Extraction of interaction potentials between amino acids from native protein structures

Journal of Chemical Physics

Volumn 112, Issue 20, 2000, Pages 9151-9166

  Dima, Ruxandra I ^a,d   Settanni, Giovanni ^b,c   Micheletti, Cristian ^b,c   Banavar, Jayanth R ^a   Maritan, Amos ^b,c  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b SISSA   (Italy)

^c ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS   (Italy)

^d UNIVERSITY OF MARYLAND   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000433089     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.481525     Document Type: Article

References (73)

1. F. Seno, C. Micheletti, A. Maritan, and J. Banavar, Phys. Rev. Lett. 81, 2172 (1998).
2. T. Creighton, Proteins, Structure, and Molecular Properties, 2nd ed. (Freeman, New York, 1993).
3. C. Branden and J. Tooze, Introduction to Protein Structure (Garland, New York, 1991).
4. C. Anfinsen, Science 181, 223 (1973).
5. A. Bauer and A. Beyer, Proteins: Struct., Funct., Genet. 18, 254 (1994).
6. J. Bowie, R. Lüthy, and D. Eisenberg, Science 253, 164 (1991).
7. S. Bryant and C. Lawrence, Proteins: Struct., Funct., Genet. 16, 92 (1993).
8. G. Casari and M. Sippl, J. Mol. Biol. 224, 725 (1992).
9. A. Godzik, A. Kolinski, and J. Skolnick, J. Mol. Biol. 227, 227 (1992).
10. R. A. Goldstein, Z. A. Luthey-Shulten, and P. G. Wolynes, Proc. Natl. Acad. Sci. USA 89, 9029 (1992).
11. N. D. Socci and J. N. Onuchic, J. Chem. Phys. 101, 1519 (1994).
12. E. Huang, S. Subbiah, and M. Levitt, J. Mol. Biol. 257, 716 (1995).
13. T. Jones, W. Taylor, and J. Thornton, Nature (London) 358, 86 (1992).
14. C. Ouzounis, C. Sander, M. Sharf, and R. Schneider, J. Mol. Biol. 232, 805 (1993).
15. J. Bowie and D. Eisenberg, Proc. Natl. Acad. Sci. USA 91, 4436 (1994).
16. T. Dandekar and P. Argos, J. Mol. Biol. 236, 844 (1994).
17. A. Kolinski and J. Skolnick, Proteins: Struct. Funct. Genet. 18, 338 (1994).
18. M. Levitt, J. Mol. Biol. 104, 59 (1976).
19. M. Levitt, J. Mol. Biol. 170, 723 (1983).
20. J. Skolnick, A. Kolinski, C. Brooks, A. Godzik, and A. Rey, Curr. Biol. 3, 414 (1993).
21. S. Sun, Protein Sci. 2, 762 (1993).
22. A. Wallqvist and M. Ullner, Proteins: Struct., Funct., Genet. 18, 267 (1994).
23. J. Deutsch and T. Kurosky, Phys. Rev. Lett. 76, 323 (1996).
24. R. Srinivasan and G. D. Rose, Proteins: Struct., Funct., Genet. 22, 81 (1995).
25. C. Micheletti, F. Seno, A. Maritan, and J. Banavar, Proteins: Struct., Funct., Genet. 32, 80 (1998).
26. P. Wolynes, J. Onuchic, and D. Thirumalai, Science 267, 1619 (1995).
27. J. Bryngelson, J. Onuchic, D. Socci, and P. Wolynes, Proteins: Struct., Funct., Genet. 21, 167 (1995).
28. D. Klimov and D. Thirumalai, Phys. Rev. Lett. 76, 4070 (1996).
29. W. F. van Gunsteren, Computer Simulation of Biomolecular Systems (ESCOM Science, B. V. Leiden, 1989).
30. Y. Duan and P. Kollman, Science 282, 740 (1998).
31. N. Go and H. Scheraga, Macromolecules 9, 535 (1976).
32. T. Lazaridis and M. Karplus, Science 278, 1928 (1997).
33. C. Micheletti, J. Banavar, A. Maritan, and F. Seno, Phys. Rev. Lett. 82, 3372 (1999).
34. O. V. Galzitskaya and A. V. Finkelstein, Proc. Natl. Acad. Sci. USA 96, 11299 (1999).
35. S. Tanaka and H. Scheraga, Macromolecules 9, 945 (1976).
36. S. Miyazawa and R. L. Jernigan, Macromolecules 18, 534 (1985).
37. S. Miyazawa and R. L. Jernigan, J. Mol. Biol. 256, 623 (1996).
38. S. Miyazawa and R. Jernigan, Proteins: Struct., Funct., Genet. 34, 49 (1999).
39. M. Sippl, J. Mol. Biol. 213, 859 (1990).
40. D. Hinds and M. Levitt, Proc. Natl. Acad. Sci. USA 89, 2536 (1992).
41. A. Godzik and J. Skolnick, Proc. Natl. Acad. Sci. USA 89, 12098 (1992).
42. A. Kolinski, A. Godzik, and J. Skolnick, J. Chem. Phys. 98, 7420 (1993).
43. P. Thomas and K. Dill, J. Mol. Biol. 257, 457 (1996).
44. P. Thomas and K. Dill, Proc. Natl. Acad. Sci. USA 93, 11628 (1996).
45. F. Seno, A. Maritan, and J. Banavar, Proteins: Struct., Funct., Genet. 30, 224 (1998).
46. F. Bernstein, T. Koetzle, G. Williams, E. J. Meyer, M. Brice, J. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi, J. Mol. Biol. 112, 535 (1977).
47. M. Friedrichs and P. Wolynes, Science 246, 371 (1989).
48. L. Mirny and E. Shakhnovich, J. Mol. Biol. 264, 1164 (1996).
49. M. Vandruscolo, R. Najmanovich, and E. Domany, Phys. Rev. Lett. 82, 656 (1999).
50. R. A. Goldstein, Z. A. Luthey-Shulten, and P. G. Wolynes, Proc. Natl. Acad. Sci. USA 89, 4918 (1992).
51. V. N. Maiorov and G. M. Crippen, J. Mol. Biol. 227, 876 (1992).
52. G. M. Crippen, Biochemistry 30, 4232 (1991).
53. J. van Mourik, C. Clementi, A. Maritan, F. Seno, and J. Banavar, J. Chem. Phys. 110, 10123 (1999).
54. C. Clementi, A. Maritan, and J. Banavar, Phys. Rev. Lett. 81, 3287 (1998).
55. B. Park and M. Levitt, J. Mol. Biol. 258, 367 (1996).
56. R. Samudrala, Y. Xia, M. Levitt, and E. Huang, in Proceedings of the Pacific Symposium on Biocomputing, 1999, pp. 505-516 (unpublished).
57. G. Ramachandran and V. Sasisekharan, Adv. Protein Chem. 28, 283 (1968).
58. S. Sun, R. Brem, H. S. Chan, and K. Dill, Protein Eng. 8, 1205 (1995).
59. W. Kabsch and C. Sander, Biopolymers 22, 2577 (1995).
60. H. Frauenfelder, Physics in a Technological World (American Institute of Physics, New York, 1988).
61. C. Micheletti, J. Banavar, F. Seno, and A. Maritan, Phys. Rev. Lett. 80, 5683 (1998).
62. F. Seno, M. Vendruscolo, A. Maritan, and J. Banavar, Phys. Rev. Lett. 77, 1901 (1996).
63. C. Orengo, T. Flores, W. Taylor, and J. Thornton, Protein Eng. 6, 485 (1993).
64. J. Desjarlais and T. Handel, Protein Sci. 4, 2006 (1995).
65. G. Lazar, J. Desjarlais, and T. Handel, Protein Sci. 6, 1167 (1995).
66. A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia, J. Mol. Biol. 247, 536 (1995).
67. W. Krauth and M. Mezard, J. Phys. A 20, L745 (1987).
68. Giugliarelli, C. Micheletti, J. Banavar, and A. Maritan (in preparation).
69. K. Lau and K. Dill, Macromolecules 22, 3986 (1989).
70. H. S. Chan and K. Dill, Proteins: Struct., Funct., Genet. 24, 335 (1996).
71. From a geometrical point of view, indeed, the transformation that let us pass from the free energy parameters with solvation to the form without them is a homeomorphism that does not preserve the scalar product, whichis used to compute the free energy.
72. In other potential extraction schemes, the potentials are shifted to make their average zero. A priori this may not be allowed, since the energy shift will typically affect the average protein solubility (Ref. 68).
73. We note that only the direction of the vector of parameters is important, because it sets the rank of the conformations that a sequence can assume, while the norm of that vector just sets an energy scale.