TY - JOUR
T1 - Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA
AU - Degtjarik, Oksana
AU - Brynda, Jiři
AU - Ettrichova, Olga
AU - Kuty, Michal
AU - Sinha, Dhiraj
AU - Kuta Smatanova, Ivana
AU - Carey, Jannette
AU - Ettrich, Rüdiger
AU - Řeha, David
N1 - Publisher Copyright:
© 2016 American Chemical Society.
PY - 2016/6/9
Y1 - 2016/6/9
N2 - 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.
AB - 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.
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U2 - 10.1021/acs.jpcb.5b11958
DO - 10.1021/acs.jpcb.5b11958
M3 - Article
C2 - 27183467
AN - SCOPUS:84974786934
SN - 1520-6106
VL - 120
SP - 4867
EP - 4877
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
IS - 22
ER -