to have at least one structural domain, a coverage of 61\% of Pfam families was achieved which is higher than the existing methods (43.36\% by SIFTS). Taxonomic analysis of the proteins revealed 493 superfamilies in all the major kingdoms of life and a few lateral gene transfers between viruses and cellular organisms. The distribution of remote homologues across different classes, folds and superfamilies was studied and reveals that sequences are unequally distributed across structural classes. Finally, domain architectures were computed for the homologues and these data were compiled for each superfamily and organism.

}, issn = {2515-4184}, doi = {10.1039/c8mo00008e}, author = {Iyer, Meenakshi S and Joshi, Adwait G and Sowdhamini, Ramanathan} } @article {29621, title = {Investigating the effect of key mutations on the conformational dynamics of Toll-like receptor dimers through molecular dynamics simulations and protein structure networks.}, journal = {Proteins}, year = {2018}, month = {2018 Jan 31}, abstract = {

The Toll-like receptors (TLRs) are critical components of the innate immune system due to their ability to detect conserved pathogen-associated molecular patterns, present in bacteria, viruses and other microorganisms. Ligand detection by TLRs leads to a signalling cascade, mediated by interactions among TIR domains present in the receptors, the bridging adaptors as well as sorting adaptors. The BB loop is a highly conserved region present in the TIR domain and is crucial for mediating interactions among TIR domain-containing proteins. Mutations in the BB loop of the Toll-like receptors, such as the A795P mutation in TLR3 and the P712H mutation (Lpsd mutation) in TLR4, have been reported to disrupt or alter downstream signalling. While the phenotypic effect of these mutations is known, the underlying effect of these mutations on the structure, dynamics and interactions with other TIR domain-containing proteins is not well understood. Here, we have attempted to investigate the effect of the BB loop mutations on the dimer form of TLRs, using TLR2 and TLR3 as case studies. Our results based on molecular dynamics simulations, protein-protein interaction analyses and protein structure network analyses highlight significant differences between the dimer interfaces of the wild-type and mutant forms and provide a logical reasoning for the effect of these mutations on adaptor binding to TLRs. Furthermore, it also leads us to propose a hypothesis for the differential requirement of signalling and bridging adaptors by TLRs. This could aid in further understanding of the mechanisms governing such signalling pathways. This article is protected by copyright. All rights reserved.

}, issn = {1097-0134}, doi = {10.1002/prot.25467}, author = {Mahita, Jarjapu and Sowdhamini, Ramanathan} } @article {29620, title = {Probing subtle conformational changes induced by phosphorylation and point mutations in the TIR domains of TLR2 and TLR3.}, journal = {Proteins}, year = {2018}, month = {2018 Jan 31}, abstract = {

Extensive research performed on Toll-like receptor (TLR) signalling has identified residues in the Toll/interleukin-1 receptor (TIR) domains that are essential for its proper functioning. Among these residues, those in BB loop are particularly significant as single amino acid mutations in this region can cause drastic changes in downstream signalling. However, while the effect of these mutations on the function is well studied (like the P681H mutation in TLR2, the A795P mutation in TLR3, and the P714H mutation in TLR4), their influence on the dynamics and inter-residue networks is not well understood. The effects of local perturbations induced by these mutations could propagate throughout the TIR domain, influencing interactions with other TIR domain-containing proteins. The identification of these subtle changes in inter-residue interactions can provide new insights and structural rationale for how single-point mutations cause drastic changes in TIR-TIR interactions. We employed molecular dynamics simulations and protein structure network (PSN) analyses to investigate the structural transitions with special emphasis on TLR2 and TLR3. Our results reveal that phosphorylation of the Tyr 759 residue in the TIR domain of TLR3 introduces rigidity to its BB loop. Subtle differences in the intra BB loop hydrogen bonding network between TLR3 and TLR2 are also observed. The PSN analyses indicate that the TIR domain is highly connected and pinpoints key differences in the inter-residue interactions between the wild-type and mutant TIR domains, suggesting that TIR domain structure is prone to allosteric effects, consistent with the current view of the influence of allostery on TLR signaling. This article is protected by copyright. All rights reserved.

}, issn = {1097-0134}, doi = {10.1002/prot.25471}, author = {Mahita, Jarjapu and Sowdhamini, Ramanathan} } @article {22812, title = {Bioinformatics comparisons of RNA-binding proteins of pathogenic and non-pathogenic Escherichia coli strains reveal novel virulence factors.}, journal = {BMC Genomics}, volume = {18}, year = {2017}, month = {2017 Aug 24}, pages = {658}, abstract = {

BACKGROUND: Pathogenic bacteria have evolved various strategies to counteract host defences. They are also exposed to environments that are undergoing constant changes. Hence, in order to survive, bacteria must adapt themselves to the changing environmental conditions by performing regulations at the transcriptional and/or post-transcriptional levels. Roles of RNA-binding proteins (RBPs) as virulence factors have been very well studied. Here, we have used a sequence search-based method to compare and contrast the proteomes of 16 pathogenic and three non-pathogenic E. coli strains as well as to obtain a global picture of the RBP landscape (RBPome) in E. coli.

RESULTS: Our results show that there are no significant differences in the percentage of RBPs encoded by the pathogenic and the non-pathogenic E. coli strains. The differences in the types of Pfam domains as well as Pfam RNA-binding domains, encoded by these two classes of E. coli strains, are also insignificant. The complete and distinct RBPome of E. coli has been established by studying all known E. coli strains till date. We have also identified RBPs that are exclusive to pathogenic strains, and most of them can be exploited as drug targets since they appear to be non-homologous to their human host proteins. Many of these pathogen-specific proteins were uncharacterised and their identities could be resolved on the basis of sequence homology searches with known proteins. Detailed structural modelling, molecular dynamics simulations and sequence comparisons have been pursued for selected examples to understand differences in stability and RNA-binding.

CONCLUSIONS: The approach used in this paper to cross-compare proteomes of pathogenic and non-pathogenic strains may also be extended to other bacterial or even eukaryotic proteomes to understand interesting differences in their RBPomes. The pathogen-specific RBPs reported in this study, may also be taken up further for clinical trials and/or experimental validations.

