Downhill kinetics of biomolecular interface binding: Globally connected scenario

Biophysical Journal

Volumn 87, Issue 4, 2004, Pages 2187-2194

  Wang, Jin ^a,b   Huang, Weimin ^a   Lu, Hongyang ^a   Wang, Erkang ^a  

^a CHANGCHUN INSTITUTE OF APPLIED CHEMISTRY   (China)

^b STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING AFFINITY; ENERGY; HIGH TEMPERATURE; KINETICS; LANDSCAPE; LOW TEMPERATURE; MATHEMATICAL COMPUTING; TEMPERATURE MEASUREMENT; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENERGY TRANSFER; EVALUATION; PROTEIN BINDING; STATISTICAL MODEL; STRUCTURE ACTIVITY RELATION; TEMPERATURE;

BIOPOLYMER; PROTEIN;

BINDING SITES; BIOPOLYMERS; COMPUTER SIMULATION; ENERGY TRANSFER; KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; PROTEIN BINDING; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; TEMPERATURE;

EID: 10044249730     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.042747     Document Type: Article

References (55)

1. Abkevich, V. I., A. M. Gutin, and E. I. Shakhnovich. 1994. Free energy landscape for protein folding kinetics: intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 109:6052-6062.
2. Agmon, N., and J. J. Hopfield. 1983. CO binding to heme proteins: a model for barrier height distributions and slow conformational changes. J. Chem. Phys. 79:2042-2053.
3. Cherfils, J., and J. Janin. 1993. Protein docking algorithms: simulating molecular recognition. Curr. Opin. Struct. Biol. 3:265-269.
4. Clackson, T., and J. A. Wells. 1995. A hot-spot of binding energy in a hormone-receptor interface. Science. 267:383-386.
5. Deniz, A. A., T. A. Laurence, G. S. Beligere, M. Dahan, A. B. Martin, D. S. Chemla, P. E. Dawson, P. G. Schultz, and S. Weiss. 2000. Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. USA. 97:5179-5184.
6. Dill, K. A., S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan. 1995. Principles of protein folding - a perspective from simple exact models. Protein Sci. 4:561-602.
7. Ferry, J. D., L. D. Grandine, and E. R. Fitzgerald. 1953. The relaxation distribution function of polyisobutylene in the transition from rubber-like to glass-like behavior. J. Appl. Phys. 24:911-916.
8. Frauenfelder, H., G. A. Petsko, and D. Tsernoglou. 1979. Temperature-dependent x-ray diffraction as a probe of protein structure dynamics. Nature. 280:558-563.
9. Frauenfelder, H., S. G. Sligar, and P. G. Wolynes. 1991. The energy landscapes and motions of proteins. Science. 254:1598-1603.
10. Gallop, M. A., R. W. Barrett, W. J. Dower, S. P. A. Fodor, and E. M. Gordon. 1994. Applications of combinatorial technologies to drug discovery. I. Background and peptide combinatorial libraries. J. Med. Chem. 37:1233-1251.
11. Goldstein, R. A., Z. A. Luthey-Schulten, and P. G. Wolynes. 1992. Optimal protein-folding codes from spin-glass theory. Proc. Natl. Acad. Sci. USA. 89:4918-1922.
12. Gordon, E. M., R. W. Barrett, W. J. Dower, S. P. A. Fodor, and M. A. Gallop. 1994. Applications of combinatorial technologies to drug discovery. II. Combinatorial organic synthesis, library screening strategies, and future directions. J. Med. Chem. 37:1385-1401.
13. Gutin, A. M., V. I. Abkevich, and E. I. Shakhnovich. 1995. Evolution-like selection of fast-folding model proteins. Proc. Natl. Acad. Sci. USA. 92:1282-1286.
14. Jia, Y. W., D. S. Talaga, W. L. Lau, H. S. M. Lu, W. F. DeGrado, and R. M. Hochstrasser. 1999. Folding dynamics of single GCN-4 peptides by fluorescence resonant energy transfer confocal microscopy. Chem. Phys. 247:69-83.
15. Klimov, D. K., and D. Thirumalai. 1998. Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics. J. Chem. Phys. 109:4119-4125.
16. Kaya, H., and H. S. Chan. 2000. Energetic components of cooperative protein folding. Phys. Rev. Lett. 85:4823-4826.
17. Kaya, H., and H. S. Chan. 2002. Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: how applicable is the transition state picture to folding and unfolding? J. Mol. Biol. 315:899-909.
18. Koshland, D. E., Jr. 1958. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA. 44:98-104.
19. Lee, C. L., C. T. Lin, G. Stell, and J. Wang. 2003. Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules. Phys. Rev. E. 67:041905.
20. Leopold, P. E., M. Montal, and J. N. Onuchic. 1992. Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc. Natl. Acad. Sci. USA. 89:8721-8725.
21. Levinthal, C. 1969. Mössbauer Spectroscopy in Biological Systems. P. DeBrunner, J. Tsibris, and E. Munck, editors. University of Illinois Press, Urbana, IL. 22.
22. Levy, Y., P. G. Wolynes, and J. N. Onuchic. 2004. Protein topology determines the binding mechanism. Proc. Natl. Acad. Sci. USA. 101:511-516.
23. Lipman, E. A., B. Schuler, O. Bakajin, and W. A. Eaton. 2003. Single-molecule measurement of protein folding kinetics. Science. 301:1233-1235.
24. Lu, H. P., L. Y. Xun, and X. S. Xie. 1998. Single-molecule enzymatic dynamics. Science. 282:1877-1882.
