Simulation of mutation: Influence of a “side group” on global minimum structure and dynamics of a protein model

Abstract

The 46-bead, three-color model of a β-barrel-forming protein is modified by the addition of a single side group, represented by a bead which may be hydrophilic or hydrophobic. Molecular dynamics and quenching simulations show how the nature and location of the bead influence both the structure at the global minimum of internal energy and the relaxation processes by which the system finds its minima. The most drastic effects occur with a hydrophobic side group in the middle of a sequence of hydrophobes.