}, issn = {1471-2164}, doi = {10.1186/s12864-017-4045-3}, author = {Ghosh, Pritha and Sowdhamini, Ramanathan} } @article {16560, title = {Integrative modelling of TIR domain-containing adaptor molecule inducing interferon-β (TRIF) provides insights into its autoinhibited state.}, journal = {Biol Direct}, volume = {12}, year = {2017}, month = {2017 Apr 20}, pages = {9}, abstract = {

BACKGROUND: TRIF is a key protein in antiviral innate immunity, operating downstream of TLRs. TRIF activation leads to the production of interferon-β and pro-inflammatory cytokines. There is evidence from experiments to suggest that the N-terminal domain of TRIF binds to its TIR domain to avoid constitutive activation. However, no structure of a complex between the N-terminal domain and the TIR domain exists till date. The disordered nature of the region connecting the N-terminal domain and the TIR domain compounds the issue of elucidating the mechanism of autoinhibition of TRIF. In this study, we have employed an integrative approach consisting of mutual information analysis, docking, molecular dynamics simulations and residue network analysis, in combination with existing experimental data to provide a glimpse of TRIF in its autoinhibited state.

RESULTS: Our extensive docking approach reveals that the N-terminal domain binds to the BB loop-B helix region of the TIR domain, consistent with experimental observations. Long length molecular dynamics simulations of 1 microsecond performed on the docked model highlights residues participating in hydrogen bonding and hydrophobic interactions at the interface. A pair of residues present in the vicinity of the interface is also predicted by mutual information analysis, to co-evolve. Residues mediating long-range interactions within the TIR domain of TRIF were identified using residue network analysis.

CONCLUSIONS: Based on the results of the modelling and residue network analysis, we propose that the N-terminal domain binds to the BB loop region of the TIR domain, thereby preventing its homodimersation. The binding of TRIF to TLR3 or TRAM could induce a slight conformational change, causing the interactions between the N-terminal domain and TIR domain to disrupt, thereby exposing the BB loop and rendering it amenable for higher-order oligomerisation.

REVIEWERS: This article was reviewed by Michael Gromiha, Srikrishna Subramaniam and Peter Bond (nominated by Chandra Verma).

}, issn = {1745-6150}, doi = {10.1186/s13062-017-0179-0}, author = {Mahita, Jarjapu and Sowdhamini, Ramanathan} } @article {24294, title = {Molecular mechanisms and structural features of cardiomyopathy-causing troponin T mutants in the tropomyosin overlap region.}, journal = {Proc Natl Acad Sci U S A}, year = {2017}, month = {2017 Oct 02}, abstract = {

Point mutations in genes encoding sarcomeric proteins are the leading cause of inherited primary cardiomyopathies. Among them are mutations in the TNNT2 gene that encodes cardiac troponin T (TnT). These mutations are clustered in the tropomyosin (Tm) binding region of TnT, TNT1 (residues 80-180). To understand the mechanistic changes caused by pathogenic mutations in the TNT1 region, six hypertrophic cardiomyopathy (HCM) and two dilated cardiomyopathy (DCM) mutants were studied by biochemical approaches. Binding assays in the absence and presence of actin revealed changes in the affinity of some, but not all, TnT mutants for Tm relative to WT TnT. HCM mutants were hypersensitive and DCM mutants were hyposensitive to Ca(2+) in regulated actomyosin ATPase activities. To gain better insight into the disease mechanism, we modeled the structure of TNT1 and its interactions with Tm. The stability predictions made by the model correlated well with the affinity changes observed in vitro of TnT mutants for Tm. The changes in Ca(2+) sensitivity showed a strong correlation with the changes in binding affinity. We suggest the primary reason by which these TNNT2 mutations between residues 92 and 144 cause cardiomyopathy is by changing the affinity of TnT for Tm within the TNT1 region.

}, issn = {1091-6490}, doi = {10.1073/pnas.1710354114}, author = {Gangadharan, Binnu and Sunitha, Margaret S and Mukherjee, Souhrid and Chowdhury, Ritu Roy and Haque, Farah and Sekar, Narendrakumar and Sowdhamini, Ramanathan and Spudich, James A and Mercer, John A} } @article {12269, title = {Specificity and stability of transient protein-protein interactions.}, journal = {Curr Opin Struct Biol}, volume = {44}, year = {2017}, month = {2017 Jan 11}, pages = {77-86}, abstract = {

Remarkable features that are achieved in a protein-protein complex to precise levels are stability and specificity. Deviation from the normal levels of specificity and stability, which is often caused by mutations, could result in disease conditions. Chemical nature, 3-D arrangement and dynamics of interface residues code for both specificity and stability. This article reviews roles of interfacial residues in transient protein-protein complexes. It is proposed that aside from hotspot residues conferring stability to the complex, a small set of {\textquoteright}rigid{\textquoteright} residues at the interface that maintain conformation between complexed and uncomplexed forms, play a major role in conferring specificity. Exceptionally, {\textquoteright}super hotspot{\textquoteright} residues, which confer both stability and specificity, are attractive sites for interaction with small molecule inhibitors.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2016.12.010}, author = {Vishwanath, Sneha and Sukhwal, Anshul and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {3545, title = {An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016}, pages = {e0151323}, abstract = {

The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs). Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS), which also provides a web service API (Application Programming Interface) for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0151323}, author = {Dhanyalakshmi, K H and Naika, Mahantesha B N and Sajeevan, R S and Mathew, Oommen K and Shafi, K Mohamed and Sowdhamini, Ramanathan and N Nataraja, Karaba} } @article {6134, title = {Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016}, pages = {e0159627}, abstract = {

3D-domain swapping is one of the mechanisms of protein oligomerization and the proteins exhibiting this phenomenon have many biological functions. These proteins, which undergo domain swapping, have acquired much attention owing to their involvement in human diseases, such as conformational diseases, amyloidosis, serpinopathies, proteionopathies etc. Early realisation of proteins in the whole human genome that retain tendency to domain swap will enable many aspects of disease control management. Predictive models were developed by using machine learning approaches with an average accuracy of 78\% (85.6\% of sensitivity, 87.5\% of specificity and an MCC value of 0.72) to predict putative domain swapping in protein sequences. These models were applied to many complete genomes with special emphasis on the human genome. Nearly 44\% of the protein sequences in the human genome were predicted positive for domain swapping. Enrichment analysis was performed on the positively predicted sequences from human genome for their domain distribution, disease association and functional importance based on Gene Ontology (GO). Enrichment analysis was also performed to infer a better understanding of the functional importance of these sequences. Finally, we developed hinge region prediction, in the given putative domain swapped sequence, by using important physicochemical properties of amino acids.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0159627}, author = {Upadhyay, Atul Kumar and Sowdhamini, Ramanathan} } @article {8107, title = {Genome-wide survey and phylogeny of S-Ribosylhomocysteinase (LuxS) enzyme in bacterial genomes.}, journal = {BMC Genomics}, volume = {17}, year = {2016}, month = {2016}, pages = {742}, abstract = {

BACKGROUND: The study of survival and communication of pathogenic bacteria is important to combat diseases caused by such micro-organisms. Bacterial cells communicate with each other using a density-dependent cell-cell communication process called Quorum Sensing (QS). LuxS protein is an important member of interspecies quorum-sensing system, involved in the biosynthesis of Autoinducer-2 (AI-2), and has been identified as a drug target. Despite the above mentioned significance, their evolution has not been fully studied, particularly from a structural perspective.

