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Title: H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle

Abstract

Recent investigations into ferredoxin-dependent transhydrogenases, a class of enzymes responsible for electron transport, have highlighted the biological importance of flavin-based electron bifurcation (FBEB). FBEB generates biomolecules with very low reduction potential by coupling the oxidation of an electron donor with intermediate potential to the reduction of high and low potential molecules. Bifurcating systems can generate biomolecules with very low reduction potentials, such as reduced ferredoxin (Fd), from species such as NADPH. Metabolic systems that use bifurcation are more efficient and confer a competitive advantage for the organisms that harbor them. Structural models are now available for two NADH-dependent ferredoxin-NADP+ oxidoreductase (Nfn) complexes. These models, together with spectroscopic studies, have provided considerable insight into the catalytic process of FBEB. However, much about the mechanism and regulation of these multi-subunit proteins remains unclear. Using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and statistical coupling analysis (SCA), we identified in this work specific pathways of communication within the model FBEB system, Nfn from Pyrococus furiosus, under conditions at each step of the catalytic cycle. HDX-MS revealed evidence for allosteric coupling across protein subunits upon nucleotide and ferredoxin binding. SCA uncovered a network of co-evolving residues that can provide connectivity across the complex. Together, the HDX-MSmore » and SCA data show that protein allostery occurs across the ensemble of iron-sulfur cofactors and ligand binding sites using specific pathways that connect domains allowing them to function as dynamically coordinated units.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [2];  [2];  [3];  [1];  [1]
  1. Montana State Univ., Bozeman, MT (United States)
  2. Univ. of Georgia, Athens, GA (United States)
  3. Washington State Univ., Pullman, WA (United States)
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Center for Biological Electron Transfer and Catalysis (BETCy)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)
OSTI Identifier:
1469904
Alternate Identifier(s):
OSTI ID: 1549363
Grant/Contract Number:  
SC0012518; P20GM103474
Resource Type:
Accepted Manuscript
Journal Name:
Biochimica et Biophysica Acta - General Subjects
Additional Journal Information:
Journal Volume: 1862; Journal Issue: 1; Related Information: BETCy partners with Montana State University (lead); Arizona State University; National Renewable Energy Laboratory; University of Georgia; University of Kentucky; University of Washington; Utah State University; Journal ID: ISSN 0304-4165
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; solar (fuels); biofuels (including algae and biomass); bio-inspired; hydrogen and fuel cells; HDX-MS; SCA; Electron bifurcation; Allostery; Ferredoxin-dependent transhydrogenase; Flavin-based electron bifurcation

