Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA

Oksana Degtjarik, Jiři Brynda, Olga Ettrichova, Michal Kuty, Dhiraj Sinha, Ivana Kuta Smatanova, Jannette Carey, Rüdiger Ettrich, David Řeha

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3 Scopus citations

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 NAD(P)H: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.

Original languageEnglish (US)
Pages (from-to)4867-4877
Number of pages11
JournalJournal of Physical Chemistry B
Volume120
Issue number22
DOIs
StatePublished - Jun 9 2016

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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