RESULTS: Search for LuxS in the non-redundant database of protein sequences yielded 3106 sequences. Phylogenetic analysis of these sequences revealed grouping of sequences into five distinct clusters belonging to different phyla and according to their habitat. A majority of the neighbouring genes of LuxS have been found to be hypothetical proteins. However, gene synteny analyses in different bacterial genomes reveal the presence of few interesting gene neighbours. Moreover, LuxS gene was found to be a component of an operon in only six out of 36 genomes. Analysis of conserved motifs in representative LuxS sequences of different clusters revealed the presence of conserved motifs common to sequences of all the clusters as well as motifs unique to each cluster. Homology modelling of LuxS protein sequences of each cluster revealed few structural features unique to protein of each cluster. Analyses of surface electrostatic potentials of the homology models of each cluster showed the interactions that are common to all the clusters, as well as cluster-specific potentials and therefore interacting partners, which may be unique to each cluster.

CONCLUSIONS: LuxS protein evolved early during the course of bacterial evolution, but has diverged into five subtypes. Analysis of sequence motifs and homology models of representative members reveal cluster-specific structural properties of LuxS. Further, it is also shown that LuxS protein may be involved in various protein-protein or protein-RNA interactions, which may regulate the activity of LuxS proteins in bacteria.

}, issn = {1471-2164}, doi = {10.1186/s12864-016-3002-x}, author = {Rao, Rajas M and Pasha, Shaik Naseer and Sowdhamini, Ramanathan} } @article {16565, title = {Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera.}, journal = {Genome Biol Evol}, volume = {8}, year = {2016}, month = {2016 Sep 26}, pages = {2879-2895}, abstract = {

We developed a computational pipeline for homology based identification of the complete repertoire of olfactory receptor (OR) genes in the Asian honey bee species, Apis florea Apis florea is phylogenetically the most basal honey bee species and also the most distant sister species to the Western honey bee Apis mellifera, for which all OR genes had been identified before. Using our pipeline, we identified 180 OR genes in A. florea, which is very similar to the number of ORs identified in A. mellifera (177 ORs). Many characteristics of the ORs including gene structure, synteny of tandemly repeated ORs and basic phylogenetic clustering are highly conserved. The composite phylogenetic tree of A. florea and A. mellifera ORs could be divided into 21 clades which are in harmony with the existing Hymenopteran tree. However, we found a few nonorthologous OR relationships between both species as well as independent pseudogenization of ORs suggesting separate evolutionary changes. Particularly, a subgroup of the OR gene clade XI, which had been hypothesized to code cuticular hydrocarbon receptors showed a high number of species-specific ORs RNAseq analysis detected a total number of 145 OR transcripts in male and 162 in female antennae. Most of the OR genes were highly expressed on the female antennae. However, we detected five distinct male-biased OR genes, out of which three genes (AfOr11, AfOr18, AfOr170P) were shown to be male-biased in A. mellifera, too, thus corroborating a behavioral function in sex-pheromone communication.

}, issn = {1759-6653}, doi = {10.1093/gbe/evw202}, author = {Karpe, Snehal D and Jain, Rikesh and Brockmann, Axel and Sowdhamini, Ramanathan} } @article {8344, title = {An in silico approach towards the identification of novel inhibitors of the TLR-4 signaling pathway.}, journal = {J Biomol Struct Dyn}, volume = {34}, year = {2016}, month = {2016 Jun}, pages = {1345-62}, abstract = {

Precise functioning and fine-tuning of Toll-like receptor 4 (TLR4) signaling is a critical requirement for the smooth functioning of the innate immune system, since aberrant TLR4 activation causes excessive production of pro-inflammatory cytokines and interferons. This can result in life threatening conditions such as septic shock and other inflammatory disorders. The TRIF-related adaptor molecule (TRAM) adaptor protein is unique to the TLR4 signaling pathway and abrogation of TRAM-mediated TLR4 signaling is a promising strategy for developing therapeutics aimed at disrupting TRAM interactions with other components of the TLR4 signaling complex. The VIPER motif from the vaccinia virus-producing protein, A46 has been reported to disrupt TRAM-TLR4 interactions. We have exploited this information, in combination with homology modeling and docking approaches, to identify a potential binding site on TRAM lined by the BB loop and αC helix. Virtual screening of commercially available small molecules targeting the binding site enabled to short-list 12 small molecules to abrogate TRAM-mediated TLR4 signaling. Molecular dynamics and molecular mechanics calculations have been performed for the analysis of these receptor-ligand interactions.

}, issn = {1538-0254}, doi = {10.1080/07391102.2015.1079243}, author = {Mahita, Jarjapu and Harini, K and Rao Pichika, Mallikarjuna and Sowdhamini, Ramanathan} } @article {11622, title = {Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.}, journal = {Brief Bioinform}, volume = {17}, year = {2016}, month = {2016 Sep}, pages = {841-62}, abstract = {

Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics. Ascribing functional roles and/or clinical significances to single nucleotide variants identified from a next-generation sequencing study is an important step in genome interpretation. Experimental characterization of all the observed functional variants is yet impractical; thus, the prediction of functional and/or regulatory impacts of the various mutations using in silico approaches is an important step toward the identification of functionally significant or clinically actionable variants. The relationships between genotypes and the expressed phenotypes are multilayered and biologically complex; such relationships present numerous challenges and at the same time offer various opportunities for the design of in silico variant assessment strategies. Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions. In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants. We discuss the currently available approaches and major challenges from the perspective of protein sequence, structure, function and interactions that require consideration when interpreting the impact of putatively functional variants. We also discuss the relevance of incorporating integrated workflows for predicting the biomedical impact of the functionally important variations encoded in a genome, exome or transcriptome. Finally, we propose a framework to classify variant assessment approaches and strategies for incorporation of variant assessment within electronic health records.

