Understanding Protein Flexibility through Dimensionality Reduction

Journal of Computational Biology

Volumn 10, Issue 3-4, 2003, Pages 617-634

  Teodoro, Miguel L ^a   Phillips Jr , George N ^b   Kavraki, Lydia E ^c  

^a RICE UNIVERSITY   (United States)

^b University of Wisconsin Madison   (United States)

^c Rice University   (United States)

Author keywords

Dimensionality reduction; Principal component analysis; Protein flexibility; Protein motion

Indexed keywords

ALDEHYDE REDUCTASE; LIGAND; NUCLEIC ACID; PROTEIN; PROTEINASE;

ACCURACY; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR DYNAMICS; MOTION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN STRUCTURE; SIMULATION; X RAY CRYSTALLOGRAPHY;

ALDEHYDE REDUCTASE; BINDING SITES; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATA INTERPRETATION, STATISTICAL; HIV PROTEASE; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0042894239     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/10665270360688228     Document Type: Conference Paper

References (57)

1. Amadei, A., Linssen, A.B., and Berendsen, H.J. 1993. Essential dynamics of proteins. Proteins 17, 412-425.
2. Amadei, A., Linssen, A.B., de Groot, B.L., van Aalten, D.M., and Berendsen, H.J. 1996. An efficient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dyn. 13, 615-625.
3. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A., and Haak, J.R. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690.
4. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucl. Acids Res. 28, 235-242.
5. Bishop, C.M., Svensen, M., and Williams, C.K. 1998. GTM: The Generative Topographic Mapping. Neural Computation 10, 215-234.
6. Brooks, C.L., Montgomery, B., and Karplus, M. 1988. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, John Wiley, New York.
7. Byrne, B., and Iwata, S. 2002. Membrane protein complexes. Curr. Opin. Struct. Biol. 12, 239-243.
8. Caves, L.S., Evanseck, J.D., and Karplus, M. 1998. Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin. Protein Sci. 7, 649-666.
9. Collins, J.R., Burt, S.K., and Erickson, J.W. 1995. Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics. Nat. Struct. Biol. 2, 334-338.
10. de Groot, B.L., Amadei, A., van Aalten, D.M., and Berendsen, H.J. 1996b. Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. J. Biomol. Struct. Dyn. 13, 741-751.
11. de Groot, B.L., Amadei, A., Scheek, R.M., van Nuland, N.A., and Berendsen, H.J. 1996a. An extended sampling of the configurational space of HPr from E. coli. Proteins 26, 314-322.
12. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., and Kollman, P.A. 1995. A second generation force field for the simulation of proteins and nucleic acids. J. Am. Chem. Soc. 117, 5179-5197.
13. de Groot, B.L., Hayward, S., van Aalten, D.M., Amadei, A., and Berendsen, H.J. 1998. Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data. Proteins 31, 116-127.
14. de Groot, B.L., van Aalten, D.M., Amadei, A., and Berendsen, H.J. 1996c. The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophys. J. 71, 1707-1713.
15. Duan, Y., and Kollman, P.A. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282, 740-744.
16. Finn, P., and Kavraki, L. 1999. Computational approaches to drug design. Algorithmica 25, 347-371.
17. Garcia, A.E. 1992. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 68, 2696-2699.
18. Gerstein, M., and Krebs, W. 1998. A database of macromolecular motions. Nucl. Acids Res. 26, 4280-4290.
19. Go, N., Noguti, T., and Nishikawa, T. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA 80, 3696-3700.
20. Gogonea, V., Suarez, D., van der Vaart, A., and Merz, Jr., K.M. 2001. New developments in applying quantum mechanics to proteins. Curr. Opin. Struct. Biol. 11, 217-223.
21. Guntert, P., Braun, W., and Wüthrich, K. 1991. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517-530.
22. Hastie, T., and Stuetzle, W. 1989. Principal curves. J. Am. Statist. Ass. 84, 502-516.
23. Hotelling, H. 1933. Analysis of a complex of statistical variables into principal components. J. Educational Psychol. 24, 441.
24. Isralewitz, B., Gao, M., and Schulten, K. 2001. Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11, 224-230.
25. Kabsch, W. 1976. A solution for the best rotation to relate two sets of vectors. Acta Cryst. 32, 922-923.
26. Kalé, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., and Schulten, K. 1999. NAMD2: Greater scalability for parallel molecular dynamics. J. Comp. Phys. 151, 283-312.
27. Kambhatla, N., and Leen, T.K. 1997. Dimension reduction by local principal component analysis. Neural Computation 9, 1493-1516.
