Coulomb soup of bioenergetics: Electron transfer in a bacterial bc 1 complex

Journal of Physical Chemistry Letters

Volumn 4, Issue 21, 2013, Pages 3602-3606

  Martin, Daniel R ^a   Lebard, David N ^b   Matyushov, Dmitry V ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

^b YESHIVA UNIVERSITY   (United States)

Author keywords

bioenergetics; non Gaussian statistics; nonergodic chemical kinetics; protein dynamics; protein electron transfer

Indexed keywords

ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS; BIOENERGETICS; ELECTRON TRANSFER; ELECTRON TRANSPORT CHAIN; MEMBRANE-BOUND PROTEINS; NON-GAUSSIAN STATISTICS; PROTEIN DYNAMICS; REORGANIZATION ENERGIES;

BIOCHEMISTRY; ELECTRON TRANSITIONS; PROTEINS;

ELECTRON TRANSPORT PROPERTIES;

EID: 84887751722     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz401910e     Document Type: Article

References (38)

1. Nicholls, D. G.; Ferguson, S. J. Bioenergetics 3; Academic Press: London, 2002.
2. Barja, G. Mitochondrial Oxygen Radical Generation and Leak: Sites of Production in States 4 and 3, Organ Specificity, and Relation to Aging and Longevity J. Bioenerg. Biomembr. 1999, 31, 347-366
3. Moser, C. C.; Farid, T. A.; Chobot, S. E.; Dutton, P. L. Electron Tunneling Chains of Mitochondria Biochim. Biophys. Acta 2006, 1757, 1096-1109
4. 1 Complex Biochim. Biophys. Acta: Bioenerg. 2013, 1827, 365-386
5. 1 Complex Predicted by Atomistic Molecular Dynamics Simulations Biochim. Biophys. Acta 2013, 1827, 761-768
6. 1 Complex J. Biol. Chem. 2010, 285, 9233-9248
7. Marcus, R. A.; Sutin, N. Electron Transfer in Chemistry and Biology Biochim. Biophys. Acta 1985, 811, 265-322
8. Moser, C. C.; Keske, J. M.; Warncke, K.; Farid, R. S.; Dutton, P. L. Nature of Biological Electron Transfer Nature 1992, 335, 796-802
9. Page, C. C.; Moser, C. C.; Chen, X. X.; Dutton, P. L. Natural Engineering Principles of Electron Tunneling in Biological Oxidation-Reduction Nature 1999, 402, 47-52
10. 1 Complex in Rhodobacter sphaeroides J. Biol. Chem. 1999, 274, 33931-33944
11. 1 Complex Controls the Rate of Ubihydroquinone Oxidation Biochim. Biophys. Acta 2004, 1655, 77-92
12. LeBard, D. N.; Matyushov, D. V. Protein-Water Electrostatics and Principles of Bioenergetics Phys. Chem. Chem. Phys. 2010, 12, 15335-15348
13. Warshel, A.; Parson, W. W. Computer Simulations of Electron-Transfer Reactions in Solution and in Photosynthetic Reaction Centers Annu. Rev. Phys. Chem. 1991, 42, 279-309
14. 3+ Redox Reaction Theor. Chem. Acc. 2006, 115, 113-126
15. Small, D. W.; Matyushov, D. V.; Voth, G. A. The Theory of Electron Transfer: What May Be Missing? J. Am. Chem. Soc. 2003, 125, 7470-7478
16. LeBard, D. N.; Matyushov, D. V. Glassy Protein Dynamics and Gigantic Solvent Reorganization Energy of Plastocyanin J. Phys. Chem. B 2008, 112, 5218-5227
17. Matyushov, D. V. Protein Electron Transfer: Dynamics and Statistics J. Chem. Phys. 2013, 139, 025102
