title: Excited States and Photochemistry of Chromophores in the Photoactive Proteins Explored by the Combined Quantum Mechanical and Molecular Mechanical Calculations.
abstract: A photoactive protein usually contains a unique chromophore that is responsible for the initial photoresponse and functions of the photoactive protein are determined by the interaction between the chromophore and its protein surroundings. The combined quantum mechanical and molecular mechanical (QM/MM) approach is demonstrated to be a very useful tool for exploring structures and functions of a photoactive protein with the chromophore and its protein surroundings treated by the QM and MM methods, respectively. In this review, we summarize the basic formulas of the QM/MM approach and emphasize its applications to excited states and photoreactions of chromophores in rhodopsin protein, photoactive yellow protein, and green fluorescent protein.
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China. Electronic address: lihong.liu@bnu.edu.cn.
authors.forename: Lihong
authors.initials: L
authors.lastname: Liu
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Ganglong
authors.initials: G
authors.lastname: Cui
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
authors.forename: Wei-Hai
authors.initials: WH
authors.lastname: Fang
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D049452:Green Fluorescent Proteins / Q000737:chemistry*; D020607:Halorhodospira halophila / Q000737:chemistry / Q000235:genetics; D006801:Humans; D037402:Hydrozoa / Q000737:chemistry / Q000235:genetics; D007700:Kinetics; D008027:Light; D008164:Luminescent Proteins / Q000737:chemistry* / Q000235:genetics; D056004:Molecular Dynamics Simulation; D009154:Mutation; D055668:Photochemical Processes; D011789:Quantum Theory; D012243:Rhodopsin / Q000737:chemistry* / Q000235:genetics; D012545:Schiff Bases / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D008164:Luminescent Proteins; D012545:Schiff Bases; C485192:green fluorescent protein, Aequorea victoria; C054562:yellow fluorescent protein, Bacteria; D049452:Green Fluorescent Proteins; D012243:Rhodopsin
keywords: Chromophore; Electrostatic effect; Protein; QM/MM approach; Steric effect