Unfolded-state dynamics and structure of protein L characterized by simulation and experiment

Journal of the American Chemical Society

Volumn 132, Issue 13, 2010, Pages 4702-4709

  Voelz, Vincent A ^a   Singh, Vijay R ^b   Wedemeyer, William J ^b,c   Lapidus, Lisa J ^b   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c Michigan State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCELERATED CALCULATION; ALL-ATOM SIMULATIONS; CONTACT QUENCHING; DENATURED CHAINS; DIFFUSION RATE; DISTRIBUTED COMPUTING; EXPERIMENTAL TECHNIQUES; GRAPHICS PROCESSOR UNITS; HIGH TEMPERATURE; MOLECULAR DYNAMICS TRAJECTORIES; MOLECULAR SIMULATIONS; POLYMER THEORY; PREDICTIVE TOOLS; QUANTITATIVE COMPARISON; QUENCHING RATE; SIMULATION TIME; STATE DYNAMICS; STRUCTURE AND DYNAMICS; TIME-SCALES; TOTAL AGGREGATES;

AGGREGATES; DYNAMICS; EXPERIMENTS; MOLECULAR DYNAMICS; PROTEINS; QUENCHING; REACTION RATES;

DIFFUSION;

CYSTEINE; DIHYDROLIPOAMIDE DEHYDROGENASE; POLYMER; TRYPTOPHAN;

ARTICLE; CALCULATION; COMPARATIVE STUDY; CONTROLLED STUDY; DENATURATION; DIFFUSION; HIGH TEMPERATURE; MOLECULAR DYNAMICS; MUTATION; PREDICTOR VARIABLE; PROTEIN DETERMINATION; PROTEIN FOLDING; PROTEIN STRUCTURE; QUANTITATIVE ANALYSIS; REACTION TIME; SIMULATION;

CALIBRATION; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEINS; TEMPERATURE; THERMODYNAMICS;

EID: 77950789652     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja908369h     Document Type: Article

References (64)

