A simulated cooling process for proteins

We have developed a molecular dynamics simulation method to cool proteins in. The method uses a stochastic boundary layer which surrounds the protein and simulates a contact with a coolant. The atoms in this layer are subject to fluctuating and dissipative forces and follow a prescribed temperature schedule. In this arrangement the protein is cooled from the boundary into the interior. The temperature change can be described by the heat conduction equation assuming a thermal diffusivity D=7×10^-4 cm² s^-1. We have applied the cooling method suggested to a segment of the photosynthetic reaction center of Rhodopseudomonas viridis. Cooling leads to a contraction of this structure, evidenced by a decrease in the radius of gyration.