Protein Grabs a Ligand by Extending Anchor Residues: Molecular Simulation for Ca^sup 2+^ 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 Ca^sup 2+^ 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 …