@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 {91672, title = {Influence of Disease-Causing Mutations on Protein Structural Networks.}, journal = {Front Mol Biosci}, volume = {7}, year = {2021}, month = {2020}, pages = {620554}, abstract = {

The interactions between residues in a protein tertiary structure can be studied effectively using the approach of protein structure network (PSN). A PSN is a node-edge representation of the structure with nodes representing residues and interactions between residues represented by edges. In this study, we have employed weighted PSNs to understand the influence of disease-causing mutations on proteins of known 3D structures. We have used manually curated information on disease mutations from UniProtKB/Swiss-Prot and their corresponding protein structures of wildtype and disease variant from the protein data bank. The PSNs of the wildtype and disease-causing mutant are compared to analyse variation of global and local dissimilarity in the overall network and at specific sites. We study how a mutation at a given site can affect the structural network at a distant site which may be involved in the function of the protein. We have discussed specific examples of the disease cases where the protein structure undergoes limited structural divergence in their backbone but have large dissimilarity in their all atom networks and vice versa, wherein large conformational alterations are observed while retaining overall network. We analyse the effect of variation of network parameters that characterize alteration of function or stability.

}, issn = {2296-889X}, doi = {10.3389/fmolb.2020.620554}, author = {Prabantu, Vasam Manjveekar and Naveenkumar, Nagarajan and Srinivasan, Narayanaswamy} } @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 {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 {1000, title = {Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold.}, journal = {Proteins}, volume = {83}, year = {2015}, month = {2015 Oct}, pages = {1766-86}, abstract = {

Heterodimeric proteins with homologous subunits of same fold are involved in various biological processes. The objective of this study is to understand the evolution of structural and functional features of such heterodimers. Using a non-redundant dataset of 70 such heterodimers of known 3D structure and an independent dataset of 173 heterodimers from yeast, we note that the mean sequence identity between interacting homologous subunits is only 23-24\% suggesting that, generally, highly diverged paralogues assemble to form such a heterodimer. We also note that the functional roles of interacting subunits/domains are generally quite different. This suggests that, though the interacting subunits/domains are homologous, the high evolutionary divergence characterize their high functional divergence which contributes to a gross function for the heterodimer considered as a whole. The inverse relationship between sequence identity and RMSD of interacting homologues in heterodimers is not followed. We also addressed the question of formation of homodimers of the subunits of heterodimers by generating models of fictitious homodimers on the basis of the 3D structures of the heterodimers. Interaction energies associated with these homodimers suggests that, in overwhelming majority of the cases, such homodimers are unlikely to be stable. Majority of the homologues of heterodimers of known structures form heterodimers (51.8\%) and a small proportion (14.6\%) form homodimers. Comparison of 3D structures of heterodimers with homologous homodimers suggests that interfacial nature of residues is not well conserved. In over 90\% of the cases we note that the interacting subunits of heterodimers are co-localized in the cell.

}, issn = {1097-0134}, doi = {10.1002/prot.24849}, author = {Sudha, Govindarajan and Naveenkumar, Nagarajan and Srinivasan, Narayanaswamy} }