Literature DB >> 27995927

Mechanism of O2 diffusion and reduction in FeFe hydrogenases.

Adam Kubas1,2, Christophe Orain3, David De Sancho4,5,6, Laure Saujet7,8, Matteo Sensi3, Charles Gauquelin9, Isabelle Meynial-Salles9, Philippe Soucaille9, Hervé Bottin7,8, Carole Baffert3, Vincent Fourmond3, Robert B Best10, Jochen Blumberger1, Christophe Léger3.   

Abstract

FeFe hydrogenases are the most efficient H2-producing enzymes. However, inactivation by O2 remains an obstacle that prevents them being used in many biotechnological devices. Here, we combine electrochemistry, site-directed mutagenesis, molecular dynamics and quantum chemical calculations to uncover the molecular mechanism of O2 diffusion within the enzyme and its reactions at the active site. We propose that the partial reversibility of the reaction with O2 results from the four-electron reduction of O2 to water. The third electron/proton transfer step is the bottleneck for water production, competing with formation of a highly reactive OH radical and hydroxylated cysteine. The rapid delivery of electrons and protons to the active site is therefore crucial to prevent the accumulation of these aggressive species during prolonged O2 exposure. These findings should provide important clues for the design of hydrogenase mutants with increased resistance to oxidative damage.

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Year:  2016        PMID: 27995927      PMCID: PMC5597964          DOI: 10.1038/nchem.2592

Source DB:  PubMed          Journal:  Nat Chem        ISSN: 1755-4330            Impact factor:   24.427


  48 in total

1.  O2 reactions at the six-iron active site (H-cluster) in [FeFe]-hydrogenase.

Authors:  Camilla Lambertz; Nils Leidel; Kajsa G V Havelius; Jens Noth; Petko Chernev; Martin Winkler; Thomas Happe; Michael Haumann
Journal:  J Biol Chem       Date:  2011-09-19       Impact factor: 5.157

2.  Intrinsic rates and activation free energies from single-molecule pulling experiments.

Authors:  Olga K Dudko; Gerhard Hummer; Attila Szabo
Journal:  Phys Rev Lett       Date:  2006-03-15       Impact factor: 9.161

3.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

Authors:  Sander Pronk; Szilárd Páll; Roland Schulz; Per Larsson; Pär Bjelkmar; Rossen Apostolov; Michael R Shirts; Jeremy C Smith; Peter M Kasson; David van der Spoel; Berk Hess; Erik Lindahl
Journal:  Bioinformatics       Date:  2013-02-13       Impact factor: 6.937

4.  Electrocatalytic O₂ reduction by [Fe-Fe]-hydrogenase active site models.

Authors:  Subal Dey; Atanu Rana; Danielle Crouthers; Biswajit Mondal; Pradip Kumar Das; Marcetta Y Darensbourg; Abhishek Dey
Journal:  J Am Chem Soc       Date:  2014-06-10       Impact factor: 15.419

5.  A redox hydrogel protects hydrogenase from high-potential deactivation and oxygen damage.

Authors:  Nicolas Plumeré; Olaf Rüdiger; Alaa Alsheikh Oughli; Rhodri Williams; Jeevanthi Vivekananthan; Sascha Pöller; Wolfgang Schuhmann; Wolfgang Lubitz
Journal:  Nat Chem       Date:  2014-08-03       Impact factor: 24.427

6.  On understanding proton transfer to the biocatalytic [Fe-Fe](H) sub-cluster in [Fe-Fe]H(2)ases: QM/MM MD simulations.

Authors:  G Hong; A J Cornish; E L Hegg; R Pachter
Journal:  Biochim Biophys Acta       Date:  2011-02-04

7.  Relating diffusion along the substrate tunnel and oxygen sensitivity in hydrogenase.

Authors:  Pierre-Pol Liebgott; Fanny Leroux; Bénédicte Burlat; Sébastien Dementin; Carole Baffert; Thomas Lautier; Vincent Fourmond; Pierre Ceccaldi; Christine Cavazza; Isabelle Meynial-Salles; Philippe Soucaille; Juan Carlos Fontecilla-Camps; Bruno Guigliarelli; Patrick Bertrand; Marc Rousset; Christophe Léger
Journal:  Nat Chem Biol       Date:  2009-12-06       Impact factor: 15.040

8.  Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases.

