title: Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor.
abstract: The AppA protein with the BLUF (blue light using flavin adenine dinucleotide) domain is a blue light photoreceptor that cycle between dark-adapted and light-induced functional states. We characterized possible reaction intermediates in the photocycle of AppA BLUF. Molecular dynamics (MD), quantum chemical and quantum mechanical-molecular mechanical (QM/MM) calculations were carried out to describe several stable structures of a molecular system modeling the protein. The coordinates of heavy atoms from the crystal structure (PDB code 2IYG) of the protein in the dark state served as starting point for 10 ns MD simulations. Representative MD frames were used in QM(B3LYP/cc-pVDZ)/MM(AMBER) calculations to locate minimum energy configurations of the model system. Vertical electronic excitation energies were estimated for the molecular clusters comprising the quantum subsystems of the QM/MM optimized structures using the SOS-CIS(D) quantum chemistry method. Computational results support the occurrence of photoreaction intermediates that are characterized by spectral absorption bands between those of the dark and light states. They agree with crystal structures of reaction intermediates (PDB code 2IYI) observed in the AppA BLUF domain. Transformations of the Gln63 side chain stimulated by photo-excitation and performed with the assistance of the chromophore and the Met106 side chain are responsible for these intermediates.
authors.affiliation: Department of Chemistry, M V Lomonosov Moscow State University, Moscow, Russia. wasabiko13@gmail.com
authors.forename: Maria G
authors.initials: MG
authors.lastname: Khrenova
authors.forename: Tatiana
authors.initials: T
authors.lastname: Domratcheva
authors.forename: Ilme
authors.initials: I
authors.lastname: Schlichting
authors.forename: Bella L
authors.initials: BL
authors.lastname: Grigorenko
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Nemukhin
mesh_terms: D001419:Bacteria / Q000737:chemistry / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D001696:Biomechanical Phenomena; D003460:Crystallization; D015226:Dinucleoside Phosphates / Q000737:chemistry / Q000378:metabolism; D005182:Flavin-Adenine Dinucleotide / Q000378:metabolism; D005420:Flavoproteins / Q000737:chemistry / Q000378:metabolism*; D005973:Glutamine / Q000378:metabolism*; D008027:Light; D008715:Methionine / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D055668:Photochemical Processes / Q000528:radiation effects; D020283:Photoreceptors, Microbial / Q000737:chemistry / Q000378:metabolism*; D017434:Protein Structure, Tertiary / Q000528:radiation effects*; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D015226:Dinucleoside Phosphates; D005420:Flavoproteins; D020283:Photoreceptors, Microbial; D005973:Glutamine; D005182:Flavin-Adenine Dinucleotide; C012276:diadenosine pyrophosphate; D008715:Methionine