PIMA: Protein-Protein Interactions in Macromolecular Assembly - a web server for its Analysis and Visualization

Abstract

Protein-protein interactions are essential for the basic biological machinery of the cell. This is important for processes like protein synthesis, enzyme kinetics, molecular assembly and signal transduction. A high number of macromolecular structural complexes are known due to recent advances in structure determination techniques. Therefore, it is of interest to develop an interactive tool to objectively analyze large protein complexes. Hence, we describe the development and utility of a web enabled application named 'Protein-Protein Interaction in Macro-molecular Assembly' (PIMA) for the analysis of large protein assemblies. The intricate details of physical interactions amongst protein subunits in a large complex are presented as simple user preferred interactive network diagrams. Availability: PIMA server is available for free at http://caps.ncbs.res.in/pima/ Background: Many biological processes in the cell are driven by protein subunit assemblies [1]. Therefore, it is important to understand inter-chain interactions and their contribution to the overall three-dimensional structure for macro-molecular stability. Earlier studies have provided insights on their interaction principles using known multi-meric protein structural complexes in the Protein Data Bank (PDB) [2]. The steric complementarity [3], inter atomic hydrogen bonds, salt bridges, hydrophobic effects and change in solvent accessible surface area (ASA) upon complex formation [4] has been noted as features of protein-protein interfaces in several complex molecular assemblies for cellular functions. Visual examination of various such aspects for each interaction in an assembly is often perplexing and frequently tedious to explain. Hence, there is need for a tool that can enable user defined interactive visualization of such parameters with corresponding quantitative values to illustrate several important binding features. Therefore, we describe a simple yet a powerful visualization interface (web driven) to objectively analyze and examine large protein assemblies.