}, issn = {1477-4054}, doi = {10.1093/bib/bbv084}, author = {Shameer, Khader and Tripathi, Lokesh P and Kalari, Krishna R and Dudley, Joel T and Sowdhamini, Ramanathan} } @article {5299, title = {Molecular Dynamics Simulations and Structural Analysis to Decipher Functional Impact of a Twenty Residue Insert in the Ternary Complex of Mus musculus TdT Isoform.}, journal = {PLoS One}, volume = {11}, year = {2016}, month = {2016}, pages = {e0157286}, abstract = {

Insertions/deletions are common evolutionary tools employed to alter the structural and functional repertoire of protein domains. An insert situated proximal to the active site or ligand binding site frequently impacts protein function; however, the effect of distal indels on protein activity and/or stability are often not studied. In this paper, we have investigated a distal insert, which influences the function and stability of a unique DNA polymerase, called terminal deoxynucleotidyl transferase (TdT). TdT (EC:2.7.7.31) is a monomeric 58 kDa protein belonging to family X of eukaryotic DNA polymerases and known for its role in V(D)J recombination as well as in non-homologous end-joining (NHEJ) pathways. Two murine isoforms of TdT, with a length difference of twenty residues and having different biochemical properties, have been studied. All-atom molecular dynamics simulations at different temperatures and interaction network analyses were performed on the short and long-length isoforms. We observed conformational changes in the regions distal to the insert position (thumb subdomain) in the longer isoform, which indirectly affects the activity and stability of the enzyme through a mediating loop (Loop1). A structural rationale could be provided to explain the reduced polymerization rate as well as increased thermosensitivity of the longer isoform caused by peripherally located length variations within a DNA polymerase. These observations increase our understanding of the roles of length variants in introducing functional diversity in protein families in general.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0157286}, author = {Mutt, Eshita and Sowdhamini, Ramanathan} } @article {5302, title = {PIMA: Protein-Protein interactions in Macromolecular Assembly - a web server for its Analysis and Visualization.}, journal = {Bioinformation}, volume = {12}, year = {2016}, month = {2016}, pages = {9-11}, abstract = {

Protein-protein interactions are essential for the basic biological machinery of the cell. This is important for processes like protein synthesis, enzyme kinetics, molecular assembly and signal transduction. A high number of macromolecular structural complexes are known due to recent advances in structure determination techniques. Therefore, it is of interest to develop an interactive tool to objectively analyze large protein complexes. Hence, we describe the development and utility of a web enabled application named {\textquoteright}Protein-Protein Interaction in Macro-molecular Assembly{\textquoteright} (PIMA) for the analysis of large protein assemblies. The intricate details of physical interactions amongst protein subunits in a large complex are presented as simple user preferred interactive network diagrams.

}, issn = {0973-2063}, doi = {10.6026/97320630012009}, author = {Kaleeckal Mathew, Oommen and Sowdhamini, Ramanathan} } @article {7043, title = {PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.}, journal = {Bioinform Biol Insights}, volume = {10}, year = {2016}, month = {2016}, pages = {105-9}, abstract = {

Protein-protein interactions play a very important role in the process of cellular functionality. Intricate details about the interactions between the proteins in a macromolecular assembly are important to understand the function and significance of protein complexes. We are reporting about a database of protein-protein interactions in huge macromolecular assemblies (PIMADb) that records the intrinsic details of 189,532 interchain interactions in 40,049 complexes from the Protein Data Bank. These details include the results of the quantification and analysis of all the interactions in the complex. The availability of interprotomer interaction networks can enable the design of point mutation experiments. PIMADb can be accessed from the URL: http://caps.ncbs.res.in/pimadb.

}, issn = {1177-9322}, doi = {10.4137/BBI.S38416}, author = {Mathew, Oommen K and Sowdhamini, Ramanathan} } @article {5311, title = {Protein sequence design and its applications.}, journal = {Curr Opin Struct Biol}, volume = {37}, year = {2016}, month = {2016 Apr}, pages = {71-80}, abstract = {

Design of proteins has far-reaching potentials in diverse areas that span repurposing of the protein scaffold for reactions and substrates that they were not naturally meant for, to catching a glimpse of the ephemeral proteins that nature might have sampled during evolution. These non-natural proteins, either in synthesized or virtual form have opened the scope for the design of entities that not only rival their natural counterparts but also offer a chance to visualize the protein space continuum that might help to relate proteins and understand their associations. Here, we review the recent advances in protein engineering and design, in multiple areas, with a view to drawing attention to their future potential.

}, issn = {1879-033X}, doi = {10.1016/j.sbi.2015.12.004}, author = {Sandhya, Sankaran and Mudgal, Richa and Kumar, Gayatri and Sowdhamini, Ramanathan and Srinivasan, Narayanaswamy} } @article {807, title = {Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space.}, journal = {Bioinformatics}, volume = {32}, year = {2016}, month = {2015 Oct 10}, pages = {338-44}, chapter = {338}, abstract = {

MOTIVATION: In the post-genomic era, automatic annotation of protein sequences using computational homology-based methods is highly desirable. However, often protein sequences diverge to an extent where detection of homology and automatic annotation transfer is not straightforward. Sophisticated approaches to detect such distant relationships are needed. We propose a new approach to identify deep evolutionary relationships of proteins to overcome shortcomings of the available methods.

RESULTS: We have developed a method to identify remote homologues more effectively from any protein sequence database by using several cascading events with Hidden Markov Models (C-HMM). We have implemented clustering of hits and profile generation of hit clusters to effectively reduce the computational timings of the cascaded sequence searches. Our C-HMM approach could cover 94, 83 and 40\% coverage at family, superfamily and fold levels, respectively, when applied on diverse protein folds. We have compared C-HMM with various remote homology detection methods and discuss the trade-offs between coverage and false positives.

AVAILABILITY AND IMPLEMENTATION: A standalone package implemented in Java along with a detailed documentation can be downloaded from https://github.com/RSLabNCBS/C-HMMSupplementary information: Supplementary data are available at Bioinformatics online.

