Internal friction in enzyme reactions

IUBMB Life

Volumn 65, Issue 1, 2013, Pages 35-42

  Rauscher, Anna ^a   Derényi, Imre ^a   Gráf, Lászlõ ^a   Málnási Csizmadia, András ^a  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

Arrhenius plot; energy landscape; enzyme mechanisms; internal friction; Kramers theory; roughness; viscosity dependence

Indexed keywords

ENERGY; ENZYME MECHANISM; ENZYME STRUCTURE; EXPERIMENTAL STUDY; FRICTION; INTERNAL FRICTION; REVIEW; THEORETICAL STUDY; VISCOSITY;

ENZYMES; FRICTION; VISCOSITY;

EID: 84871654210     PISSN: 15216543     EISSN: 15216551     Source Type: Journal    
DOI: 10.1002/iub.1101     Document Type: Review

References (61)

1. Frauenfelder, H., Chen, G., Berendzen, J., Fenimore, P. W., Jansson, H., et al. (2009) A unified model of protein dynamics. Proc. Natl. Acad. Sci. U S A 106, 5129-5134.
2. Henzler-Wildman, K., and, Kern, D., (2007) Dynamic personalities of proteins. Nature 450, 964-972.
3. Hagen, S. J., (2010) Solvent viscosity and friction in protein folding dynamics. Curr. Protein Pept. Sci. 11, 385-395.
4. Kramers, H. A., (1940) Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7, 284-304.
5. Hänggi, P., Talkner, P., and, Borkovec, M., (1990) Reaction-rate theory: fifty years after Kramers. Rev. Mod. Phys. 62, 251-342.
6. Beece, D., Eisenstein, L., Frauenfelder, H., Good, D., Marden, M. C., et al. (1980) Solvent viscosity and protein dynamics. Biochemistry 19, 5147-5157.
7. Ansari, A., Jones, C. M., Henry, E. R., Hofrichter, J., and, Eaton, W. A., (1992) The role of solvent viscosity in the dynamics of protein conformational changes. Science 256, 1796-1798.
8. Frauenfelder, H., Chan, S. S. e., Chan, W. S. e., (Contributor), R. H. A., (Contributor), C. E. S., et al. (2010) The Physics of Proteins. Springer, New York.
9. Ivkovic-Jensen, M. M., and, Kostic, N. M., (1997) Effects of viscosity and temperature on the kinetics of the electron-transfer reaction between the triplet state of zinc cytochrome c and cupriplastocyanin. Biochemistry 36, 8135-8144.
10. Ansari, A., Jones, C. M., Henry, E. R., Hofrichter, J., and, Eaton, W. A., (1994) Conformational relaxation and ligand binding in myoglobin. Biochemistry 33, 5128-5145.
11. Goldbeck, R. A., Paquette, S. J., and, Kliger, D. S., (2001) The effect of water on the rate of conformational change in protein allostery. Biophys. J. 81, 2919-2934.
12. Tian, W. D., Sage, J. T., Champion, P. M., Chien, E., and, Sligar, S. G., (1996) Probing heme protein conformational equilibration rates with kinetic selection. Biochemistry 35, 3487-3502.
13. Shibata, Y., Kurita, A., and, Kushida, T., (1999) Solvent effects on conformational dynamics of Zn-substituted myoglobin observed by time-resolved hole-burning spectroscopy. Biochemistry 38, 1789-1801.
14. Rauscher, A. A., Simon, Z., Szollosi, G. J., Graf, L., Derenyi, I., et al. (2011) Temperature dependence of internal friction in enzyme reactions. FASEB J. 25, 2804-2813.
15. Toth, J., Simon, Z., Medveczky, P., Gombos, L., Jelinek, B., et al. (2007) Site directed mutagenesis at position 193 of human trypsin 4 alters the rate of conformational change during activation: role of local internal viscosity in protein dynamics. Proteins 67, 1119-1127.
16. Liu, L., Hong, J., and, Ogawa, M. Y., (2004) Gated electron transfer as a probe of the configurational dynamics of peptide-protein complexes. J. Am. Chem. Soc. 126, 50-51.
17. Qin, L., and, Kostic, N. M., (1994) Photoinduced electron transfer from the triplet state of zinc cytochrome c to ferricytochrome b5 is gated by configurational fluctuations of the diprotein complex. Biochemistry 33, 12592-12599.
18. Grove, T. Z., Ullmann, G. M., and, Kostic, N. M., (2012) Simultaneous true, gated, and coupled electron-transfer reactions and energetics of protein rearrangement. J. Inorg. Biochem. 106, 143-150.
