Understanding the principles of protein protein interactions Designing novel means for virtual proteomics

Abstract

Proteins are the basic functional units in the cellular world of life. They are nano- newlinemachines programmed to associate with other biomolecules in order to enact an array newlineof molecular functions in response to biological events at cellular and system levels. newlineUnderstanding the biomolecular phenomenon governing such associations may newlineprovide insights into the principles of protein chemistry that have a wide-range of newlineapplications. In the current work, two databases (PPInS and NRDB) in which the newlineinformation of interacting protein chains from the experimentally determined protein- newlineprotein complexes (PPCs) for which structural information in terms of SCOP newlinesuperfamily was available, is demarcated in the form of protein-protein interaction newlineinterfaces (PPIIs) were developed. The PPIIs contained in these databases were made newlineavailable on a web server for public use. These were analysed w.r.t. physicochemical newlineand geometrical characteristics of PPI sites. With the belief that designing of newlinecomputational tools with prediction ability must be trained and tested on real instances newlineof the phenomenon for which it is designed, the analytical information obtained from newlinethe analysis of PPIIs from NRDB was incorporated in development of a computational newlinetool, Anveshan, for prediction of putative protein-protein interaction (PPI) sites. The newlinetraining and test datasets for Anveshan development were obtained from the PPInS. newlinePPInS is a high-performance database of PPIIs in which atomic-level newlineinformation of the molecular interactions amongst various protein chains in PPCs newlinetogether with their evolutionary information in Structural Classification of Proteins newline(SCOPe release 2.06), is made available. Total 32,468 PDB files representing X-ray newlinecrystallized multimeric PPCs with structural resolution better than 2.5 Å were shortlisted newlineto demarcate the PPIIs. Total 111,857 PPIIs with approximately 32.24 million atomic newlinecontact pairs were generated and made available on a web server, named PPInS, newline(http://www.cup.edu.in:99/ppins/home.php) for on-site analysis