CONTACT: mini@ncbs.res.in.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btv538}, author = {Kaushik, Swati and Nair, Anu G and Mutt, Eshita and Subramanian, Hari Prasanna and Sowdhamini, Ramanathan} } @article {7679, title = {Revisiting Myosin Families Through Large-scale Sequence Searches Leads to the Discovery of New Myosins.}, journal = {Evol Bioinform Online}, volume = {12}, year = {2016}, month = {2016}, pages = {201-11}, abstract = {

Myosins are actin-based motor proteins involved in many cellular movements. It is interesting to study the evolutionary patterns and the functional attributes of various types of myosins. Computational search algorithms were performed to identify putative myosin members by phylogenetic analysis, sequence motifs, and coexisting domains. This study is aimed at understanding the distribution and the likely biological functions of myosins encoded in various taxa and available eukaryotic genomes. We report here a phylogenetic analysis of around 4,064 myosin motor domains, built entirely from complete or near-complete myosin repertoires incorporating many unclassified, uncharacterized sequences and new myosin classes, with emphasis on myosins from Fungi, Haptophyta, and other Stramenopiles, Alveolates, and Rhizaria (SAR). The identification of large classes of myosins in Oomycetes, Cellular slime molds, Choanoflagellates, Pelagophytes, Eustigmatophyceae, Fonticula, Eucoccidiorida, and Apicomplexans with novel myosin motif variants that are conserved and thus presumably functional extends our knowledge of this important family of motor proteins. This work provides insights into the distribution and probable function of myosins including newly identified myosin classes.

}, issn = {1176-9343}, doi = {10.4137/EBO.S39880}, author = {Pasha, Shaik Naseer and Meenakshi, Iyer and Sowdhamini, Ramanathan} } @article {8756, title = {RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.}, journal = {BMC Bioinformatics}, volume = {17}, year = {2016}, month = {2016 Oct 7}, pages = {411}, abstract = {

BACKGROUND: RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information.

RESULTS: The web server employs Hidden Markov Model scan (hmmscan) to enable association to a back-end database of structural and sequence families. The database (HMMRBP) comprises of 437 HMMs of RBP families of known structure that have been generated using structure-based sequence alignments and 746 sequence-centric RBP family HMMs. The input protein sequence is associated with structural or sequence domain families, if structure or sequence signatures exist. In case of association of the protein with a family of known structures, output features like, multiple structure-based sequence alignment (MSSA) of the query with all others members of that family is provided. Further, cognate RNA partner(s) for that protein, Gene Ontology (GO) annotations, if any and a homology model of the protein can be obtained. The users can also browse through the database for details pertaining to each family, protein or RNA and their related information based on keyword search or RNA motif search.

CONCLUSIONS: RStrucFam is a web server that exploits structurally conserved features of RBPs, derived from known family members and imprinted in mathematical profiles, to predict putative RBPs from sequence information. Proteins that fail to associate with such structure-centric families are further queried against the sequence-centric RBP family HMMs in the HMMRBP database. Further, all other essential information pertaining to an RBP, like overall function annotations, are provided. The web server can be accessed at the following link: http://caps.ncbs.res.in/rstrucfam .

}, issn = {1471-2105}, doi = {10.1186/s12859-016-1289-x}, author = {Ghosh, Pritha and Mathew, Oommen K and Sowdhamini, Ramanathan} } @article {11590, title = {Three-dimensional modelling of the voltage-gated sodium ion channel from Anopheles gambiae reveals spatial clustering of evolutionarily conserved acidic residues at the extracellular sites.}, journal = {Curr Neuropharmacol}, year = {2016}, month = {2016 Dec 05}, abstract = {

The eukaryotic voltage-gated sodium channel(e-Nav) is a large asymmetric transmembrane protein with important functions concerning neurological function. No structure has been resolved at high resolution for this protein. A homology model of the transmembrane and extracellular regions of an Anopheles gambiae para-like channel with emphasis on the pore entrance has been constructed, based upon the templates provided by a prokaryotic sodium channel and a potassium two-pore channel. The latter provides a template for the extracellular regions, which are located above the entrance to the pore, which is likely to open at a side of a dome formed by these loops. A model created with this arrangement shows a structure similar to low-resolution cryo-electron microscope images of a related structure. The pore entrance also shows favorable electrostatic interface. Residues responsible for the negative charge around the pore have been traced in phylogeny to highlight their importance. This model is intended for the study of pore-blocking toxins.

}, issn = {1875-6190}, author = {Vinekar, Rithvik S and Sowdhamini, Ramanathan} } @article {5312, title = {Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses.}, journal = {Nucleic Acids Res}, volume = {44}, year = {2016}, month = {2016 Apr 20}, pages = {3147-64}, abstract = {

Differentially evolved responses to various stress conditions in plants are controlled by complex regulatory circuits of transcriptional activators, and repressors, such as transcription factors (TFs). To understand the general and condition-specific activities of the TFs and their regulatory relationships with the target genes (TGs), we have used a homogeneous stress gene expression dataset generated on ten natural ecotypes of the model plantArabidopsis thaliana, during five single and six combined stress conditions. Knowledge-based profiles of binding sites for 25 stress-responsive TF families (187 TFs) were generated and tested for their enrichment in the regulatory regions of the associated TGs. Condition-dependent regulatory sub-networks have shed light on the differential utilization of the underlying network topology, by stress-specific regulators and multifunctional regulators. The multifunctional regulators maintain the core stress response processes while the transient regulators confer the specificity to certain conditions. Clustering patterns of transcription factor binding sites (TFBS) have reflected the combinatorial nature of transcriptional regulation, and suggested the putative role of the homotypic clusters of TFBS towards maintaining transcriptional robustness againstcis-regulatory mutations to facilitate the preservation of stress response processes. The Gene Ontology enrichment analysis of the TGs reflected sequential regulation of stress response mechanisms in plants.

}, issn = {1362-4962}, doi = {10.1093/nar/gkv1463}, author = {Barah, Pankaj and B N, Mahantesha Naika and Jayavelu, Naresh Doni and Sowdhamini, Ramanathan and Shameer, Khader and Bones, Atle M} } @article {1004, title = {172 Computational analysis and prediction of proteins that undergo domain swapping.}, journal = {J Biomol Struct Dyn}, volume = {33 Suppl 1}, year = {2015}, month = {2015}, pages = {112-3}, issn = {1538-0254}, doi = {10.1080/07391102.2015.1032809}, author = {Shingate, Prashant and Upadhyay, Atul and Khader, Shameer and Sowdhamini, Ramanathan} } @article {874, title = {Collation and analyses of DNA-binding protein domain families from sequence and structural databanks.}, journal = {Mol Biosyst}, volume = {11}, year = {2015}, month = {2015 Apr}, pages = {1110-8}, abstract = {

DNA-protein interactions govern several high fidelity cellular processes like DNA-replication, transcription, DNA repair, etc. Proteins that have the ability to recognise and bind DNA sequences can be classified either according to their DNA-binding motif or based on the sequence of the target nucleotides. We have collated the DNA-binding families by integrating information from both protein sequence family and structural databases. This resulted in a dataset of 1057 DNA-binding protein domain families. Their family properties (the number of members, percent identity distribution and length of members) and domain architectures were examined. Further, sequence domain families were mapped to structures in the protein databank (PDB) and the protein domain structure classification database (SCOP). The DNA-binding families, with no structural information, were clustered together into potential superfamilies based on sequence associations. On the basis of functions attributed to DNA-binding protein folds, we observe that a majority of the DNA-binding proteins follow divergent evolution. This study can serve as a basis for annotation and distribution of DNA-binding proteins in genome(s) of interest. The entire collated set of DNA-binding protein domains is available for download as Hidden Markov Models.

