PROTEIN SIMULATION BELOW THE GLASS-TRANSITION TEMPERATURE - DEPENDENCE ON COOLING PROTOCOL

To examine the discrepancy between experimentally observed and computer-simulated low-temperature protein motion, molecular dynamics (MD) simulations of hydrated and dry carboxymyoglobin (MbCO) were performed at 100 K following cooling at different rates and from different temperatures. Simulations were also performed at nine temperatures, from 100 to 300 K, after cooling both systems from 300 K at 0.2 K/ps. 'Slow' cooling resulted in low-energy structures that exhibited atomic fluctuation 25% closer to experimental levels than those employed in previous simulations. The additional electrostatic interactions accompanying hydration increased the need to cool slowly. Cooling hydrated MbCO from 400 K at 2 K/ps balanced realism and efficiency.