@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 {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 {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} }