Dissecting the Structural Plasticity and Dynamics of Cytochrome P450 2B4 by Molecular Dynamics Simulations

• Published in: Journal of chemical information and modeling 2020-10, Vol.60 (10), p.5026-5035
• Main Authors: Li, Junhao, Zhou, Yang, Tang, Yun, Li, Weihua, Tu, Yaoquan
• Format: Article
• Language: English
• Subjects: Computational Biochemistry; Crystal structure; Cytochromes P450; Dimers; Dynamic structural analysis; Membranes; Molecular dynamics; Molecular structure; Network analysis; Plastic properties; Simulation; Substrates
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/acs.jcim.0c00482

The plasticity of cytochromes P450 (P450s) is known to contribute significantly to their catalytic capacity of metabolizing various substrates. Although numerous studies have been performed, factors governing the plasticity and dynamics of P450s are still not fully understood. In this study, taking CYP2B4 as an example, we dissect the protein plasticity and dynamics in different environments. CYP2B4 is featured by a high degree of plasticity, which exhibits open, closed, and intermediate states. By analyzing the CYP2B4 crystal structures, we identified the structural features for the closed, open, and intermediate states. Interestingly, formation of the dimer structure was found in the open and intermediate states. The subsequent molecular dynamics (MD) simulations of the open structure in water confirmed the importance of the dimer form in stabilizing the open conformations. MD simulations of the closed and open structures in the membrane environment and the free energies for opening the F–G cassette obtained from the umbrella sampling calculations indicate that the membrane environment is important for stabilizing the F–G cassette. The dynamical network analysis indicates that Asp105 on the B–C loop plays an important role in transiting the structure from the open to the intermediate state. Our results thus unveil the mechanisms of dimer formation and open-to-intermediate transition for CYP2B4 in the water and membrane environments.