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Title: Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli [Q-Band ENDOR Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli]

Abstract

The respiratory cytochrome bo3 ubiquinol oxidase from E. coli has a high affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQH), which is a transient intermediate during the electron mediated reduction of O2 to water. It is known that SQH is stabilized by two strong hydrogen bonds from R71 and D75 to the ubiquinone carbonyl oxygen O1, and weak hydrogen bonds from H98 and Q101 to O4. In the current work, SQH was investigated with orientation selective Q-band (~34 GHz) pulsed 1H ENDOR spectroscopy on fully deuterated cyt bo3 in an H2O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor Tz' = 11.8 MHz, whereas for H2 Tz' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (~70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by about 25°. Equilibrium molecular dynamics (MD) simulations onmore » a membrane-embedded model of the cyt bo3 QH site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Here, density functional theory (DFT) calculations support that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone« less

Authors:
 [1];  [2];  [3];  [4];  [4];  [1];  [1];  [1]
+ Show Author Affiliations
  1. Univ. of Illinois at Urbana-Champagne, Urbana, IL (United States)
  2. Univ. of Illinois at Urbana-Champagne, Urbana, IL (United States); Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
  3. Univ. of Illinois at Urbana-Champagne, Urbana, IL (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
  4. The Univ. of Manchester, Manchester (United Kingdom)
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champagne, Urbana, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1465174
Grant/Contract Number:  
FG02-08ER15960
Resource Type:
Accepted Manuscript
Journal Name:
Biochemistry
Additional Journal Information:
Journal Volume: 55; Journal Issue: 40; Journal ID: ISSN 0006-2960
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Sun, Chang, Taguchi, Alexander T., Vermaas, Josh V., Beal, Nathan J., O’Malley, Patrick J., Tajkhorshid, Emad, Gennis, Robert B., and Dikanov, Sergei A. Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli [Q-Band ENDOR Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli]. United States: N. p., 2016. Web. doi:10.1021/acs.biochem.6b00669.
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Sun, Chang, Taguchi, Alexander T., Vermaas, Josh V., Beal, Nathan J., O’Malley, Patrick J., Tajkhorshid, Emad, Gennis, Robert B., & Dikanov, Sergei A. Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli [Q-Band ENDOR Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli]. United States. https://doi.org/10.1021/acs.biochem.6b00669
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Sun, Chang, Taguchi, Alexander T., Vermaas, Josh V., Beal, Nathan J., O’Malley, Patrick J., Tajkhorshid, Emad, Gennis, Robert B., and Dikanov, Sergei A. Tue . "Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli [Q-Band ENDOR Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli]". United States. https://doi.org/10.1021/acs.biochem.6b00669. https://www.osti.gov/servlets/purl/1465174.
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@article{osti_1465174,
title = {Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli [Q-Band ENDOR Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli]},
author = {Sun, Chang and Taguchi, Alexander T. and Vermaas, Josh V. and Beal, Nathan J. and O’Malley, Patrick J. and Tajkhorshid, Emad and Gennis, Robert B. and Dikanov, Sergei A.},
abstractNote = {The respiratory cytochrome bo3 ubiquinol oxidase from E. coli has a high affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQH), which is a transient intermediate during the electron mediated reduction of O2 to water. It is known that SQH is stabilized by two strong hydrogen bonds from R71 and D75 to the ubiquinone carbonyl oxygen O1, and weak hydrogen bonds from H98 and Q101 to O4. In the current work, SQH was investigated with orientation selective Q-band (~34 GHz) pulsed 1H ENDOR spectroscopy on fully deuterated cyt bo3 in an H2O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor Tz' = 11.8 MHz, whereas for H2 Tz' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (~70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by about 25°. Equilibrium molecular dynamics (MD) simulations on a membrane-embedded model of the cyt bo3 QH site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Here, density functional theory (DFT) calculations support that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone},
doi = {10.1021/acs.biochem.6b00669},
journal = {Biochemistry},
number = 40,
volume = 55,
place = {United States},
year = {Tue Sep 13 00:00:00 EDT 2016},
month = {Tue Sep 13 00:00:00 EDT 2016}
}
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