O2 migration rates in [NiFe] hydrogenases. A joint approach combining free-energy calculations and kinetic modeling

Journal of Physical Chemistry B

Volumn 118, Issue 3, 2014, Pages 676-681

  Topin, Jérémie ^a   Diharce, Julien ^a   Fiorucci, Sébastien ^a   Antonczak, Serge ^a   Golebiowski, Jéroîme ^a  

^a UNIVERSITÉ DE NICE SOPHIA ANTIPOLIS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AEROBIC CONDITION; CATALYTIC PRODUCTION; FREE-ENERGY CALCULATIONS; KINETIC MODELING; MIGRATION PATHWAY; MODEL-BASED OPC; POTENTIAL OF MEAN FORCE; TRANSITION STATE THEORIES;

PHYSICAL CHEMISTRY; PHYSICS;

FREE ENERGY;

HYDROGENASE; NICKEL IRON HYDROGENASE; NICKEL-IRON HYDROGENASE; OXYGEN;

ARTICLE; CHEMISTRY; DESULFOVIBRIO; DIFFUSION; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; MOLECULAR DYNAMICS; MOVEMENT (PHYSIOLOGY); MUTATION; PROTEIN CONFORMATION; THERMODYNAMICS;

DESULFOVIBRIO; DIFFUSION; HYDROGENASE; KINETICS; MOLECULAR DYNAMICS SIMULATION; MOVEMENT; MUTATION; OXYGEN; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 84893086387     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp4093964     Document Type: Article

References (27)

