Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations.

ABSTRACT: Conformational changes of proteins upon ligand binding are usually explained in terms of several mechanisms including the induced fit, conformational selection, or their mixtures. Due to the slow time scales, conventional molecular dynamics (cMD) simulations based on the atomistic models cannot easily simulate the open-to-closed conformational transition in proteins. In our previous study, we have developed an enhanced sampling scheme (generalized replica exchange with solute tempering selected surface charged residues: gREST_SSCR) for multidomain proteins and applied it to ligand-mediated conformational changes in the G134R mutant of ribose-binding protein (RBP_G134R) in solution. The free-energy landscape (FEL) of RBP_G134R in the presence of a ribose at the binding s

SUBMITTER: Ren W 

PROVIDER: S-EPMC10954230 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature