Molecular dynamics of native protein. II. Analysis and nature of motion

The 132 picosecond simulation of atomic motion in bovine pancreatic trypsin inhibitor protein generated in the accompanying paper is analysed here using a variety of different methods. Together, these techniques, many of which have been used before in analyses of protein co-ordinate refinement, give a complete and comprehensible description of the trajectory. Some highlights of the simulation are as follows. (1) The atoms vibrate about a time-averaged conformation that is close to the X-ray structure (within 1.1 A root-mean-square deviation for the main-chain of all residues except the first and last two). The vibration amplitude is least for main-chain atoms in alpha-helix or beta-sheet secondary structure and most for side-chain atoms in the charged polar side-chains (Asp, Glu, Lys and Arg). The overall extent and distribution of atomic motion is in agreement with the temperature factors derived from the X-ray refinement: the reorientation of bond vectors is much less than observed by nuclear magnetic resonance. (2) The protein explores four distinct regions of conformational space in the 132 picoseconds simulated. The conformational change from region III to IV and back again lasts 40 picoseconds and is of particular interest as it is reversible and involves an increase in the hydrogen bond energy. (3) The changes in main-chain torsion angles show the expected cooperativity of phi i + 1 and psi i; side-chains that are close in space also change their conformational angles in unison. (4) Hydrogen bonds are variable and many break and reform again in the 132 picoseconds. Certain hydrogen bonds are much less stable than others; with particular variability seen in the alpha-helices and at the ends of the beta-hairpin. Most noticeable are the co-operative changes of hydrogen bonds at both ends of the beta-hairpin that occur in going from region III to IV of the conformational space. (5) The overall solvent-accessible area remains close to that of the X-ray structure but polar charged residues become less exposed while non-polar hydrophobic residues become more exposed. Together these results give a conceptual model for protein dynamics in which the molecule vibrates about a particular conformation but then suddenly changes conformation, jumping over an energy barrier into a new region of conformational space.