1. Vignais, P. M.; Billoud, B. Occurrence, Classification, and Biological Function of Hydrogenases: An Overview Chem. Rev. 2007, 107, 4206-4272
2. Jones, A. K.; Sillery, E.; Albracht, S. P.; Armstrong, F. A. Direct Comparison of the Electrocatalytic Oxidation of Hydrogen by an Enzyme and a Platinum Catalyst Chem. Commun. 2002, 866-867
3. Kim, S.; Lu, D.; Park, S.; Wang, G. Production of Hydrogenases as Biocatalysts Int. J. Hydrogen Energy 2012, 37, 15833-15840
4. 2-Photoproducing Organisms and Processes Biochem. Soc. Trans. 2005, 33, 70-72
5. Tye, J. W.; Hall, M. B.; Darensbourg, M. Y. Better Than Platinum? Fuel Cells Energized by Enzymes Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 16911-16912
6. Fontecilla-Camps, J. C.; Volbeda, A.; Cavazza, C.; Nicolet, Y. Structure/Function Relationships of [NiFe]- and [FeFe]-Hydrogenases Chem. Rev. 2007, 107, 4273-4303
7. Wang, P.-h.; Best, R. B.; Blumberger, J. A Microscopic Model for Gas Diffusion Dynamics in a [NiFe]-Hydrogenase Phys. Chem. Chem. Phys. 2011, 13, 7708-7719
8. Wang, P. H.; Blumberger, J. Mechanistic Insight into the Blocking of CO Diffusion in [NiFe]-Hydrogenase Mutants through Multiscale Simulation Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 6399-6404
9. 2-Tolerance in [Ni-Fe] Hydrogenases Energy Environ. Sci. 2011, 4, 33-41
10. Liebgott, P. P.; de Lacey, A. L.; Burlat, B.; Cournac, L.; Richaud, P.; Brugna, M.; Fernandez, V. M.; Guigliarelli, B.; Rousset, M.; Leger, C. Original Design of an Oxygen-Tolerant [NiFe] Hydrogenase: Major Effect of a Valine-to-Cysteine Mutation near the Active Site J. Am. Chem. Soc. 2011, 133, 986-997
11. Leroux, F.; Dementin, S.; Burlat, B.; Cournac, L.; Volbeda, A.; Champ, S.; Martin, L.; Guigliarelli, B.; Bertrand, P.; Fontecilla-Camps, J. Experimental Approaches to Kinetics of Gas Diffusion in Hydrogenase Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 11188-11193
12. Armstrong, F. A.; Belsey, N. A.; Cracknell, J. A.; Goldet, G.; Parkin, A.; Reisner, E.; Vincent, K. A.; Wait, A. F. Dynamic Electrochemical Investigations of Hydrogen Oxidation and Production by Enzymes and Implications for Future Technology Chem. Soc. Rev. 2009, 38, 36-51
13. Hong, G.; Pachter, R. Inhibition of Biocatalysis in [Fe-Fe] Hydrogenase by Oxygen: Molecular Dynamics and Density Functional Theory Calculations ACS Chem. Biol. 2012, 7, 1268-1275
14. 2 Transport in a [NiFe]-Hydrogenase J. Am. Chem. Soc. 2011, 133, 3548-3556
15. Topin, J.; Rousset, M.; Antonczak, S.; Golebiowski, J. Kinetics and Thermodynamics of Gas Diffusion in a NiFe Hydrogenase Proteins: Struct., Funct., Bioinf. 2012, 80, 677-682
16. Shomura, Y.; Yoon, K. S.; Nishihara, H.; Higuchi, Y. Structural Basis for a [4Fe-3S] Cluster in the Oxygen-Tolerant Membrane-Bound [NiFe]-Hydrogenase Nature 2011, 479, 253-256
17. Fritsch, J.; Scheerer, P.; Frielingsdorf, S.; Kroschinsky, S.; Friedrich, B.; Lenz, O.; Spahn, C. M. The Crystal Structure of an Oxygen-Tolerant Hydrogenase Uncovers a Novel Iron-Sulphur Centre Nature 2011, 479, 249-52
18. Liebgott, P.-P.; Leroux, F.; Burlat, B.; Dementin, S.; Baffert, C.; Lautier, T.; Fourmond, V.; Ceccaldi, P.; Cavazza, C.; Meynial-Salles, I. Relating Diffusion Along the Substrate Tunnel and Oxygen Sensitivity in Hydrogenase Nat. Chem. Biol. 2010, 6, 63-70
19. Dementin, S.; Leroux, F.; Cournac, L.; de Lacey, A. L.; Volbeda, A.; Leger, C.; Burlat, B.; Martinez, N.; Champ, S.; Martin, L. Introduction of Methionines in the Gas Channel Makes [NiFe] Hydrogenase Aero-Tolerant J. Am. Chem. Soc. 2009, 131, 10156-64
20. 2-Resistant Enzymes? Int. J. Hydrogen Energy 2010, 35, 10770-10777
21. Zhang, Y.; Lu, M.; Cheng, Y.; Li, Z. H-NOX Domains Display Different Tunnel Systems for Ligand Migration J. Mol. Graphics Modell. 2010, 28, 814-819
22. Abbruzzetti, S.; Spyrakis, F.; Bidon-Chanal, A.; Luque, F. J.; Viappiani, C. Ligand Migration through Hemeprotein Cavities: Insights from Laser Flash Photolysis and Molecular Dynamics Simulations Phys. Chem. Chem. Phys. 2013, 15, 10686-10701
23. Guex, N.; Peitsch, M. C. SWISS-MODEL and the Swiss-PdbViewer: An Environment for Comparative Protein Modeling Electrophoresis 1997, 18, 2714-23
24. 2 Affinity and Low Autooxidation Rate J. Biol. Chem. 1992, 15, 14443-50
25. Johnson, K.; Simpson, Z.; Blom, T. Global Kinetic Explorer: A New Computer Program for Dynamic Simulation and Fitting of Kinetic Data Anal. Biochem. 2009, 387, 20-29
26. Eyring, H. The Activated Complex and the Absolute Rate of Chemical Reactions Chem. Rev. 1935, 17, 65-77
27. 2 into Human Ferritin Chem. Phys. Lett. 2004, 390, 491-495