@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 {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} }