title: Ground-state structures and vertical excitations for the kindling fluorescent protein asFP595.
abstract: Geometry configurations of a large fraction of the kindling fluorescent protein asFP595 around the chromophore region were optimized by using the effective fragment potential quantum mechanical-molecular mechanical (QM/MM) method. The initial coordinates of heavy atoms were taken from the structure from the Protein Data Bank archive corresponding to the dark-adapted state of the Ala143 --> Gly mutant of asFP595. Optimization of geometry parameters was performed for all internal coordinates in the QM part composed of the chromophore unit and the side chains of His197, Glu215, and Arg92 as well as for positions of effective fragments constituting the MMpart. The structures corresponding to the anion trans, anion cis, and zwitterion trans moieties were considered among various alternatives for the chromophore unit inside the protein matrix. The QM/MM simulations show that the protein environment provides stabilization for the trans-zwitterion isomer compared to the gas-phase conditions. By using the multiconfigurational CASSCF and the time-dependent density functional theory calculations, we estimated positions of spectral bands corresponding to vertical S(0)-S(1) transitions. The results of simulations support the assumption that the dark state of asFP595 corresponds to the anionic or zwitterionic trans-conformation, while the kindled state corresponds to the anionic cis-conformation.
authors.affiliation: Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow 119992, Russian Federation.
authors.forename: Bella
authors.initials: B
authors.lastname: Grigorenko
authors.forename: Alexander
authors.initials: A
authors.lastname: Savitsky
authors.forename: Igor
authors.initials: I
authors.lastname: Topol
authors.forename: Stanley
authors.initials: S
authors.lastname: Burt
authors.forename: Alexander
authors.initials: A
authors.lastname: Nemukhin
mesh_terms: D000409:Alanine / Q000737:chemistry; D000818:Animals; D000838:Anions; D001703:Biophysics / Q000379:methods*; D030562:Databases, Protein; D007477:Ions; D008164:Luminescent Proteins / Q000737:chemistry*; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012615:Sea Anemones; D012984:Software
chemical_list: D000838:Anions; C430876:FP595 protein, Anemonia sulcata; D007477:Ions; D008164:Luminescent Proteins; D011506:Proteins; D000409:Alanine