28. Kitao, A., and Go, N. 1999. Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol. 9, 164-169.
29. Kramer, M.A. 1991. Nonlinear principal component analysis using autoassociative neural networks. AIChE J. 37, 233-243.
30. Kruskal, J.B. 1964. Nonmetric multidimensional scaling: A numerical method. Psychometrika 29, 115-129.
31. Larson, E.R., Lipinski, C.A., and Sarges, R. 1988. Medicinal chemistry of aldose reductase inhibitors. Med. Res. Rev. 8, 159-186.
32. Lehoucq, R.B., and Sorensen, D.C. 1996. Deflation techniques for an implicitly restarted Arnoldi iteration. SIAM J. Matrix Analysis and Applications 17, 789-821.
33. Lehoucq, R., Sorensen, D.C., and Yang, C. 1998. Arpack User's Guide: Solution of Large-Scale Eigenvalue Problems With Implicitly Restorted Arnoldi Methods, SIAM, Philadelphia.
34. Levitt, M., Sander, C., and Stern, P.S. 1985. Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181, 423-447.
35. Levy, R.M., and Karplus, M. 1979. Vibrational approach to the dynamics of an alpha-helix. Biopolymers 18, 2465-2495.
36. MacKerell, A.D., Bashford, D., Bellot, M., Dunbrack, R.L., Jr., Evanseck, J.D., Field, M.J., et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616.
37. Martin, Y.C., and Willett, P., eds. 1998. Designing Bioactive Molecules: Three Dimensional Techniques and Applications, American Chemical Society, Washington D.C.
38. Miller, M., Schneider, J., Sathyanarayana, B.K., Toth, M.V., Marshall, G.R., Clawson, L., Selk, L., Kent, S.B., and Wlodawer, A. 1989. Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. Science 246, 1149-1152.
39. Muegge, I., and Rarey, M. 2001. Small molecule docking and scoring. Reviews in Computational Chemistry 17, 1-60.
40. Pearson, K. 1901. On lines and planes of closest fit to systems of points in space. The London, Edinburgh and Dublin Philosophical Magazine and Journal of Science 2, 572.
41. Rhodes, G. 1993. Crystallography Made Crystal Clear, Academic Press, London.
42. Romo, T. 1998. Identification and modeling of protein conformational substates, p. 235, Department of Biochemistry and Cell Biology, Rice University, Houston.
43. Romo, T.D., Clarage, J.B., Sorensen, D.C., and Phillips, Jr., G.N. 1995. Automatic identification of discrete substates in proteins: Singular value decomposition analysis of time-averaged crystallographic refinements. Proteins 22, 311-321.
44. Roweis, S., and Saul, L. 2000. Nonlinear dimensionality reduction by locally linear embedding. Science 290, 2323-2326.
45. Rutenber, E., Fauman, E.B., Keenan, R.J., Fong, S., Furth, P.S., Ortiz de Montellano, P.R., Meng, E., Kuntz, I.D., DeCamp, D.L., Salto, R., et al. 1993. Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design. J. Biol. Chem. 268, 15343-15346.
46. Shepard, R.N. 1962. The analysis of proximities: Multidimensional scaling with an unknown distance function. Psychometrika 27, 125-140.
47. Tenenbaum, J.B., de Silva, V., and Langford, J.C. 2000. A global geometric framework for nonlinear dimensionality reduction. Science 290, 2319-2323.
48. Teodoro, M., Phillips, G.N.J., and Kavraki, L.E. 2001. Molecular docking: A problem with thousands of degrees of freedom. IEEE International Conference on Robotics and Automation.
49. Teodoro, M.L., Phillips, G.N., and Kavraki, L.E. 2000. Singular value decomposition of protein conformational motions, 198-199, in Satoru, M., Shamir, R., and Tagaki, T., eds., Currents in Computational Molecular Biology, Universal Academy Press, Tokyo.
50. Tibshirani, R. 1992. Principal curves revisited. Statistics and Computing 2, 183-190.
51. Urzhumtsev, A., Tete-Favier, F., Mitschler, A., Barbanton, J., Barth, P., Urzhumtseva, L., Biellmann, J.F., Podjarny, A., and Moras, D. 1997. A 'specificity' pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil. Structure 5, 601-612.
52. van Aalten, D.M., Conn, D.A., de Groot, B.L., Berendsen, H.J., Findlay, J.B., and Amadei, A. 1997. Protein dynamics derived from clusters of crystal structures. Biophys. J. 73, 2891-2896.
53. Van Eldik, L.J., and Watterson, D.M., eds. 1998. Calmodulin and Signal Transduction, Academic Press, London.
54. Wilson, D.K., Tarle, I., Petrash, J.M., and Quiocho, F.A. 1993. Refined 1.8 A structure of human aldose reductase complexed with the potent inhibitor zopolrestat. Proc. Natl. Acad. Sci. USA 90, 9847.
55. Wolfram, S. 1999. The Mathematica Book, Cambridge University Press, New York.
56. Wüthrich, K. 1986. NMR of Proteins and Nucleic Acids, Wiley, New York.
57. Zacharias, M., and Sklenar, H. 1999. Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex. J. Comp. Chem. 20, 287-300.