DRAMATIC DIFFERENCES IN THE MOTIONS OF THE MOUTH OF OPEN AND CLOSED CYTOCHROME P450BM-3 BY MOLECULAR-DYNAMICS SIMULATIONS

Molecular dynamics trajectories were calculated separately for each of the two molecules in the asymmetric unit of the crystal structure of the hemoprotein domain of cytochrome P450BM-3, Each simulation was 200 ps in length and included a 10 Angstrom layer of explicit solvent. Th e simulated time-average structure of each P450BM-3 molecule is closer to its crystal structure than the two molecular dynamics time-average d structures are to each other. In the crystal structure, molecule 2 h as a more accessible substrate binding pocket than molecule 1, and thi s difference is maintained throughout the simulations presented here. In particular, the substrate docking regions of molecule 1 and molecul e 2 diverge in the solution state simulations, The mouth of the substr ate binding pocket is significantly more mobile in the simulation of m olecule 2 than in the simulation of molecule 1. For molecule 1, the wi dth of the mouth is only slightly larger than its X-ray value of 8.7 A ngstrom and undergoes fluctuations of about 1 Angstrom. However, in mo lecule 2, the mouth of the substrate binding pocket is dramatically mo re open in the time-average molecular dynamics structure (14.7 Angstro m) than in the X-ray structure (10.9 Angstrom). Furthermore, this regi on of the protein undergoes large amplitude motions during the traject ory that are not seen in the trajectory of molecule 1, repeatedly open ing and closing up to 7 Angstrom. Presumably, the binding of different substrates will induce the mouth region to adopt different conformati ons from within the wide range of structures that are accessible. (C) 1995 Wiley-Lies, Inc.