title: Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA.
abstract: Quantum mechanical calculations using the Marcus equation are applied to compare the electron-transfer probability for two distinct crystal structures of the Escherichia coli protein WrbA, an FMN-dependent
  
  
  
  quinone oxidoreductase, with the bound substrate benzoquinone. The calculations indicate that the position of benzoquinone in a new structure reported here and solved at 1.33 Å resolution is more likely to be relevant for the physiological reaction of WrbA than a previously reported crystal structure in which benzoquinone is shifted by ∼5 Å. Because the true electron-acceptor substrate for WrbA is not yet known, the present results can serve to constrain computational docking attempts with potential substrates that may aid in identifying the natural substrate(s) and physiological role(s) of this enzyme. The approach used here highlights a role for quantum mechanical calculations in the interpretation of protein crystal structures.
authors.affiliation: Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.|Faculty of Sciences, University of South Bohemia in Ceske Budejovice , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.
authors.forename: Oksana
authors.initials: O
authors.lastname: Degtjarik
authors.affiliation: Institute of Molecular Genetics and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 16610 Prague 6, Czech Republic.
authors.forename: Jiři
authors.initials: J
authors.lastname: Brynda
authors.affiliation: Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.
authors.forename: Olga
authors.initials: O
authors.lastname: Ettrichova
authors.affiliation: Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.|Faculty of Sciences, University of South Bohemia in Ceske Budejovice , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Kuty
authors.affiliation: Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.|Faculty of Sciences, University of South Bohemia in Ceske Budejovice , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.
authors.forename: Dhiraj
authors.initials: D
authors.lastname: Sinha
authors.affiliation: Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.|Faculty of Sciences, University of South Bohemia in Ceske Budejovice , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.
authors.forename: Ivana
authors.initials: I
authors.lastname: Kuta Smatanova
authors.affiliation: Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.|Chemistry Department, Princeton University , Princeton, New Jersey 08544-1009, United States.
authors.forename: Jannette
authors.initials: J
authors.lastname: Carey
authors.affiliation: Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.|Faculty of Sciences, University of South Bohemia in Ceske Budejovice , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.
authors.forename: Rüdiger
authors.initials: R
authors.lastname: Ettrich
authors.affiliation: Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.|Faculty of Sciences, University of South Bohemia in Ceske Budejovice , Zamek 136, CZ-373 33 Nove Hrady, Czech Republic.
authors.forename: David
authors.initials: D
authors.lastname: Řeha
mesh_terms: D016227:Benzoquinones / Q000737:chemistry*; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004579:Electron Transport; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D005486:Flavin Mononucleotide / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D012097:Repressor Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D016227:Benzoquinones; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; C081759:WrbA protein, E coli; D005486:Flavin Mononucleotide