19. Khajehpour, M., Troxler, T., and, Vanderkooi, J. M., (2003) Effect of protein dynamics upon reactions that occur in the heme pocket of horseradish peroxidase. Biochemistry 42, 2672-2679.
20. Heyes, D. J., Sakuma, M., and, Scrutton, N. S., (2009) Solvent-slaved protein motions accompany proton but not hydride tunneling in light-activated protochlorophyllide oxidoreductase. Angew. Chem. Int. Ed. Engl. 48, 3850-3853.
21. Kawai, Y., Matsuo, T., and, Ohno, A., (2000) Kinetic study on conformational effect in hydrolysis of p-nitroanilides catalyzed by [small alpha]-chymotrypsin. J. Chem. Soc. Perkin Trans. 2, 887-891.
22. Khoshtariya, D. E., Hammerstad-Pedersen, J. M., and, Ulstrup, J., (1991) Substrate specificity of solvent viscosity effects in carboxypeptidase A catalyzed peptide hydrolysis. Biochim. Biophys. Acta 1076, 359-363.
23. Steinbach, P. J., Ansari, A., Berendzen, J., Braunstein, D., Chu, K., et al. (1991) Ligand binding to heme proteins: connection between dynamics and function. Biochemistry 30, 3988-4001.
24. Zhou, J. S., and, Kostic, N. M., (1993) Gating of photoinduced electron transfer from zinc cytochrome c and tin cytochrome c to plastocyanin. Effects of solution viscosity on rearrangement of the metalloprotein complex. J. Am. Chem. Soc. 115, 10796-10804.
25. Blacklow, S. C., Raines, R. T., Lim, W. A., Zamore, P. D., and, Knowles, J. R., (1988) Triosephosphate isomerase catalysis is diffusion controlled. Appendix: analysis of triose phosphate equilibria in aqueous solution by 31P NMR. Biochemistry 27, 1158-1167.
26. Kao, Y. T., Zhu, X., and, Min, W., (2012) Protein-flexibility mediated coupling between photoswitching kinetics and surrounding viscosity of a photochromic fluorescent protein. Proc. Natl. Acad. Sci. U S A 109, 3220-3225.
27. Yedgar, S., Tetreau, C., Gavish, B., and, Lavalette, D., (1995) Viscosity dependence of O2 escape from respiratory proteins as a function of cosolvent molecular weight. Biophys. J. 68, 665-670.
28. Uribe, S., and, Sampedro, J. G., (2003) Measuring solution viscosity and its effect on enzyme activity. Biol. Proced. Online 5, 108-115.
29. Finkelstein, I. J., Massari, A. M., and, Fayer, M. D., (2007) Viscosity-dependent protein dynamics. Biophys. J. 92, 3652-3662.
30. Almagor, A., Yedgar, S., and, Gavish, B., (1992) Viscous cosolvent effect on the ultrasonic absorption of bovine serum albumin. Biophys. J. 61, 480-486.
31. Lavalette, D., Tetreau, C., Tourbez, M., and, Blouquit, Y., (1999) Microscopic viscosity and rotational diffusion of proteins in a macromolecular environment. Biophys. J. 76, 2744-2751.
32. Somogyi, B., Norman, J. A., Zempel, L., and, Rosenberg, A., (1988) Viscosity and transient solvent accessibility of Trp-63 in the native conformation of lysozyme. Biophys. Chem. 32, 1-13.
33. Ohta, Y., Mukouyama, E. B., and, Suzuki, H., (2006) Kinetic isotope effect of the L-phenylalanine oxidase from Pseudomonas sp. P-501. J. Biochem. 139, 551-555.
34. Kleinert, T., Doster, W., Leyser, H., Petry, W., Schwarz, V., et al. (1998) Solvent composition and viscosity effects on the kinetics of CO binding to horse myoglobin. Biochemistry 37, 717-733.
35. Vitkup, D., Ringe, D., Petsko, G. A., and, Karplus, M., (2000) Solvent mobility and the protein 'glass' transition. Nat. Struct. Biol. 7, 34-38.
36. Ivkovic-Jensen, M. M., and, Kostic, N. M., (1996) Effects of temperature on the kinetics of the gated electron-transfer reaction between zinc cytochrome c and plastocyanin. Analysis of configurational fluctuation of the diprotein complex. Biochemistry 35, 15095-15106.
37. Schlarb-Ridley, B. G., Mi, H., Teale, W. D., Meyer, V. S., Howe, C. J., et al. (2005) Implications of the effects of viscosity, macromolecular crowding, and temperature for the transient interaction between cytochrome f and plastocyanin from the cyanobacterium Phormidium laminosum. Biochemistry 44, 6232-6238.
