title: A comprehensive study of isomerization and protonation reactions in the photocycle of the photoactive yellow protein.
abstract: The light-activated photoactive yellow protein (PYP) chromophore uses a series of reactions to trigger photo-motility and biological responses, and generate a wide range of structural signals. To provide a comprehensive mechanism of the overall process at the atomic level, we apply a CASPT2//CASSCF/AMBER QM/MM protocol to investigate the relaxation pathways for a variety of possible isomerization and proton transfer reactions upon photoexcitation of the wild-type PYP. The nonadiabatic relay through an S1/S0 conical intersection [CI(S1/S0)] is found to play a decisive major role in bifurcating the excited state relaxation into a complete and short photocycle. Two major and one minor deactivation channels were found starting from the CI(S1/S0)-like intermediate IT, producing the cis isomers pR1, ICP, and ICT through "hula twist", "bicycle pedal" and one-bond flip isomerization reactions. The overall photocycle can be achieved by competitive parallel/sequential reactions, in which the ground state recovery is controlled by a series of slow volume-conserving bicycle pedal/hula twist and one-bond flip isomerization reactions, as well as fast protonation-deprotonation processes and the hydrophobic-hydrophilic state transformation.
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education, Department of Chemistry, Beijing Normal University, Xin-wai-da-jie No. 19, Beijing, 100875, China. xuebochen@bnu.edu.cn.
authors.forename: Lili
authors.initials: L
authors.lastname: Wei
authors.forename: Hongjuan
authors.initials: H
authors.lastname: Wang
authors.forename: Xuebo
authors.initials: X
authors.lastname: Chen
authors.forename: Weihai
authors.initials: W
authors.lastname: Fang
authors.forename: Haobin
authors.initials: H
authors.lastname: Wang
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007536:Isomerism; D008958:Models, Molecular; D055668:Photochemical Processes; D020283:Photoreceptors, Microbial / Q000737:chemistry*; D011487:Protein Conformation; D011522:Protons; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D020283:Photoreceptors, Microbial; D011522:Protons; C050162:photoactive yellow protein, Bacteria