Citation Formats

Berry, Luke, Poudel, Saroj, Tokmina-Lukaszewska, Monika, Colman, Daniel R., Nguyen, Diep M. N., Schut, Gerrit J., Adams, Michael W. W., Peters, John W., Boyd, Eric S., and Bothner, Brian. H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle. United States: N. p., 2017. Web. doi:10.1016/j.bbagen.2017.10.002.
Berry, Luke, Poudel, Saroj, Tokmina-Lukaszewska, Monika, Colman, Daniel R., Nguyen, Diep M. N., Schut, Gerrit J., Adams, Michael W. W., Peters, John W., Boyd, Eric S., & Bothner, Brian. H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle. United States. https://doi.org/10.1016/j.bbagen.2017.10.002
Berry, Luke, Poudel, Saroj, Tokmina-Lukaszewska, Monika, Colman, Daniel R., Nguyen, Diep M. N., Schut, Gerrit J., Adams, Michael W. W., Peters, John W., Boyd, Eric S., and Bothner, Brian. Fri . "H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle". United States. https://doi.org/10.1016/j.bbagen.2017.10.002. https://www.osti.gov/servlets/purl/1469904.
@article{osti_1469904,
title = {H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle},
author = {Berry, Luke and Poudel, Saroj and Tokmina-Lukaszewska, Monika and Colman, Daniel R. and Nguyen, Diep M. N. and Schut, Gerrit J. and Adams, Michael W. W. and Peters, John W. and Boyd, Eric S. and Bothner, Brian},
abstractNote = {Recent investigations into ferredoxin-dependent transhydrogenases, a class of enzymes responsible for electron transport, have highlighted the biological importance of flavin-based electron bifurcation (FBEB). FBEB generates biomolecules with very low reduction potential by coupling the oxidation of an electron donor with intermediate potential to the reduction of high and low potential molecules. Bifurcating systems can generate biomolecules with very low reduction potentials, such as reduced ferredoxin (Fd), from species such as NADPH. Metabolic systems that use bifurcation are more efficient and confer a competitive advantage for the organisms that harbor them. Structural models are now available for two NADH-dependent ferredoxin-NADP+ oxidoreductase (Nfn) complexes. These models, together with spectroscopic studies, have provided considerable insight into the catalytic process of FBEB. However, much about the mechanism and regulation of these multi-subunit proteins remains unclear. Using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and statistical coupling analysis (SCA), we identified in this work specific pathways of communication within the model FBEB system, Nfn from Pyrococus furiosus, under conditions at each step of the catalytic cycle. HDX-MS revealed evidence for allosteric coupling across protein subunits upon nucleotide and ferredoxin binding. SCA uncovered a network of co-evolving residues that can provide connectivity across the complex. Together, the HDX-MS and SCA data show that protein allostery occurs across the ensemble of iron-sulfur cofactors and ligand binding sites using specific pathways that connect domains allowing them to function as dynamically coordinated units.},
doi = {10.1016/j.bbagen.2017.10.002},
journal = {Biochimica et Biophysica Acta - General Subjects},
number = 1,
volume = 1862,
place = {United States},
year = {Fri Oct 06 00:00:00 EDT 2017},
month = {Fri Oct 06 00:00:00 EDT 2017}
}

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Works referenced in this record:

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation
journal, February 2013

  • Buckel, Wolfgang; Thauer, Rudolf K.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 2
  • DOI: 10.1016/j.bbabio.2012.07.002

Energy Conservation via Electron-Transferring Flavoprotein in Anaerobic Bacteria
journal, November 2007

  • Herrmann, G.; Jayamani, E.; Mai, G.
  • Journal of Bacteriology, Vol. 190, Issue 3
  • DOI: 10.1128/JB.01422-07

Insights into Flavin-based Electron Bifurcation via the NADH-dependent Reduced Ferredoxin:NADP Oxidoreductase Structure
journal, July 2015

  • Demmer, Julius K.; Huang, Haiyan; Wang, Shuning
  • Journal of Biological Chemistry, Vol. 290, Issue 36
  • DOI: 10.1074/jbc.M115.656520

Mechanistic insights into energy conservation by flavin-based electron bifurcation
journal, April 2017

  • Lubner, Carolyn E.; Jennings, David P.; Mulder, David W.
  • Nature Chemical Biology, Vol. 13, Issue 6
  • DOI: 10.1038/nchembio.2348

Two functionally distinct NADP + -dependent ferredoxin oxidoreductases maintain the primary redox balance of Pyrococcus furiosus
journal, July 2017

  • Nguyen, Diep M. N.; Schut, Gerrit J.; Zadvornyy, Oleg A.
  • Journal of Biological Chemistry, Vol. 292, Issue 35
  • DOI: 10.1074/jbc.M117.794172

Ligand binding and conformational dynamics in a flavin-based electron-bifurcating enzyme complex revealed by Hydrogen-Deuterium Exchange Mass Spectrometry
journal, December 2016

  • Demmer, Julius K.; Rupprecht, Fiona A.; Eisinger, Martin L.
  • FEBS Letters, Vol. 590, Issue 24
  • DOI: 10.1002/1873-3468.12489

Studies on the Mechanism of Electron Bifurcation Catalyzed by Electron Transferring Flavoprotein (Etf) and Butyryl-CoA Dehydrogenase (Bcd) of Acidaminococcus fermentans
journal, December 2013