25. McCammon, J. A. 1998. Theory of biomolecular recognition. Curr. Opin. Struct. Biol. 8:245-249.
26. Mezard, M., E. Parisi, and M. A. Virasoro. 1987. Spin Glass Theory. World Scientific, Singapore.
27. Moemer, W. E. 1996. High-resolution optical spectroscopy of single molecules in solids. Acc. Chem. Res. 29:563-571.
28. Nguyen, H., M. Jäger, A. Moretto, M. Gruebele, and J. W. Kelly. 2003. Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation. Proc. Natl. Acad. Sci. USA. 100:3948-3953.
29. Oshiro, C. M., I. D. Kuntz, and J. S. Dixon. 1995. Flexible ligand docking using a genetic algorithm. J. Comput. Aid. Mol. Des. 9:113-130.
30. Panchenko, A. R., J. Wang, G. U. Nienhaus, and P. G. Wolynes. 1995. Analysis of ligand binding to heme proteins using a fluctuating path description. J. Phys. Chem. 99:9278-9282.
31. Papoian, G. A., and P. G. Wolynes. 2003. The physics and bioinformatics of binding and folding - an energy landscape perspective. Biopolymers. 68:333-349.
32. Plotkin, S. S., J. Wang, and P. G. Wolynes. 1997. Statistical mechanics of a corcelated energy landscape model for protein folding funnels. J. Chem. Phys. 106:2932-2948.
33. Plotkin, S. S., J. Wang, and P. G. Wolynes. 1996. Correlated energy landscape model for finite, random heteropolymers. Phys. Rev. E. 53:6271-6296.
34. Post, F., W. Doster, G. Karvounis, and M. Settles. 1993. Structural relaxation and nonexponential kinetics of CO-binding to horse myoglobin. Multiple flash photolysis experiments. Biophys. J. 64:1833-1842.
35. Rejto, P. A., and G. M. Verkhivker. 1996. Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors. Proc. Natl. Acad. Sci. USA. 93:8945-8950.
36. Saven, J. G., J. Wang, and P. G. Wolynes. 1994. Kinetics of protein folding: the dynamics of globally connected rough energy landscapes with biases. J. Chem. Phys. 101:11037-11043.
37. Schuler, B., E. A. Lipman, and W. A. Eaton. 2002. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature. 419:743-747.
38. Shoemaker, B. A., J. J. Portman, and P. G. Wolynes. 2000. Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. Proc. Natl. Acad. Sci. USA. 97:8868-8873.
39. Steinbach, P. J., A. Ansari, J. Berendzen, D. Braunstein, K. Chu, B. R. Cowen, D. Ehrenstein, H. Frauenfelder, J. B. Johnson, D. C. Lamb, S. Luck, J. R. Mourant, G. U. Nienhaus, P. Ormos, R. Philipp, A. Xie, and R. D. Young. 1991. Ligand binding to heme proteins: connection between dynamics and function. Biochemistry. 30:3988-4001.
40. Tovchigrechko, A., and I. A. Vakser. 2001. How common is the funnel-like enemy landscape in protein-protein interactions? Protein Sci. 10:1572-1583.
41. Tsai, C. J., S. Kumar, B. Ma, and R. Nussinov. 1999. Folding funnels, binding funnels, and protein function. Protein Sci. 8:1181-1190.
42. Tsai, C. J., D. Xu, and R. Nussinov. 1998. Protein folding via binding and vice versa. Folding Des. 3:R71-R80.
43. Wang, J., J. Onuchic, and P. Wolynes. 1996. Statistics of kinetic pathways on biased rough energy landscapes with applications to protein folding. Phys. Rev. Lett. 76:4861-4864.
44. Wang, J., J. G. Saven, and P. G. Wolynes. 1996. Kinetics in a globally connected, correlated random energy model. J. Chem. Phys. 105:11276-11284.
45. Wang, J. 2003. Statistics, pathways and dynamics of single molecule folding. J. Chem. Phys. 118:952-958.
46. Wang, J., and G. M. Verkhivker. 2003. Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding. Phys. Rev. Lett. 90:188101.
47. Wlodawer, A., and J. W. Erickson. 1993. Structure-based inhibitors of HIV-1 protease. Annu. Rev. Biochem. 62:543-585.
48. Wolynes, P. G., J. N. Onuchic, and D. Thirumalai. 1995. Navigating the folding routes. Science. 267:1619-1620.
49. Xie, X. S. 2002. Single molecule approach to dispersed kinetics and dynamic disorder: probing conformational fluctuation and enzymatic dynamics. J. Chem. Phys. 117:11024-11032.
50. Yang, H., and X. S. Xie. 2002a. Probing single molecule dynamics photon by photon. J. Chem. Phys. 117:10965-10979.
51. Yang, H., and X. S. Xie. 2002b. Statistical approaches for probing single molecule dynamics photon by photon. Chem. Phys. 284:423-437.
52. Yang, H., G. Luo, P. Karnchanaphanurach, T. M. Louie, I. Rech, S. Cova, L. Xun, and X. S. Xie. 2003. Protein conformational dynamics probed by single molecule electron transfer. Science. 302:262-266.
53. Zhou, Y., C. Zhang, G. Stell, and J. Wang. 2003. Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second-hairpin fragment of protein G. J. Am. Chem. Soc. 125:6300-6305.
54. Zhuang, X. W., L. E. Bartley, H. P. Babcock, R. Russell, T. Ha, D. Herschlag, and S. Chu. 2000. A single-molecule study of RNA catalysis and folding. Science. 288:2048-2051.
55. Zhuang, X. W., H. Kim, M. J. B. Pereira, H. P. Babcock, N. G. Walter, and S. Chu. 2002. Correlating structural dynamics and function in single ribozyme molecules. Science. 296:1473-1476.