1. Meier, S., Blackledge, M., and Grzesiek, S. J. Chem. Phys. 2008, 128 052204
2. Mittag, T. and Forman-Kay, J. D. Curr. Opin. Struct. Biol. 2007, 17, 3 - 14
3. Plaxco, K. W., Millett, I. S., Segel, D. J., Doniach, S., and Baker, D. Nat. Struct. Biol. 1999, 6, 554 - 556
4. Kohn, J. E., Millett, I. S., Jacob, J., Zagrovic, B., Dillon, T. M., Cingel, N., Dothager, R. S., Seifert, S., Thiyagarajan, P., Sosnick, T. R., Hasan, M. Z., Pande, V. S., Ruczinski, I., Doniach, S., and Plaxco, K. W. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 12495
5. Mohana-Borges, R., Goto, N. K., Kroon, G. J. A., Dyson, H. J., and Wright, P. E. J. Mol. Biol. 2004, 340, 1131 - 1142
6. Ohnishi, S., Lee, A. L., Edgell, M. H., and Shortle, D. Biochemistry 2004, 43, 4064 - 4070
7. Shortle, D. and Ackerman, M. S. Science 2001, 293, 487 - 489
8. Felitsky, D. J., Lietzow, M. A., Dyson, H. J., and Wright, P. E. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 6278 - 6283
9. Song, J., Guo, L.-W., Muradov, H., Artemyev, N. O., Ruoho, A. E., and Markley, J. L. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1505 - 1510
10. Schuler, B., Lipman, E. A., and Eaton, W. A. Nature 2002, 419, 743 - 747
11. Sherman, E. and Haran, G. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 11539 - 11543
12. Merchant, K. A., Best, R. B., Louis, J. M., Gopich, I. V., and Eaton, W. A. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1528 - 1533
13. Sherman, E., Itkin, A., Kuttner, Y. Y., Rhoades, E., Amir, D., Haas, E., and Haran, G. Biophys. J. 2008, 94, 4819 - 4827
14. Bieri, O., Wirz, J., Hellrung, B., Schutkowski, M., Drewello, M., and Kiefhaber, T. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9597 - 9601
15. Hudgins, R. R., Huang, F., Gramlich, G., and Nau, W. M. J. Am. Chem. Soc. 2002, 124, 556 - 564
16. Lapidus, L. J., Eaton, W. A., and Hofrichter, J. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7220 - 7225
17. Lee, J. C., Langen, R., Hummel, P. A., Gray, H. B., and Winkler, J. R. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 16466 - 16471
18. Neuweiler, H., Schulz, A., Bhmer, M., Enderlein, J., and Sauer, M. J. Am. Chem. Soc. 2003, 125, 5324 - 5330
19. Buscaglia, M., Schuler, B., Lapidus, L. J., Eaton, W. A., and Hofrichter, J. J. Mol. Biol. 2003, 332, 9 - 12
20. Singh, V. R., Kopka, M., Chen, Y., Wedemeyer, W. J., and Lapidus, L. J. Biochemistry 2007, 46, 10046 - 10054
21. Nettels, D., Gopich, I. V., Hoffmann, A., and Schuler, B. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 2655 - 2660
22. Guo, L., Chowdhury, P., Glasscock, J. M., and Gai, F. J. Mol. Biol. 2008, 384, 1029 - 1036
23. Lee, J. C., Lai, B. T., Kozak, J. J., Gray, H. B., and Winkler, J. R. J. Phys. Chem. B 2007, 111, 2107 - 2112
24. Wang, Z., Plaxco, K. W., and Makarov, D. E. Biopolymers 2007, 86, 321 - 328
25. Buscaglia, M., Lapidus, L. J., Eaton, W. A., and Hofrichter, J. Biophys. J. 2006, 91, 276 - 288
26. Lapidus, L. J., Steinbach, P. J., Eaton, W. A., Szabo, A., and Hofrichter, J. J. Phys. Chem. B 2002, 106, 11628 - 11640
27. Jha, A. K., Colubri, A., Freed, K. F., and Sosnick, T. R. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13099 - 13104
28. Lindorff-Larsen, K., Kristjansdottir, S., Teilum, K., Fieber, W., Dobson, C. M., Poulsen, F. M., and Vendruscolo, M. J. Am. Chem. Soc. 2004, 126, 3291 - 3299
29. Zagrovic, B., Snow, C. D., Khaliq, S., Shirts, M. R., and Pande, V. S. J. Mol. Biol. 2002, 323, 153 - 164
30. Camilloni, C., Sutto, L., Provasi, D., Tiana, G., and Broglia, R. A. Protein Sci. 2008, 17, 1424 - 1433
31. Marsh, J. A., Neale, C., Jack, F. E., Choy, W.-Y., Lee, A. Y., Crowhurst, K. A., and Forman-Kay, J. D. J. Mol. Biol. 2007, 367, 1494 - 1510
32. DeSimone, A., Richter, B., Salvatella, X., and Vendruscolo, M. J. Am. Chem. Soc. 2009, 131, 3810 - 3811
33. Dedmon, M. M., Lindorff-Larsen, K., Christodoulou, J., Vendruscolo, M., and Dobson, C. M. J. Am. Chem. Soc. 2005, 127, 476 - 477
34. Brown, S., Fawzi, N. J., and Head-Gordon, T. Proc. Natl. Acad. Sci. U.S.A. 2004, 100, 10712 - 10717
35. Das, P., Matysiak, S., and Clementi, C. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 10141 - 10146
36. OBrien, E. P., Ziv, G., Haran, G., Brooks, B. R., and Thirumalai, D. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 13403 - 13408
37. van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., and Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701 - 1718
38. Friedrichs, M. S., Eastman, P., Vaidyanathan, V., Houston, M., Legrand, S., Beberg, A. L., Ensign, D. L., Bruns, C. M., and Pande, V. S. J. Comput. Chem. 2009, 30, 864 - 872
39. Wang, J., Cieplak, P., and Kollman, P. A. J. Comput. Chem. 2000, 21, 1049 - 1074
40. Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J., and Kollman, P. J. Comput. Chem. 2003, 24, 1999 - 2012
41. Onufriev, A., Bashford, D., and Case, D. Proteins 2004, 55, 383 - 394
42. Shell, M. S., Ritterson, R., and Ai, K. J. Phys. Chem. B 2008, 112, 6878 - 6886
43. Scalley, M. L., Yi, Q., Gu, H., McCormack, A., Yates, J. R., III, and Baker, D. Biochemistry 1997, 36, 3373 - 3382
44. Sadqi, M., Lapidus, L. J., and Muoz, V. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12117 - 12122
45. Waldauer, S. A., Bakajin, O., Ball, T., Chen, Y., DeCamp, S. J., Kopka, M., Jäger, M., Singh, V. R., Wedemeyer, W. J., Weiss, S., Yao, S., and Lapidus, L. J. HFSP J. 2008, 2, 388 - 395
46. Ziv, G. and Haran, G. J. Am. Chem. Soc. 2009, 131, 2942 - 2947
47. Ziv, G., Thirumalai, D., and Haran, G. Phys. Chem. Chem. Phys. 2009, 11, 83 - 93
48. Sanchez, I. C. Macromolecules 1979, 12, 980 - 988
49. Dill, K. A. Biochemistry 1985, 24, 1501 - 1509
50. Pitera, J. W. and Swope, W. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7587 - 7592
51. Chen, J. and Brooks, C. L., III. Phys. Chem. Chem. Phys. 2008, 10, 471 - 481
52. McCarney, E. R., Kohn, J. E., and Plaxco, K. W. Crit. Rev. Biochem. Mol. Biol. 2005, 40, 181 - 189
53. Yi, Q., Scalley-Kim, M. L., Alm, E. J., and Baker, D. J. Mol. Biol. 2000, 299, 1341 - 1351
54. Fitzkee, N. C. and Rose, G. D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 12497 - 12502
55. Le Guillou, J. C. and Zinn-Justin, J. Phys. Rev. Lett. 1977, 39, 95 - 98
56. Kabsch, W. and Sander, C. Biopolymers 1983, 22, 2577 - 2637
57. Wishart, D. S. and Sykes, B. D. J. Biomol. NMR 1994, 4, 171 - 180
58. Cho, J.-H. and Raleigh, D. P. J. Mol. Biol. 2006, 359, 1437 - 1446
59. Brewer, S. H., Vu, D. M., Tang, Y., Li, Y., Franzen, S., Raleigh, D. P., and Dyer, R. B. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 16662 - 16667
60. Wright, P. E. and Dyson, H. J. Curr. Opin. Struct. Biol. 2009, 19, 31 - 38
61. Dyson, H. J. and Wright, P. E. Nat. Rev. Mol. Cell Biol. 2005, 6, 197 - 208
62. Szabo, A., Schulten, K., and Schulten, Z. J. Chem. Phys. 1980, 72, 4350 - 4357
63. Lapidus, L. J., Eaton, W. A., and Hofrichter, J. Phys. Rev. Lett. 2001, 87, 258101
64. Frembgen-Kesner, T. and Elcock, A. H. J. Chem. Theory Comput. 2009, 5, 242 - 256