18. Martin, D. R.; Matyushov, D. V. Non-Gaussian Statistics and Nanosecond Dynamics of Electrostatic Fluctuations Affecting Optical transitions in a Green Fluorescent Protein J. Phys. Chem. B 2012, 116, 10294-10300
19. Zhang, L.; Yang, Y.; Kao, Y.-T.; Wang, L.; Zhong, D. Protein Hydration Dynamics and Molecular Mechanism of Coupled Water -Protein Fluctuations J. Am. Chem. Soc. 2009, 131, 10677-10691
20. Frauenfelder, H.; Chen, G.; Berendzen, J.; Fenimore, P. W.; Jansson, H.; McMahon, B. H.; Stroe, I. R.; Swenson, J.; Young, R. D. A Unified Model of Protein Dynamics Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5129-5134
21. Henzler-Wildman, K. A.; Thai, V.; Lei, M.; Ott, M.; Wolf-Watz, M.; Fenn, T.; Pozharski, E.; Wilson, M. A.; Petsko, G. A.; Karplus, M. Intrinsic Motions along an Enzymatic Reaction Trajectory Nature 2007, 450, 838-844
22. Sumi, H.; Marcus, R. A. Dynamical Effects in Electron Transfer Reactions J. Chem. Phys. 1986, 84, 4894-4914
23. Chen, P.; Meyer, T. J. Electron Transfer in Frozen Media Inorg. Chem. 1996, 35, 5520-5524
24. Barbara, P. F.; Meyer, T. J.; Ratner, M. A. Contemporary Issues in Electron Transfer Research J. Phys. Chem. 1996, 100, 13148-13168
25. Matyushov, D. V. Energetics of Electron Transfer Reactions in Soft Condensed Media Acc. Chem. Res. 2007, 40, 294-301
26. Mukamel, S. Principles of Nonlinear Optical Spectroscopy; Oxford University Press: New York, 1995.
27. Hansen, J. P.; McDonald, I. R. Theory of Simple Liquids; Academic Press: Amsterdam, 2003.
28. Ceccarelli, M.; Marchi, M. Simulation and Modeling of the Rhodobacter spaheroides Bacterial Reaction Center II: Primary Charge Separation J. Phys. Chem. B 2003, 107, 5630-5641
29. LeBard, D. N.; Kapko, V.; Matyushov, D. V. Energetics and Kinetics of Primary Charge Separation in Bacterial Photosynthesis J. Phys. Chem. B 2008, 112, 10322-10342
30. LeBard, D. N.; Matyushov, D. V. Energetics of Bacterial Photosynthesis J. Phys. Chem. B 2009, 113, 12424-12437
31. Matyushov, D. V. Nanosecond Stokes Shift Dynamics, Dynamical Transition, and Gigantic Reorganization Energy of Hydrated Heme Proteins J. Phys. Chem. B 2011, 115, 10715-10724
32. Andersen, H. C.; Chandler, D.; Weeks, J. D. Roles of Repulsive and Attractive Forces in Liquids: The Equilibrium Theory of Classical Fluids Adv. Chem. Phys. 1976, 34, 105-155
33. 1 Complex Biophys. J. 1999, 77, 1753-1768
34. Newton, M. D. Control of Electron Transfer Kinetics: Models for Medium Reorganization and Donor-Acceptor Coupling Adv. Chem. Phys. 1999, 106, 303
35. Li, T.; Hassanali, A. A.; Singer, S. J. Origin of Slow Relaxation Following Photoexcitation of W7 in Myoglobin and the Dynamics of Its Hydration Layer J. Phys. Chem. B 2008, 112, 16121-16134
36. Halle, B.; Nilsson, L. Does the Dynamic Stokes Shift Report on Slow Protein Dynamics? J. Phys. Chem. B 2009, 113, 8210-8213
37. Ghorai, P. K.; Matyushov, D. V. Solvent Reorganization Entropy of Electron Transfer in Polar Solvents J. Phys. Chem. A 2006, 110, 8857-8863
38. Cheng, Y.-K.; Rossky, P. J. Surface Topography Dependence of Biomolecular Hydrophobic Hydration Nature 1998, 392, 696-699