DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283

• Published in: The journal of physical chemistry. B Vol. 128; no. 28; pp. 6670 - 6683
• Main Authors: Xue, Pei, Huang, Donglian, Pu, Jingzhi, Zhou, Yan
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 18.07.2024
• Subjects: active sites; B: Biophysical and Biochemical Systems and Processes; catalytic activity; cleavage (chemistry); Cyclization; Density Functional Theory; deoxyribodipyrimidine photo-lyase; Deoxyribodipyrimidine Photo-Lyase - chemistry; Deoxyribodipyrimidine Photo-Lyase - metabolism; dissociation; DNA; electron transfer; electrostatic interactions; Gibbs free energy; hydrogen; Hydrogen Bonding; Molecular Dynamics Simulation; potential energy; protonation; Protons; Pyrimidine Dimers - chemistry; solvation; Thermodynamics
• DOI: 10.1021/acs.jpcb.4c01011
• ISSN: 1520-6106; 1520-5207

DNA photolyase targets the primary ultraviolet (UV)-induced DNA lesioncyclobutane pyrimidine dimer (CPD), attaches to it, and catalyzes its dissociation. The catalytic mechanism of DNA photolyase and the role of the conserved residue E283 remain subjects of debate. This study employs two-dimensional potential energy surface maps and minimum free energy paths calculated at the ωB97XD/6-31G/MM level to elucidate these mechanisms. Results suggest that the catalytic process follows a sequential, stepwise reaction in which the C5–C5 and C6–C6 bonds are cleaved in order, facilitated by a protonated E283. Activation free energies for these cleavages are calculated at 4.4 and 4.2 kcal·mol–1, respectively. Protonation of E283 reduces electrostatic repulsion with CPD and forms dual hydrogen bonds with it and provides better solvation, stabilizing the CPD radical anion, particularly during intermediate state. This stabilization renders the initial splitting step exergonic, slows reverse reactions of the C5–C5 bond cleavage and electron transfer, and ensures a high quantum yield. Furthermore, the protonation state of E283 significantly affects the type of bond cleavage. Other residues in the active site were also investigated for their roles in the mechanism.