Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes.

ABSTRACT: We examine the dynamic features of non-trivial allosteric binding sites to elucidate potential drug binding sites. These allosteric sites were previously found to be allosteric after determination of the protein-drug co-crystal structure. After comprehensive search in the Protein Data Bank, we identify 10 complex structures with allosteric ligands whose structures are very similar to their functional forms. Then, possible pockets on the protein surface are searched as potential ligand binding sites. To mimic ligand binding to the pocket, complex models are generated to fill out each pocket with pseudo ligand blocks consisting of spheres. Normal mode analysis of the elastic network model is performed for the complex models and unbound structures to assess the change of protein dynamics indu

SUBMITTER: Taguchi J 

PROVIDER: S-EPMC5042162 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature