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Updated: May 10, 2026

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
Published on: April 19, 2021
Car-Parrinello molecular dynamics/molecular mechanics (CPMD/MM) simulation study of coupling and uncoupling
Peng Lian1, Jue Li, Dong-Qi Wang
1State Key Laboratory of Microbial Metabolism, and College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China 200240.
Abstract:
The relevance of the pathway through which the second proton is delivered to the active site of P450cam and the subsequent coupling/uncoupling reactions has been investigated using Car-Parrinello molecular dynamics/molecular mechanics (CPMD/MM) dynamics simulations. Five models have been prepared, representing delivery pathways in the wild-type enzyme and its mutants in which Thr252 mutated into other residues with different side-chain length and hydrophobicity. In the simulations, coupling reaction is observed in the wild-type enzyme (Model A) and its T252S mutant (Model B), while the uncoupling products are obtained in the other three models (C, D, and E). Different from previous studies, a dynamic process of the last stage of coupling/uncoupling was observed. We found that the peroxide bond cleavage in coupling, the Fe-O bond stretching in uncoupling, proton transfer, and electron delivery take place spontaneously. Moreover, besides the intrinsic chemical differences between the two peroxide oxygen atoms, water molecules in the active site and the proton transfer pathway may play an important role in the determination of coupling/uncoupling. We conclude that by maintaining a specific proton transfer channel, Asp251-Thr252 channel, the wild-type enzyme could efficiently deliver the second proton to the ideal position for coupling reaction.
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