Origin of Enantioselectivity in Engineered Cytochrome c‑Catalyzed Carbon-Radical FePP Hydrolysis Revealed Using QM/MM (ABEEM Polarizable Force Field) and MD Simulations

• Published in: The journal of physical chemistry. B 2024-04, Vol.128 (16), p.3807-3823
• Main Authors: Huang, Hong, Zhao, Dong-Xia, Zhao, Jian, Chen, Xin, Liu, Cui, Yang, Zhong-Zhi
• Format: Article
• Language: English
• Subjects: amino acids; B: Biophysical and Biochemical Systems and Processes; Biocatalysis; Carbon - chemistry; catalytic activity; Cytochromes c - chemistry; Cytochromes c - metabolism; enantiomers; enantioselectivity; Hydrogen Bonding; Hydrolysis; Metalloporphyrins - chemistry; Metalloporphyrins - metabolism; molecular dynamics; Molecular Dynamics Simulation; nitrogen; Protein Engineering; quantum mechanics; Quantum Theory; stereochemistry; Stereoisomerism; styrene; van der Waals forces
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/acs.jpcb.3c07158

The origin of highly efficient asymmetric aminohydroxylation of styrene catalyzed by engineered cytochrome c is investigated by the developed Atom-Bond Electronegativity Equalization Method polarizable force field (ABEEM PFF), which is a combined outcome of electronic and steric effects. Model molecules were used to establish the charge parameters of the ABEEM PFF, for which the bond-stretching and angle-bending parameters were obtained by using a combination of modified Seminario and scan methods. The interactions between carbon-radical Fe–porphyrin (FePP) and waters are simulated by molecular dynamics, which shows a clear preference for the pre-R over the pre-S. This preference is attributed to the hydrogen-bond between the mutated 100S and 101P residues as well as van der Waals interactions, enforcing a specific conformation of the carbon-radical FePP complex within the binding pocket. Meanwhile, the hydrogen-bond between water and the nitrogen atom in the active intermediate dictates the stereochemical outcome. Quantum mechanics/molecular mechanics (QM/MM (ABEEM PFF)) and free-energy perturbation calculations elucidate that the 3RTS is characterized by sandwich-like structure among adjacent amino acid residues, which exhibits greater stability than crowed arrangement in 3STS and enables the R enantiomer to form more favorably. Thus, this study provides mechanistic insight into the catalytic reaction of hemoproteins.