Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 26, 2006, Pages 9885-9890

  Das, Payel ^a   Moll, Mark ^b,d   Stamati, Hernán ^b   Kavraki, Lydia E ^b,c   Clementi, Cecilia ^a,c  

^a RICE UNIVERSITY   (United States)

^b Rice University   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

^d UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Embedding; ISOMAP; Manifold; Reaction coordinate; Transition state

Indexed keywords

PROTEIN; PROTEIN SH3;

ARTICLE; DIAGNOSTIC VALUE; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR MODEL; NONHUMAN; NONLINEAR SYSTEM; PRIORITY JOURNAL; PROCESS MODEL; PROTEIN FOLDING; REACTION ANALYSIS; VALIDATION PROCESS;

ALGORITHMS; ENTROPY; MODELS, MOLECULAR; PROTEIN FOLDING; SRC HOMOLOGY DOMAINS;

EID: 33745611125     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0603553103     Document Type: Article

References (49)

1. Das, P., Matysiak, S. & Clementi, C. (2005) Proc. Natl. Acad. Sci. USA 102, 10141-10146.
2. Du, R., Pande, V., Grosberg, A., Tanaka, T. & Shakhnovich, E. (1998) J. Chem. Phys. 108, 334-350.
3. Hummer, G. (2004) J. Chem. Phys. 120, 516-523.
4. Best, R. & Hummer, G. (2005) Proc. Natl. Acad. Sci. USA 102, 6732-6737.
5. Cho, S., Levy, Y. & Wolynes, P. (2006) Proc. Natl. Acad. Sci. USA 103, 586-591.
6. Baumketner, A., Shea, J.-E. & Hiwatari, Y. (2004) J. Chem. Phys. 121, 1114-1120.
7. Ma, A. & Dinner, A. (2005) J. Phys. B 109, 6769-6779.
8. Rhee, Y. & Pande, V. (2005) J. Phys. B 109, 6780-6786.
9. Klimov, D. & Thirumalai, D. (2004) Chem. Phys. 307, 251-258.
10. Clementi, C., Jennings, P. & Onuchic, J. (2001) J. Mol. Biol. 311, 879-890.
11. Clementi, C. & Plotkin, S. (2004) Protein Sci. 13, 1750-1766.
12. Abkevich, V., Gutin, A. & Shakhnovich, E. (1998) Fold. Des. 3, 183-194.
13. Chavez, L., Onuchic, J. & Clementi, C. (2004) J. Am. Chem. Soc. 126, 8426-8432.
14. Dokholyan, N., Li, L., Ding, F. & Shakhnovich, E. (2002) Proc. Natl. Acad. Sci. USA 99, 8637-8641.
15. Das, P., Wilson, C., Fossati, G., Wittung-Stafshede, P., Matthews, K. & Clementi, C. (2005) Proc. Natl. Acad. Sci. USA 102, 14569-14574.
16. Bryngelson, J. & Wolynes, P. (1989) J. Phys. Chem. 93, 6902-6915.
17. Nymeyer, H., García, A. & Onuchic, J. (1998) Proc. Natl. Acad. Sci. USA 95, 7 5921-5928.
18. Onuchic, J., Luthey-Schulten, Z. & Wolynes, P. (1997) Annu. Rev. Phys. Chem. 48, 545-600.
19. Shea, J.-E. & Brooks, C., III (2001) Annu. Rev. Phys. Chem. 52, 499-535.
20. Ferst, A. & Sato, S. (2004) Proc. Natl. Acad. Sci. USA 101, 7976-7981.
21. Fersht, A., Leatherbarrow, R. & Wells, T. (1986) Nature 322, 284-286.
22. Klimov, D. K. & Thirumalai, D. (2001) Proteins: Struct. Funct. Genet. 43, 465-475.
23. Ding, F., Guo, W., Dokholyan, N. V., Shakhnovich, E. I. & Shea, J.-E. (2005) J. Mol. Biol. 350, 1035-1050.
24. Kirby, M. & Sirovich, L. (1990) IEEE Trans. Pattern Anal. Mach. Intell. 12, 103-108.
25. Turk, M. & Pentland, A. (1991) J. Cognit. Neurosci. 3, 71-86.
26. Benito, M. & Pena, D. (2004) Lect. Notes Comput. Sci. 3177, 326-332.
27. Cho, E., Kim, D. & Lee, S. (2003) Lect. Notes Comput. Sci. 2688, 946-954.
28. Jolliffe, I. (1986) Principal Components Analysis (Springer, New York).
29. Levitt, M. (1991) J. Mol. Biol. 220, 1-4.
30. Garcia, A. (1992) Phys. Rev. Lett. 68, 2696-2699.
31. Hayward, S. & Go, N. (1995) Ann. Rev. Phys. Chem. 46, 223-250.
32. Hayward, S., Kitao, A. & Go, N. (1994) Protein Sci. 3, 936-943.
33. Hayward, S., Kitao, A. & Berendsen, H. (1997) Proteins: Struct. Fund. Genet. 27, 425-437.
34. Nolde, S., Arseniev, A., Orekhov, V. & Billeter, M. (2002) Proteins: Struct. Funct. Genet. 46, 250-258.
35. Levy, Y. & Caflisch, A. (2003) J. Phys. B 107, 3068-3079.
36. Teodora, M., Phillips, Jr., G. & Kavraki, L. E. (2003) J. Comp. Biol. 10, 617-634.
37. Weinberger, K. Q. & Saul, L. K. (2004) Proceedings of the IEEE Conference in Computer Vision and Pattern Recognition (IEEE, Washington, DC), pp. 988-995.
38. Belkin, M. & Niyogi, P. (2003) Neural Comp. 15, 1373-1396.
39. Rhee, Y. & Pande, V. (2006) Chem. Phys. 323, 66-77.
40. Monahan, A. H. (2000) J. Climate 13, 821-835.
41. Gamez, A. Z., Zhou, C. S., Timmermann, A. & Kurths, J. (2004) Nonlinear Processes Geophys. 11, 393-398.
42. Tenenbaum, J., de Silva, V. & Langford, J. (2000) Science 290, 2319-2323.
43. de Silva, V. & Tenenbaum, J. (2002) in Advances in Neural Information Processing Systems 15, eds. Becker, S., Thrun, S. & Obermayer, K. (MIT Press, Cambridge, MA), pp. 705-712.
44. de Silva, V. & Tenenbaum, J. (2004) Sparse Multidimensional Scaling Using Landmark Points (Stanford Univ., Stanford, CA).
45. Ferrenberg, A. & Swendsen, R. (1989) Phys. Rev. Lett. 63, 1185-1198.
46. Ferrenberg, A. & Swendsen, R. (1988) Phys. Rev. Lett. 61, 2635-2638.
47. Arnoldi, W. (1951) Q. Applied Mathematics 9, 17-29.
48. Saad, Y. (2003) Iterative Methods for Sparse Linear Systems. (Soc. Ind. Appl. Math., Philadelphia), 2nd Ed.
49. Clementi, C., Nymeyer, H. & Onuchic, J. (2000) J. Mol. Biol. 298, 937-953.