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Geometrical and electro-static determinants of protein-protein interactions
Authors:Vicky Kumar  Ashita Sood  Anjana Munshi  Tarkeshwar Gautam  Mahesh Kulharia
Institution:1.Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India, 176206;2.Department of Computational Sciences, School of Basic and Applied Sciences, CentralUniversity of Punjab, Bathinda, India, 151001;3.Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India, 151001;4.Department of Zoology, Kalindi College, University of Delhi , Delhi, India
Abstract:Protein-protein interactions (PPI) are pivotal to the numerous processes in the cell. Therefore, it is of interest to document the analysis of these interactions in terms of binding sites, topology of the interacting structures and physiochemical properties of interacting interfaces and the of forces interactions. The interaction interface of obligatory protein-protein complexes differs from that of the transient interactions. We have created a large database of protein-protein interactions containing over100 thousand interfaces. The structural redundancy was eliminated to obtain a non-redundant database of over 2,265 interaction interfaces. Therefore, it is of interest to document the analysis of these interactions in terms of binding sites, topology of the interacting structures and physiochemical properties of interacting interfaces and the offorces interactions. The residue interaction propensity and all of the rest of the parametric scores converged to a statistical indistinguishable common sub-range and followed the similar distribution trends for all three classes of sequence-based classifications PPInS. This indicates that the principles of molecular recognition are dependent on the preciseness of the fit in the interaction interfaces. Thus, it reinforces the importance of geometrical and electrostatic complementarity as the main determinants for PPIs.
Keywords:Protein-protein interactions  protein-protein interaction interface  non-redundant database  residue interface propensity  hydrophobicity  solvation free energy  planarity  protrusion  depth
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