Molecular dynamics of subtilisin Carlsberg in aqueous and nonaqueous solutions

Crystal structures have recently appeared for the enzyme subtilisin Carlsberg in anhydrous acetonitrile and in water. To gain a mechanistic understanding of how the solvent environment affects protein structure and dynamics, we have performed molecular dynamics simulations on subtilisin Carlsberg in water and acetonitrile. We describe a 480 ps simulation of subtilisin in acetonitrile solution and a 450 ps simulation of subtilisin in water. Each simulation employed the all-atom AMBER force field. The calculated rms deviations, from their respective x-ray structures, were similar in each simulation, but ∼0.5 Å higher in the acetonitrile simulation. Only in the acetonitrile simulation does one helix undergo a reversible partial unwinding, which lasted for about 100 ps. The other secondary structure elements remain intact or undergo modest fluctuations. In the aqueous simulation, the calculated and experimental temperature factors agree very well. In the acetonitrile simulation, however, the calculated temperature factors are much higher than the experimental values. The larger rms deviation and thermal fluctuations noted in the acetonitrile simulation are consistent with the requirement for protein cross-linking in this crystal and a recent two-dimensional NH-exchange nmr study on horse heart cytochrome c in nonaqueous solution. © 1996 John Wiley & Sons, Inc.