title: An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles.
abstract: Rich data bearing on the structural and evolutionary principles of protein-protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial 'driver' mutations in oncogenesis. They also provide the foundation toward the design of protein-protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein-protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein-protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview.
authors: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address: gsudha@mbu.iisc.ernet.in.
authors: Govindarajan
authors: G
authors: Sudha
authors: Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, MD 21702, USA; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel. Electronic address: nussinor@helix.nih.gov.
authors: Ruth
authors: R
authors: Nussinov
authors: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address: ns@mbu.iisc.ernet.in.
authors: Narayanaswamy
authors: N
authors: Srinivasan
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D009154:Mutation; D025941:Protein Interaction Mapping / Q000379:methods*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D054852:Small Molecule Libraries / Q000378:metabolism / Q000494:pharmacology
chemical_list: D011506:Proteins; D054852:Small Molecule Libraries
keywords: Conformation; Evolution; Function; Interaction; Protein–protein complexes; Structure