The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics

Journal of Chemical Physics

Volumn 106, Issue 4, 1997, Pages 1495-1517

  Becker, Oren M ^a,b   Karplus, Martin ^b,c  

^a TEL AVIV UNIVERSITY   (Israel)

^b HARVARD UNIVERSITY   (United States)

^c UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000370391     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.473299     Document Type: Article

References (47)

1. E. R. Davidson, Chem. Rev. (1993), 2337-2581.
2. M. Karplus and E. Shakhnovich, in Protein Folding 127, edited by T. Creighton (Freeman, New York, 1992).
3. P. W. Anderson, B. I. Halperin, and C. M. Varma, Philos. Mag. 25, 1 (1972).
4. C. Laermans and A. Vanelstraete, Phys. Rev. B 34, 1405 (1986).
5. J. L. Green, J. Fan, and C. A. Angell, J. Phys. Chem. 98, 13780 (1994).
6. R. D. Levine and R. B. Bernstein, Molecular Reaction Dynamics and Chemical Reactivity (Oxford University Press, New York, 1987).
7. B. M. Pettitt and M. Karplus, Chem. Phys. Lett. 121, 194 (1985).
8. A. G. Anderson and J. Hermans, Proteins 3, 262 (1988).
9. F. H. Stillinger and T. A. Weber, Science 225, 983 (1984); Phys. Rev. A 25, 978 (1982).
10. F. H. Stillinger and T. A. Weber, Science 225, 983 (1984); Phys. Rev. A 25, 978 (1982).
11. F. H. Stillinger and T. A. Weber, J. Phys. Chem. 87, 2833 (1983).
12. H. Tanaka and I. Ohmine, J. Chem. Phys. 91, 6318 (1989).
13. R. S. Berry, Chem. Rev. 93, 2379 (1993).
14. R. E. Kunz and R. S. Berry, J. Chem. Phys. 103, 1904 (1995).
15. R. Elber and M. Karplus, Science 235, 318 (1987).
16. T. Noguti and N. Gô, Proteins: Structure, Function, and Genetics 5, 97, 104, 113, 125, 132 (1989).
17. N. G. van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 1981).
18. R. Czerminski and R. Elber, Proc. Natl. Acad. Sci. USA 86, 6963 (1989).
19. R. Czerminski and R. Flber, J. Chem. Phys. 92, 5580 (1990).
20. Y. S. Bay and M. D. Fayer, Phys. Rev. B 39, 11066 (1989).
21. A. Ansari et al. Proc. Natl. Acad. Sci. USA 82, 5000 (1985).
22. I. E. T. Iben et al. Phys. Rev. Lett. 62, 1916 (1989).
23. H. Frauenfelder, S. G. Sliger, and P. G. Wolynes, Science 254, 1598 (1991).
24. S. J. Hagen, J. Hofrichter, and W. A. Eaton, Science 269, 959 (1995).
25. B. R. Gelin and M. Karplus, Proc. Natl. Acad. Sci. USA 72, 2002 (1975).
26. M. Klein, Annu. Rev. Phys. Chem. 4, 23 (1991).
27. P. E. Leopold, M. Montal, and J. N. Onuchic, Proc. Natl. Acad. Sci. USA 89, 8721 (1992).
28. P. Wolynes et al. Science 267, 1618 (1995).
29. 3N, since otherwise every local minima α will formally be in an infinite equivalence class, stemming from the fact that the energy function is invariant under rigid translation and rotation.
30. S. Kirkpatric, C. D. Gelatt, Jr, and M. P. Vecchi, Science 220, 671 (1992).
31. R. M. J. Cotterill and J. U. Madsen, in Characterizing Complex Systems, edited by H. Bohr (World Scientific, Singapore, 1990), pp. 177-191.
32. R. E. Memfield and H. E. Simmons, Topological Methods in Chemistry (Wiley, New York, 1989).
33. J. R. Munkres, Topology (Prentice-Hall, Englewood Cliffs, NJ. 1975).
34. F. Harary, Graph Theory (Addison-Wesley, Reading, MA, 1969).
35. D. E. Rutherford. Introduction to Lattice Theory (Hafner, New York, 1965).
36. B. B. Mandelbrot, The Fractal Geometry of Nature (Freeman, San Francisco, 1983).
37. M. Karplus and A. Sali, Current Opinion in Structural Biology 5, 58 (1995).
38. T. L. Hill, Introduction to Statistical Thermodynamics (Addison-Wesley, Reading, MA, 1960).
39. C. L. Brooks III, M. Karplus, and B. M. Pettitt, Proteins: A Theoretical Perspective of Dynamics, Structure & Thermodynamics, Adv. Chem. Phys. LXXI (Wiley, New York, 1988).
40. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Chem. 4, 187 (1983).
41. Reference 17 reported 513 barriers. We received 502 barriers which provide an adequate picture of the surface.
42. P. H. Maccalum, R. Poel, and E. T. Milner-White. J. Mol. Biol. 248, 374 (1995); T. Lazaridis (private communication).
43. P. H. Maccalum, R. Poel, and E. T. Milner-White. J. Mol. Biol. 248, 374 (1995); T. Lazaridis (private communication).
44. W. H. Press, B. P. Flannery, S. A. Tenkolsky, and W. T. Vellerling, Numerical Recipies (Cambridge University Press, Cambridge, 1989), Chap. 11.
45. J. D. Honeycutt and D. Thirumalai, Proc. Natl. Acad. Sci. USA 87, 3526 (1990); Biopolymers 32, 695 (1992).
46. J. D. Honeycutt and D. Thirumalai, Proc. Natl. Acad. Sci. USA 87, 3526 (1990); Biopolymers 32, 695 (1992).
47. O. M. Becker, Proteins: Structure, Function, and Genetics 27 (1997).