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

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-dimensiona...