Protein grabs a ligand by extending anchor residues: molecular simulation for Ca2+ binding to calmodulin loop.

ABSTRACT: The structural difference in proteins between unbound and bound forms directly suggests the importance of the conformational plasticity of proteins. However, pathways that connect two-end structures and how they are coupled to the binding reaction are not well understood at atomic resolution. Here, we analyzed the free-energy landscape, explicitly taking into account coupling between binding and conformational change by performing atomistic molecular dynamics simulations for Ca2+ binding to a calmodulin loop. Using the AMBER force field with explicit water solvent, we conducted umbrella sampling for the free-energy surface and steered molecular dynamics for the pathway search. We found that, at an early stage of binding, some key residue side chains extend their "arms" to catch Ca2+ and, a

SUBMITTER: Kobayashi C 

PROVIDER: S-EPMC1432117 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature