Understanding how much solvents influence the structures and dynamics of proteins is important to understand functional mechanisms of solvated proteins. We propose a solvated potential model that approximates the potential energy of a solvated protein by projecting the solvent information into the protein structure. Using the model, we derive three properties of the solvent. First, the influence of the solvent on protein structure and dynamics, mostly by the bulk solvent, decays drastically (near-exponentially) as the distances of the solvent from the protein increase. Using this decay pattern, we suggest the economical size of solvent boxes in molecular dynamics simulations. Second, the hydration shell regulates the protein dynamics by effecting extra interactions within the protein structure. Lastly, the lowest frequency modes are determined mostly by protein structures.
All Science Journal Classification (ASJC) codes
- Structural Biology
- Molecular Biology
- Cell Biology