  • Chowdhury, Nilanjan Pal; Mowafy, Amr M.; Demmer, Julius K.
  • Journal of Biological Chemistry, Vol. 289, Issue 8
  • DOI: 10.1074/jbc.M113.521013

Conformational changes in proteins probed by hydrogen-exchange electrospray-ionization mass spectrometry
journal, April 1991

  • Katta, Viswanatham; Chait, Brian T.; Carr, Steven
  • Rapid Communications in Mass Spectrometry, Vol. 5, Issue 4
  • DOI: 10.1002/rcm.1290050415

Hydrogen exchange mass spectrometry for studying protein structure and dynamics
journal, January 2011

  • Konermann, Lars; Pan, Jingxi; Liu, Yu-Hong
  • Chem. Soc. Rev., Vol. 40, Issue 3
  • DOI: 10.1039/C0CS00113A

Hydrogen exchange mass spectrometry: what is it and what can it tell us?
journal, March 2010

  • Marcsisin, Sean R.; Engen, John R.
  • Analytical and Bioanalytical Chemistry, Vol. 397, Issue 3
  • DOI: 10.1007/s00216-010-3556-4

Structural Basis for Activation of Calcineurin by Calmodulin
journal, January 2012

  • Rumi-Masante, Julie; Rusinga, Farai I.; Lester, Terrence E.
  • Journal of Molecular Biology, Vol. 415, Issue 2
  • DOI: 10.1016/j.jmb.2011.11.008

Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry
journal, March 2013

  • Engen, John R.; Wales, Thomas E.; Chen, Shugui
  • International Reviews in Physical Chemistry, Vol. 32, Issue 1
  • DOI: 10.1080/0144235X.2012.751175

Allosteric regulation and catalysis emerge via a common route
journal, July 2008

  • Goodey, Nina M.; Benkovic, Stephen J.
  • Nature Chemical Biology, Vol. 4, Issue 8
  • DOI: 10.1038/nchembio.98

Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
journal, October 1999


Protein Sectors: Evolutionary Units of Three-Dimensional Structure
journal, August 2009


Methods for the analysis of high precision differential hydrogen–deuterium exchange data
journal, April 2011

  • Chalmers, Michael J.; Pascal, Bruce D.; Willis, Scooter
  • International Journal of Mass Spectrometry, Vol. 302, Issue 1-3
  • DOI: 10.1016/j.ijms.2010.08.002

Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
journal, January 2011

  • Sievers, Fabian; Wilm, Andreas; Dineen, David
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.75

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003


Cytoscape 2.8: new features for data integration and network visualization
journal, December 2010


Computing topological parameters of biological networks
journal, November 2007


Conformational Equilibria and Rates of Localized Motion within Hepatitis B Virus Capsids
journal, January 2008

  • Hilmer, Jonathan K.; Zlotnick, Adam; Bothner, Brian
  • Journal of Molecular Biology, Vol. 375, Issue 2
  • DOI: 10.1016/j.jmb.2007.10.044

Biological insights from hydrogen exchange mass spectrometry
journal, June 2013


Analysis of Protein Conformation and Dynamics by Hydrogen/Deuterium Exchange MS
journal, October 2009


Works referencing / citing this record:

On the nature of organic and inorganic centers that bifurcate electrons, coupling exergonic and endergonic oxidation–reduction reactions
journal, January 2018

  • Peters, John W.; Beratan, David N.; Schut, Gerrit J.
  • Chemical Communications, Vol. 54, Issue 33
  • DOI: 10.1039/c8cc01530a

Origin and Evolution of Flavin-Based Electron Bifurcating Enzymes
journal, August 2018


Residue-Level Allostery Propagates through the Effective Coarse-Grained Hessian
journal, April 2020

  • Lake, Peter T.; Davidson, Russell B.; Klem, Heidi
  • Journal of Chemical Theory and Computation, Vol. 16, Issue 5
  • DOI: 10.1021/acs.jctc.9b01149

Origin and Evolution of Flavin-Based Electron Bifurcating Enzymes
journal, August 2018