Authors:  Christopher H Chang; Kwiseon Kim
Journal:  J Chem Theory Comput       Date:  2009-04-14       Impact factor: 6.006

9.  Aerobic damage to [FeFe]-hydrogenases: activation barriers for the chemical attachment of O2.

Authors:  Adam Kubas; David De Sancho; Robert B Best; Jochen Blumberger
Journal:  Angew Chem Int Ed Engl       Date:  2014-03-11       Impact factor: 15.336

10.  Crystal structure of the O(2)-tolerant membrane-bound hydrogenase 1 from Escherichia coli in complex with its cognate cytochrome b.

Authors:  Anne Volbeda; Claudine Darnault; Alison Parkin; Frank Sargent; Fraser A Armstrong; Juan C Fontecilla-Camps
Journal:  Structure       Date:  2012-12-20       Impact factor: 5.006

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  26 in total

Review 1.  Evolutionary adaptations that enable enzymes to tolerate oxidative stress.

Authors:  James A Imlay; Ramakrishnan Sethu; Sanjay Kumar Rohaun
Journal:  Free Radic Biol Med       Date:  2019-02-06       Impact factor: 7.376

2.  Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways.

Authors:  Ariane Nunes-Alves; Daniel M Zuckerman; Guilherme Menegon Arantes
Journal:  Biophys J       Date:  2018-03-13       Impact factor: 4.033

3.  Absolute quantification of selected photosynthetic electron transfer proteins in Chlamydomonas reinhardtii in the presence and absence of oxygen.

Authors:  Denitsa Nikolova; Claudia Heilmann; Susan Hawat; Philipp Gäbelein; Michael Hippler
Journal:  Photosynth Res       Date:  2018-03-28       Impact factor: 3.573

Review 4.  Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists.

Authors:  Stéphane L Benoit; Chris Greening; Robert J Maier; R Gary Sawers
Journal:  Microbiol Mol Biol Rev       Date:  2020-01-29       Impact factor: 11.056

5.  Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron.

Authors:  Maryam Khademian; James A Imlay
Journal:  Mol Microbiol       Date:  2020-05-19       Impact factor: 3.501

Review 6.  Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase.

Authors:  Sven T Stripp; Benjamin R Duffus; Vincent Fourmond; Christophe Léger; Silke Leimkühler; Shun Hirota; Yilin Hu; Andrew Jasniewski; Hideaki Ogata; Markus W Ribbe
Journal:  Chem Rev       Date:  2022-07-18       Impact factor: 72.087

7.  Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.

Authors:  Sónia Zacarias; Adriana Temporão; Philippe Carpentier; Peter van der Linden; Inês A C Pereira; Pedro M Matias
Journal:  J Biol Inorg Chem       Date:  2020-08-31       Impact factor: 3.358

Review 8.  Small-Molecule Tunnels in Metalloenzymes Viewed as Extensions of the Active Site.

Authors:  Rahul Banerjee; John D Lipscomb
Journal:  Acc Chem Res       Date:  2021-04-22       Impact factor: 22.384

Review 9.  The roles of chalcogenides in O2 protection of H2ase active sites.

Authors:  Xuemei Yang; Marcetta Y Darensbourg
Journal:  Chem Sci       Date:  2020-08-12       Impact factor: 9.825

10.  Characterization of a putative sensory [FeFe]-hydrogenase provides new insight into the role of the active site architecture.

Authors:  Henrik Land; Alina Sekretareva; Ping Huang; Holly J Redman; Brigitta Németh; Nakia Polidori; Lívia S Mészáros; Moritz Senger; Sven T Stripp; Gustav Berggren
Journal:  Chem Sci       Date:  2020-09-21       Impact factor: 9.825

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