Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam

Multiple ligand binding modes are possible in many enzyme active sites; the ir presence in cytochrome P450cam (P450cam) is evident from crystallographi c studies of the binding of thiocamphor and phenylimidazoles. Here, we use multicopy molecular dynamics simulations to compare the binding modes of (1 R)- and (1S)-camphor in the active site of P450cam. Simulations with (1R)-c amphor, the natural substrate, serve to calibrate our protocol: 19 out of 2 0 copies of (1R)-camphor converged to coordinates very close to those obser ved for (1R)-camphor in its crystallographic complex with P450cam during th e simulations. Simulations with the (1S)-camphor enantiomer showed greater mobility of the substrate, consistent with spectroscopic data, and resulted in 3 major binding modes. One of these is similar to the major conformatio n (of the two conformations assigned) in a recently determined crystal stru cture, but this conformation is not correctly oriented for regiospecific hy droxylation at C-5. The simulations, however, provide evidence for reorient ation of (1S)-camphor upon formation of the reactive Fe-O intermediate to a n orientation suitable for hydroxylation. The simulations thus permit ratio nalisation of the apparent inconsistency between the crystal structure and the reaction products. (C) 2000 Elsevier Science S.A. All rights reserved.