38. Gonnelli, M., and, Strambini, G. B., (1993) Glycerol effects on protein flexibility: a tryptophan phosphorescence study. Biophys. J. 65, 131-137.
39. Pabit, S. A., Roder, H., and, Hagen, S. J., (2004) Internal friction controls the speed of protein folding from a compact configuration. Biochemistry 43, 12532-12538.
40. Hasinoff, B. B., (1981) Diffusion-controlled reaction kinetics of the binding of carbon monoxide to the heme undecapeptide of cytochrome c (microperoxidase 11) in high viscosity solvents. Arch. Biochem. Biophys. 211, 396-402.
41. Walser, R., and, van Gunsteren, W. F., (2001) Viscosity dependence of protein dynamics. Proteins 42, 414-421.
42. Qiu, L., and, Hagen, S. J., (2004) A limiting speed for protein folding at low solvent viscosity. J. Am. Chem. Soc. 126, 3398-3399.
43. Zagrovic, B., and, Pande, V., (2003) Solvent viscosity dependence of the folding rate of a small protein: distributed computing study. J. Comput. Chem. 24, 1432-1436.
44. Feig, M., (2007) Kinetics from implicit solvent simulations of biomolecules as a function of viscosity. J. Chem. Theory Comput. 3, 1734-1748.
45. Gottfried, D. S., Peterson, E. S., Sheikh, A. G., Wang, J., Yang, M., et al. (1996) Evidence for damped hemoglobin dynamics in a room temperature trehalose glass. J. Phys. Chem. 100, 12034-12042.
46. Hagen, S. J., Hofrichter, J., and, Eaton, W. A., (1996) Geminate rebinding and conformational dynamics of myoglobin embedded in a glass at room temperature. J. Phys. Chem. 100, 12008-12021.
47. Hagen, S. J., Hofrichter, J., and, Eaton, W. A., (1995) Protein reaction kinetics in a room-temperature glass. Science 269, 959-962.
48. Steinhoff, H. J., (1990) Residual motion of hemoglobin-bound spin labels and protein dynamics: viscosity dependence of the rotational correlation times. Eur. Biophys. J. 18, 57-62.
49. Gavish, B., (1979) Viscosity-dependent structural fluctuations in enzyme catalysis. Biochemistry 18, 1269-1275.
50. Viswanath, D. S., Ghosh, T. K., Prasad, D. H. L., Dutt, N. V. K., and, Rani, K. Y., (2007) Viscosity of liquids. Springer, Dordrecht.
51. Wensley, B. G., Batey, S., Bone, F. A., Chan, Z. M., Tumelty, N. R., et al. (2010) Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family. Nature 463, 685-688.
52. Zwanzig, R., (1988) Diffusion in a rough potential. Proc. Natl. Acad. Sci. U S A 85, 2029-2030.
53. Grote, R. F., and, Hynes, J. T., (1980) The stable state picture of chemical reactions. II. J. Chem. Phys. 73, 2715-2732.
54. Agmon, N., and, Hopfield, J. J., (1982) Transient kinetics of chemical reactions with bounded diffusion perpendicular to the reaction coordinate: intramolecular processes with slow conformational changes. J. Chem. Phys. 78, 6947-6959.
55. Zwanzig, R., (1992) Dynamical disorder: passage through a fluctuating bottleneck. J. Chem. Phys. 97, 3587-3589.
56. Frauenfelder, H., Fenimore, P. W., Chen, G., and, McMahon, B. H., (2006) Protein folding is slaved to solvent motions. Proc. Natl. Acad. Sci. U S A 103, 15469-15472.
57. Frauenfelder, H., Fenimore, P. W., and, Young, R. D., (2007) Protein dynamics and function: insights from the energy landscape and solvent slaving. IUBMB Life 59, 506-512.
58. Doster, W., (2010) The protein-solvent glass transition. Biochim. Biophys. Acta 1804, 3-14.
59. Lopez, M., Kurkal-Siebert, V., Dunn, R. V., Tehei, M., Finney, J. L., et al. Activity and dynamics of an enzyme, pig liver esterase, in near-anhydrous conditions. Biophys. J. 99, L62-64.
60. Koeniger, S. L., Merenbloom, S. I., Sevugarajan, S., and, Clemmer, D. E., (2006) Transfer of structural elements from compact to extended states in unsolvated ubiquitin. J. Am. Chem. Soc. 128, 11713-11719.
61. Wang, Y. S., Sabu, S., Wei, S. C., Josh Kao, C. M., Kong, X., et al. (2006) Dissociation of heme from gaseous myoglobin ions studied by infrared multiphoton dissociation spectroscopy and Fourier-transform ion cyclotron resonance mass spectrometry. J. Chem. Phys. 125, 133310.