Calculations of electrostatic properties in proteins: Analysis of contributions from induced protein dipoles

摘要: The calculation of induced dipole moments and their contribution to electrostatic effects in proteins is implemented following the approach Warshel. Isotropic polarizabilities are assigned individual atoms, resulting deviation from pairwise interactions treated by a self-consistent iterative procedure. We give detailed description how formalism molecular mechanics dynamics simulation procedures, report results based on calculations performed crystal structures crambin, liver alcohol dehydrogenase ribonuclease T1. focus our analysis evaluating polarizability protein matrix energies, local fields, peptide groups secondary structure elements polypeptide chain. Our confirm that provide important stabilizing contributions these cannot be mimicked usual approximations where either continuum dielectric constant, or distance-dependent function used. find dipoles appreciably affect magnitude direction fields manner strongly influenced microscopic environment protein. Most affected charged involved close with other groups, while influence aliphatic marginal. find, moreover, induction surrounding atoms tend average increase helix macro-dipoles about 16%, again reflecting stabilization matrix, show (at least alpha/beta domain dehydrogenase) side-chains this significant.