}, keywords = {Archaeal Proteins, Bacterial Proteins, Databases, Protein, DNA-Binding Proteins, Protein Structure, Tertiary, Viral Proteins}, issn = {1742-2051}, doi = {10.1039/c4mb00629a}, author = {Malhotra, Sony and Sowdhamini, Ramanathan} } @article {995, title = {Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0131077}, abstract = {

Olfactory receptors (ORs) belong to the class A G-Protein Coupled Receptor superfamily of proteins. Unlike G-Protein Coupled Receptors, ORs exhibit a combinatorial response to odors/ligands. ORs display an affinity towards a range of odor molecules rather than binding to a specific set of ligands and conversely a single odorant molecule may bind to a number of olfactory receptors with varying affinities. The diversity in odor recognition is linked to the highly variable transmembrane domains of these receptors. The purpose of this study is to decode the odor-olfactory receptor interactions using in silico docking studies. In this study, a ligand (odor molecules) dataset of 125 molecules was used to carry out in silico docking using the GLIDE docking tool (SCHRODINGER Inc Pvt LTD). Previous studies, with smaller datasets of ligands, have shown that orthologous olfactory receptors respond to similarly-tuned ligands, but are dramatically different in their efficacy and potency. Ligand docking results were applied on homologous pairs (with varying sequence identity) of ORs from human and mouse genomes and ligand binding residues and the ligand profile differed among such related olfactory receptor sequences. This study revealed that homologous sequences with high sequence identity need not bind to the same/ similar ligand with a given affinity. A ligand profile has been obtained for each of the 20 receptors in this analysis which will be useful for expression and mutation studies on these receptors.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131077}, author = {Harini, K and Sowdhamini, Ramanathan} } @article {1024, title = {Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.}, journal = {Database (Oxford)}, volume = {2015}, year = {2015}, month = {2015}, pages = {bav063}, abstract = {

During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting brought together the principal investigators of several specialized protein resources (such as CAZy, TCDB and MEROPS) as well as those from protein databases from the large Bioinformatics centres (including UniProt and RefSeq). The retreat was divided into five sessions: (1) key challenges, (2) the databases represented, (3) best practices for maintenance and curation, (4) information flow to and from large data centers and (5) communication and funding. An important outcome of this meeting was the creation of a Specialist Protein Resource Network that we believe will improve coordination of the activities of its member resources. We invite further protein database resources to join the network and continue the dialogue.

}, issn = {1758-0463}, doi = {10.1093/database/bav063}, author = {Babbitt, Patricia C and Bagos, Pantelis G and Bairoch, Amos and Bateman, Alex and Chatonnet, Arnaud and Chen, Mark Jinan and Craik, David J and Finn, Robert D and Gloriam, David and Haft, Daniel H and Henrissat, Bernard and Holliday, Gemma L and Isberg, Vignir and Kaas, Quentin and Landsman, David and Lenfant, Nicolas and Manning, Gerard and Nagano, Nozomi and Srinivasan, Narayanaswamy and O{\textquoteright}Donovan, Claire and Pruitt, Kim D and Sowdhamini, Ramanathan and Rawlings, Neil D and Saier, Milton H and Sharman, Joanna L and Spedding, Michael and Tsirigos, Konstantinos D and Vastermark, Ake and Vriend, Gerrit} } @article {869, title = {DOCKSCORE: a webserver for ranking protein-protein docked poses.}, journal = {BMC Bioinformatics}, volume = {16}, year = {2015}, month = {2015}, pages = {127}, abstract = {

BACKGROUND: Proteins interact with a variety of other molecules such as nucleic acids, small molecules and other proteins inside the cell. Structure-determination of protein-protein complexes is challenging due to several reasons such as the large molecular weights of these macromolecular complexes, their dynamic nature, difficulty in purification and sample preparation. Computational docking permits an early understanding of the feasibility and mode of protein-protein interactions. However, docking algorithms propose a number of solutions and it is a challenging task to select the native or near native pose(s) from this pool. DockScore is an objective scoring scheme that can be used to rank protein-protein docked poses. It considers several interface parameters, namely, surface area, evolutionary conservation, hydrophobicity, short contacts and spatial clustering at the interface for scoring.

RESULTS: We have implemented DockScore in form of a webserver for its use by the scientific community. DockScore webserver can be employed, subsequent to docking, to perform scoring of the docked solutions, starting from multiple poses as inputs. The results, on scores and ranks for all the poses, can be downloaded as a csv file and graphical view of the interface of best ranking poses is possible.

CONCLUSIONS: The webserver for DockScore is made freely available for the scientific community at: http://caps.ncbs.res.in/dockscore/ .

}, keywords = {Algorithms, Humans, Internet, Molecular Docking Simulation, Protein Binding, Protein Interaction Domains and Motifs, Proteins, ras GTPase-Activating Proteins, Software}, issn = {1471-2105}, doi = {10.1186/s12859-015-0572-6}, author = {Malhotra, Sony and Mathew, Oommen K and Sowdhamini, Ramanathan} } @article {1010, title = {Energetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0127716}, abstract = {

Domain swapping mechanism is a specialised mode of oligomerization of proteins in which part of a protein is exchanged in a non-covalent manner between constituent subunits. This mechanism is highly affected by several physiological conditions. Here, we present a detailed analysis ofthe effect of pH on different regions of the domain swapped oligomer by considering examples which are known to be sensitive to pH in transiting from monomeric to domain-swapped dimeric form. The energetic calculations were performed using a specialized method which considers changes in pH and subsequent changes in the interactions between subunits. This analysis provides definitive hints about the pH-dependence switch from monomer to domain-swapped oligomer and the steps that may be involved in the swapping mechanism.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0127716}, author = {Shingate, Prashant and Warwicker, Jim and Sowdhamini, Ramanathan} } @article {908, title = {Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function.}, journal = {Tuberculosis (Edinb)}, volume = {95}, year = {2015}, month = {2015 Jan}, pages = {14-25}, abstract = {

The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95\% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better understanding of pathogenesis and to accelerate the process of drug target discovery.

