Molecular dynamics of native protein: I. Computer simulation of trajectories

Abstract

The motion of the atoms in the small protein bovine pancreatic trypsin inhibitor has been simulated for about 60 picoseconds using two different potential energy functions. In one known as HHL the hydrogen bond is purely electrostatic, in the other, known as L79, the hydrogen bond is a directional O . . . H interaction. The energy parameters and techniques used to obtain an accurate, well-equilibrated trajectory are described in detail. The trajectories calculated here with either potential are superior to those obtained in previous simulations on the same protein in that they treat hydrogen bonding realistically and remain closer to the native X-ray structure. Comparison of the two trajectories shows that the potential energy parameters have a significant effect on the shift from the X-ray structure, the distribution of (phi, psi) torsion angles, the pattern of hydrogen bonds and the accessible surface area of individual residues. The L79 potential with directional hydrogen bonds is used to simulate a longer 132 picosecond trajectory that is analysed in the accompanying paper.