An integrated computational and experimental approach to allosteric control mechanism of biomolecular processes

Abstract

Proteins are exible and dynamic in nature and can undergo structural rearrangements to perform their functions. The motivation of this thesis is to develop a novel integrated computational and experimental approach to understand the allosteric control of conformational transitions and molecular recognition. In the rst part, a novel methodology called Collective Modes Bias Exchange Metadynamics (CM-BexMetaD) was developed and transition and allosteric control of transition of Adenylate kinase was investigated. In the second part, allosteric control of binding of proteins were studied through Elastic Network Models (ENM), Molecular Dynamics (MD), in-vitro imaging and Dynamic Force Spectroscopy (DFS) using AFM. A strong association between the hinge positions of global modes and allosteric mutations was shown by a large scale statistical analysis. The binding behavior of pyrin domain (PYD) and assembly formation of ASC protein was studied in-silico supported by in-vitro experiments and the results showed that, the ASC speck is an organized structure and the interaction of the domains are controlled via hinge residues. Further, the allosteric control of binding have been elucidated on the kinesin- a~A-tubulin and Rac1-PAK1 interactions by prediction of hinge residues that would a ect the binding behavior of proteins and then the resulting change in the binding energy landscape were investigated by DFS and last the mechanistic explanation of the alteration of the allosteric communication network was studied via MD studies. Both kinesin- -tubulin and Rac1-PAK1 protein complexes have alternative dissociation pathways where hinge residues as mechanistically key sites that allosterically control the binding behavior of molecules.