}, keywords = {Hydrolases, Mycobacterium tuberculosis, Protein Structure, Tertiary, Proteome, Sequence Analysis, Protein, Structural Homology, Protein}, issn = {1873-281X}, doi = {10.1016/j.tube.2014.10.009}, author = {Ramakrishnan, Gayatri and Ochoa-Monta{\~n}o, Bernardo and Raghavender, Upadhyayula S and Mudgal, Richa and Joshi, Adwait G and Chandra, Nagasuma R and Sowdhamini, Ramanathan and Blundell, Tom L and Srinivasan, Narayanaswamy} } @article {161, title = {Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties.}, journal = {BMC Plant Biol}, volume = {15}, year = {2015}, month = {2015}, pages = {212}, abstract = {

BACKGROUND: Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is {\textquoteright}Tulsi{\textquoteright} (or {\textquoteright}Tulasi{\textquoteright} or {\textquoteright}Thulasi{\textquoteright}) and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374~Mb, with a genome coverage of 61~\% (612~Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties.

RESULTS: The pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry.

CONCLUSIONS: The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.

}, issn = {1471-2229}, doi = {10.1186/s12870-015-0562-x}, author = {Upadhyay, Atul K and Chacko, Anita R and Gandhimathi, A and Ghosh, Pritha and Harini, K and Joseph, Agnel P and Joshi, Adwait G and Karpe, Snehal D and Kaushik, Swati and Kuravadi, Nagesh and Lingu, Chandana S and Mahita, J and Malarini, Ramya and Malhotra, Sony and Malini, Manoharan and Mathew, Oommen K and Mutt, Eshita and Naika, Mahantesha and Nitish, Sathyanarayanan and Pasha, Shaik Naseer and Raghavender, Upadhyayula S and Rajamani, Anantharamanan and Shilpa, S and Shingate, Prashant N and Singh, Heikham Russiachand and Sukhwal, Anshul and Sunitha, Margaret S and Sumathi, Manojkumar and Ramaswamy, S and Gowda, Malali and Sowdhamini, Ramanathan} } @article {884, title = {Key challenges for the creation and maintenance of specialist protein resources.}, journal = {Proteins}, volume = {83}, year = {2015}, month = {2015 Jun}, pages = {1005-13}, abstract = {

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long-term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value.

}, issn = {1097-0134}, doi = {10.1002/prot.24803}, author = {Holliday, Gemma L and Bairoch, Amos and Bagos, Pantelis G and Chatonnet, Arnaud and Craik, David J and Finn, Robert D and Henrissat, Bernard and Landsman, David and Manning, Gerard and Nagano, Nozomi and O{\textquoteright}Donovan, Claire and Pruitt, Kim D and Rawlings, Neil D and Saier, Milton and Sowdhamini, Ramanathan and Spedding, Michael and Srinivasan, Narayanaswamy and Vriend, Gert and Babbitt, Patricia C and Bateman, Alex} } @article {1041, title = {Mechanistic Basis Of Peptide-Protein Interaction In AtPep1-PEPR1 Complex In Arabidopsis thaliana.}, journal = {Protein Pept Lett}, volume = {22}, year = {2015}, month = {2015}, pages = {618-27}, abstract = {

Peptide-mediated immunity against pathogens in plants can provide information on protein-peptide interactions and drug discovery in general. The molecular structure of AtPep1, a 23-amino acid signaling peptide isolated from Arabidopsis thaliana leaves and implicated in innate immunity, has evaded structural determination by biophysical methods. The details of molecular interaction of AtPep1 peptide with its receptor (PEPR1), a 170 kDa leucine-rich repeat (LRR) kinase is also unknown. We report a computational approach to the modeling AtPep1 by conformational sampling and its interaction with the receptor PEPR1. Molecular dynamics simulations were employed to sample and cluster energetically favorable conformations of AtPep1 and modeling of PEPR1 through homology. Docking of AtPep1 to PEPR1 and filtering of the biologically relevant poses were facilitated by the computational Ala-scanning mutations and binding energy analysis of the peptide-protein complex. This study provides the first independent in silico validation of the Structure-Activity- Relationship studies carried out on the AtPep1 and provides a molecular mechanism of the peptide-protein complex system.

}, issn = {1875-5305}, author = {Raghavender, Upadhyayula S and Sowdhamini, Ramanathan} } @article {891, title = {Mechanistic heterogeneity in contractile properties of α-tropomyosin (TPM1) mutants associated with inherited cardiomyopathies.}, journal = {J Biol Chem}, volume = {290}, year = {2015}, month = {2015 Mar 13}, pages = {7003-15}, abstract = {

The most frequent known causes of primary cardiomyopathies are mutations in the genes encoding sarcomeric proteins. Among those are 30 single-residue mutations in TPM1, the gene encoding α-tropomyosin. We examined seven mutant tropomyosins, E62Q, D84N, I172T, L185R, S215L, D230N, and M281T, that were chosen based on their clinical severity and locations along the molecule. The goal of our study was to determine how the biochemical characteristics of each of these mutant proteins are altered, which in turn could provide a structural rationale for treatment of the cardiomyopathies they produce. Measurements of Ca(2+) sensitivity of human β-cardiac myosin ATPase activity are consistent with the hypothesis that hypertrophic cardiomyopathies are hypersensitive to Ca(2+) activation, and dilated cardiomyopathies are hyposensitive. We also report correlations between ATPase activity at maximum Ca(2+) concentrations and conformational changes in TnC measured using a fluorescent probe, which provide evidence that different substitutions perturb the structure of the regulatory complex in different ways. Moreover, we observed changes in protein stability and protein-protein interactions in these mutants. Our results suggest multiple mechanistic pathways to hypertrophic and dilated cardiomyopathies. Finally, we examined a computationally designed mutant, E181K, that is hypersensitive, confirming predictions derived from in silico structural analysis.

