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Energy utilization in fluctuating biological energy converters
2. A. Szoke, D. Van der Spoel, and J. Hajdu, “ Energy utilization, catalysis and evolution—The emergent principles of life,” Curr. Chem. Biol. 1, 53–57 (2007).
5. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter, Molecular Biology of the Cell, 4th ed. ( Garland, 2002).
6. J. M. Berg, J. L. Tymoczko, and L. Stryer, Biochemistry, 5th ed. ( Freeman, 2002).
8. J. Monod, Chance and Necessity ( Collins, 1970).
11. R. Dawkins, The Selfish Gene, 2nd ed. ( Oxford University Press, 1989).
12. R. Dawkins, The Blind Watchmaker ( Norton, New York, 1987).
13. M. Eigen, Steps Towards Life ( Oxford University Press, 1992).
15. L. Hand and J. Finch, Analytical Mechanics ( Cambridge University Press, Cambridge, 2008).
16. F. Jensen, Introduction to Computational Chemistry ( Wiley & Sons, Chichester, 1999).
17. D. Chandler, Introduction to Modern Statistical Mechanics ( Oxford University Press, 1987).
23. D. Collin, F. Ritort, C. Jarzynski, S. B. Smith, I. Tinoco, Jr., and C. Bustamante, “ Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies,” Nature 437, 231–234 (2005).
24. C. Jarzynski, “ Equalities and inequalities: Irreversibility and the second law of thermodynamics at the nanoscale,” Annu. Rev. Condens. Matter Phys. 2, 329–351 (2011).
25.Denoting the energy of the system by , its pressure by , its volume by , its temperature by , and its entropy by , the Gibbs free energy is defined as .
26.It is always true that the free energy difference, , between the initial and final states, and is well defined. The work depends on some “control parameter” that may not have a well defined value in states and . In that case, a fixed may not connect the “exact” states and . This point was discussed by Crooks.21
31. T. M. Schmeing, K. S. Huang, S. A. Strobel, and T. A. Steitz, “ An induced fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-RNA,” Nature 438, 520–524 (2005).
32.The quantitative expression for the free energy difference for an ion of charge is the Nernst equation: where is the potential across the membrane, is the Faraday constant, and and are the concentrations (actually the activities) of the ion on the two sides of the membrane. The constants are such that mV/pH unit.
33. F. Fassioli, A. Olaya-Castro, S. Scheuring, J. N. Sturgis, and N. F. Johnson, “ Energy transfer in light-adapted photosynthetic membranes: From active to saturated photosynthesis,” Biophys. J. 97, 2464–2473 (2009).
34. E. Daviso, S. Prakash, A. Alia, P. Gast, J. Neugebauer, G. Jeschke, and J. Matysik, “ The electronic structure of the primary electron donor of reaction centers of purple bacteria at atomic resolution as observed by photo-CIDNP C-13 NMR,” Proc. Natl. Acad. Sci. U.S.A. 106, 22281–22286 (2009).
35. R. J. Cogdell, A. Gall, and J. Koehler, “ The architecture and function of the light-harvesting apparatus of purple bacteria: From single molecules to in vivo membranes,” Q. Rev. Biophys. 39, 227–324 (2006).
36. R. Neutze, E. Pebay-Peyroula, K. Edman, A. Royant, J. Navarro, and E. Landau, “ Bacteriorhodopsin: A high-resolution structural view of vectorial proton transport,” Biochim. Biophys. Acta-Biomembr. 1565, 144–167 (2002).
37. K. Edman, P. Nollert, A. Royant, H. Belrhali, E. Pebay, J. Hajdi, R. Neutze, and E. M. Landau, “ High resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle,” Nature 401, 821–826 (1999).
38. C. Pfisterer, A. Gruia, and S. Fischer, “ The mechanism of photo-energy storage in the halorhodopsin chloride pump,” J. Biol. Chem. 284, 13562–13569 (2009).
40. D. G. Nicholls and S. J. Ferguson, Bioenergetics, 3rd ed. ( Academic Press, 2002).
41. Y.-S. Che, S. Nakamura, S. Kojima, N. Kami-ike, K. Namba, and T. Minamino, “ Suppressor analysis of the MotB(D33E) mutation to probe bacterial flagellar motor dynamics coupled with proton translocation,” J. Bacteriol. 190, 6660–6667 (2008).
43. K.-I. Okazaki and G. Hummer, “ Elasticity, friction, and pathway of -subunit rotation in FoF1-ATP synthase,” Proc. Natl. Acad. Sci. U.S.A. 112, 10720–10725 (2015).
46. J. Lipfert, M. M. van Oene, M. Lee, F. Pedaci, and N. H. Dekker, “ Torque spectroscopy for the study of rotary motion in biological systems,” Chem. Rev. 115, 1449–1474 (2015).
48.In some cases, part of the free energy is applied against a chemical potential, in a manner very similar to the way chemical reactions use the free energy to synthesize new compounds.
49. M. V. Vinogradova, V. S. Reddy, A. S. N. Reddy, E. P. Sablin, and R. J. Fletterick, “ Crystal structure of kinesin regulated by - calmodulin,” J. Biol. Chem. 279, 23504–23509 (2004).
53. M. Nishiyama, H. Higuchi, and T. Yanagida, “ Chemomechanical coupling of the forward and backward steps of single kinesin molecules,” Nat. Cell Biol. 4, 790–797 (2002).
56. B. E. Clancy, W. M. Behnke-Parks, J. O. L. Andreasson, S. S. Rosenfeld, and S. M. Block, “ A universal pathway for kinesin stepping,” Nat. Struct. Mol. Biol. 18, 1020–1027 (2011).
59. W. Wang, L. Cao, C. Wang, B. Gigant, and M. Knossow, “ Kinesin, 30 years later: Recent insights from structural studies,” Protein Sci. 24, 1047–1056 (2015).
61. R. P. Feynman, R. B. Leighton, and M. Sands, The Feynman Lectures in Physics ( Addison-Wesley, 1963), Vol. I, Sec. 46.
62. A. Yildiz and R. D. Vale, “ Tracking movements of the microtubule motors kinesin and dynein using total internal reflection fluorescence microscopy,” Cold Spring Harbor protocols (2015).
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We have argued previously [Szoke et al., FEBS Lett. 553, 18–20 (2003); Curr. Chem. Biol. 1, 53–57 (2007)] that energy utilization and evolution are emergent properties based on a small number of established laws of physics and chemistry. The relevant laws constitute a framework for biology on a level intermediate between quantum chemistry and cell biology. There are legitimate questions whether these concepts are valid at the mesoscopic level. Such systemsfluctuate appreciably, so it is not clear what their efficiency is. Advances in fluctuation theorems allow the description of such systems on a molecular level. We attempt to clarify this topic and bridge the biochemical and physical descriptions of mesoscopic systems.
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