}, keywords = {Actins, Adenosine Triphosphatases, Calcium, Cardiomyopathies, Humans, Models, Molecular, Myosins, Point Mutation, Protein Stability, Tropomyosin}, issn = {1083-351X}, doi = {10.1074/jbc.M114.596676}, author = {Gupte, Tejas M and Haque, Farah and Gangadharan, Binnu and Sunitha, Margaret S and Mukherjee, Souhrid and Anandhan, Swetha and Rani, Deepa Selvi and Mukundan, Namita and Jambekar, Amruta and Thangaraj, Kumarasamy and Sowdhamini, Ramanathan and Sommese, Ruth F and Nag, Suman and Spudich, James A and Mercer, John A} } @article {901, title = {NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection.}, journal = {Nucleic Acids Res}, volume = {43}, year = {2015}, month = {2015 Jan}, pages = {D300-5}, abstract = {

NrichD (http://proline.biochem.iisc.ernet.in/NRICHD/) is a database of computationally designed protein-like sequences, augmented into natural sequence databases that can perform hops in protein sequence space to assist in the detection of remote relationships. Establishing protein relationships in the absence of structural evidence or natural {\textquoteright}intermediately related sequences{\textquoteright} is a challenging task. Recently, we have demonstrated that the computational design of artificial intermediary sequences/linkers is an effective approach to fill naturally occurring voids in protein sequence space. Through a large-scale assessment we have demonstrated that such sequences can be plugged into commonly employed search databases to improve the performance of routinely used sequence search methods in detecting remote relationships. Since it is anticipated that such data sets will be employed to establish protein relationships, two databases that have already captured these relationships at the structural and functional domain level, namely, the SCOP database and the Pfam database, have been {\textquoteright}enriched{\textquoteright} with these artificial intermediary sequences. NrichD database currently contains 3,611,010 artificial sequences that have been generated between 27,882 pairs of families from 374 SCOP folds. The data sets are freely available for download. Additional features include the design of artificial sequences between any two protein families of interest to the user.

}, keywords = {Computational Biology, Databases, Protein, Internet, Molecular Sequence Annotation, Protein Structure, Tertiary, Sequence Analysis, Protein, Sequence Homology, Amino Acid}, issn = {1362-4962}, doi = {10.1093/nar/gku888}, author = {Mudgal, Richa and Sandhya, Sankaran and Kumar, Gayatri and Sowdhamini, Ramanathan and Chandra, Nagasuma R and Srinivasan, Narayanaswamy} } @article {1032, title = {PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots.}, journal = {Bioinform Biol Insights}, volume = {9}, year = {2015}, month = {2015}, pages = {141-51}, abstract = {

BACKGROUND: Modeling protein-protein interactions (PPIs) using docking algorithms is useful for understanding biomolecular interactions and mechanisms. Typically, a docking algorithm generates a large number of docking poses, and it is often challenging to select the best native-like pose. A further challenge is to recognize key residues, termed as hotspots, at protein-protein interfaces, which contribute more in stabilizing a protein-protein interface.

RESULTS: We had earlier developed a computer algorithm, called PPCheck, which ascribes pseudoenergies to measure the strength of PPIs. Native-like poses could be successfully identified in 27 out of 30 test cases, when applied on a separate set of decoys that were generated using FRODOCK. PPCheck, along with conservation and accessibility scores, was able to differentiate {\textquoteright}native-like and non-native-like poses from 1883 decoys of Critical Assessment of Prediction of Interactions (CAPRI) targets with an accuracy of 60\%. PPCheck was trained on a 10-fold mixed dataset and tested on a 10-fold mixed test set for hotspot prediction. We obtain an accuracy of 72\%, which is in par with other methods, and a sensitivity of 59\%, which is better than most existing methods available for hotspot prediction that uses similar datasets. Other relevant tests suggest that PPCheck can also be reliably used to identify conserved residues in a protein and to perform computational alanine scanning.

CONCLUSIONS: PPCheck webserver can be successfully used to differentiate native-like and non-native-like docking poses, as generated by docking algorithms. The webserver can also be a convenient platform for calculating residue conservation, for performing computational alanine scanning, and for predicting protein-protein interface hotspots. While PPCheck can differentiate the generated decoys into native-like and non-native-like decoys with a fairly good accuracy, the results improve dramatically when features like conservation and accessibility are included. The method can be successfully used in ranking/scoring the decoys, as obtained from docking algorithms.

}, issn = {1177-9322}, doi = {10.4137/BBI.S25928}, author = {Sukhwal, Anshul and Sowdhamini, Ramanathan} } @article {3537, title = {Sequence Analysis and Evolutionary Studies of Reelin Proteins.}, journal = {Bioinform Biol Insights}, volume = {9}, year = {2015}, month = {2015}, pages = {187-93}, abstract = {

The reelin gene is conserved across many vertebrate species, including humans. The protein product of this gene plays several important roles in early brain development and regulation of neural network plasticity of a matured brain structure. With an extended structure of 3461 amino acid sequences, consisting of eight reelin repeats, the human reelin sequence stands out as an exceptional model for evolutionary studies. In this study, sequence analysis of the human reelin and its homologues and reelin sequences from 104 other species is described in detail. Interesting sequence conservation patterns of individual repeats have been highlighted. Sequence phylogeny of the reelin sequences indicates a pattern similar to the evolution of the species, thereby serving as a highly conserved family for evolutionary purposes. Multiple sequence alignment of different reelin domain repeats, derived from homologues, suggests specific functions for individual repeats and high sequence conservation across reelin repeats from different organisms, albeit with few unusual domain architectures. A three-dimensional structural model of the full-length human reelin is now available that provides clues on residues at the dimer interface.

}, issn = {1177-9322}, doi = {10.4137/BBI.S26530}, author = {Manoharan, Malini and Muhammad, Sayyed Auwn and Sowdhamini, Ramanathan} } @article {1002, title = {SInCRe-structural interactome computational resource for Mycobacterium tuberculosis.}, journal = {Database (Oxford)}, volume = {2015}, year = {2015}, month = {2015}, pages = {bav060}, abstract = {

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein-protein and protein-small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein-protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host-pathogen protein-protein interactions. Together they provide prerequisites for identification of off-target binding.

}, issn = {1758-0463}, doi = {10.1093/database/bav060}, author = {Metri, Rahul and Hariharaputran, Sridhar and Ramakrishnan, Gayatri and Anand, Praveen and Raghavender, Upadhyayula S and Ochoa-Monta{\~n}o, Bernardo and Higueruelo, Alicia P and Sowdhamini, Ramanathan and Chandra, Nagasuma R and Blundell, Tom L and Srinivasan, Narayanaswamy} }