Unusual compactness of a polyproline type II structure

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

Volumn 102, Issue 33, 2005, Pages 11698-11703

  Zagrovic, Bojan ^a   Lipfert, Jan ^b   Sorin, Eric J ^b   Millett, Ian S ^b   Van Gunsteren, Wilfred F ^a   Doniach, Sebastian ^b   Pande, Vijay S ^b  

^a ETH ZURICH   (Switzerland)

^b STANFORD UNIVERSITY   (United States)

Author keywords

Molecular dynamics; Small angle x ray scattering; Unfolded state of proteins

Indexed keywords

PEPTIDE; POLYPROLINE II; PROLINE; UNCLASSIFIED DRUG;

ARTICLE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

CIRCULAR DICHROISM; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; SCATTERING, RADIATION; X-RAYS;

EID: 23844465902     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0409693102     Document Type: Article

References (62)

1. Flanagan, J. M., Kataoka, M., Shortle, D. & Engelman, D. M. (1992) Proc. Natl. Acad. Sci. USA 89, 748-752.
2. Gillespie, J. R. & Shortle, D. (1997) J. Mol. Biol. 268, 170-184.
3. Gillespie, J. R. & Shortle, D. (1997) J. Mol. Biol. 268, 158-169.
4. Zhang, O., Kay, L. E., Shortle, D. & Forman-Kay, J. D. (1997) J. Mol. Biol. 272, 9-20.
5. Schwarzinger, S., Kroon, G. J., Foss, T. R., Wright, P. E. & Dyson, H. J. (2000) J. Biomol. NMR 18, 43-48.
6. Plaxco, K. W. & Gross, M. (2001) Nat. Struct. Biol. 8, 659-660.
7. Bai, Y., Chung, J., Dyson, H. J. & Wright, P. E. (2001) Protein Sci. 10, 1056-1066.
8. Shortle, D. & Ackerman, M. S. (2001) Science 293, 487-489.
9. Ackerman, M. S. & Shortle, D. (2002) Biochemistry 41, 13791-13797.
10. Choy, W. Y., Mulder, F. A., Crowhurst, K. A., Muhandiram, D. R., Millett, I. S., Doniach, S., Forman-Kay, J. D. & Kay, L. E. (2002) J. Mol. Biol. 316, 101-112.
11. Millett, I. S., Doniach, S. & Plaxco, K. W. (2002) Adv. Protein Chem. 62, 241-262.
12. Shi, Z., Woody, R. W. & Kallenbach, N. R. (2002) Adv. Protein Chem. 62, 163-240.
13. Kohn, J. E., Millet, I. S., Jacob, J., Zagrovic, B., Dillon, T. M., Cingel, N., Dothager, R. S., Seifert, S., Thiyagarajan, P., Sosnick, T. R., et al. (2004) Proc. Natl. Acad. Sci. USA 101, 12491-12496.
14. Kazmirski, S. L. & Daggett, V. (1998) J. Mol. Biol. 277, 487-506.
15. Fersht, A. R. & Daggett, V. (2002) Cell 108, 573-582.
16. Daura, X., Glattli, A., Gee, P., Peter, C. & van Gunsteren, W. F. (2002) Adv. Protein Chem. 62, 341-360.
17. Zagrovic, B., Snow, C., Khaliq, S., Shirts, M. & Pande, V. (2002) J. Mol. Biol. 323, 153-164.
18. Pappu, R. V. & Rose, G. D. (2002) Protein Sci. 11, 2437-2455.
19. Zagrovic, B. & Pande, V. S. (2003) Nat. Struct. Biol. 10, 955-961.
20. Kentsis, A., Mezei, M., Gindin, T. & Osman, R. (2004) Proteins 55, 493-501.
21. Mezei, M., Fleming, P. J., Srinivasan, R. & Rose, G. D. (2004) Proteins 55, 502-507.
22. Shi, Z., Olson, C. A., Rose, G. D., Baldwin, R. L. & Kallenbach, N. R. (2002) Proc. Natl. Acad. Sci. USA 99, 9190-9195.
23. Creamer, T. P. & Campbell, M. N. (2002) Adv. Protein Chem. 62, 263-282.
24. Rucker, A. L. & Creamer, T. P. (2002) Protein Sci. 11, 980-985.
25. Asher, S. A., Mikhonin, A. V. & Bykov, S. (2004) J. Am. Chem. Soc. 126, 8433-8440.
26. Schweitzer-Stenner, R., Eker, F., Griebenow, K., Cao, X. & Nafie, L. A. (2004) J. Am. Chem. Soc. 126, 2768-2776.
27. Maiti, N. C., Apetri, M. M., Zagorski, M. G., Carey, P. R. & Anderson, V. E. (2004) J. Am. Chem. Soc. 126, 2399-2408.
28. Eker, F., Griebenow, K., Cao, X., Nafie, L. A. & Schweitzer-Stenner, R. (2004) Proc. Natl. Acad. Sci. USA 101, 10054-10059.
29. Zaman, M. H., Shen, M. Y., Berry, R. S., Freed, K. F. & Sosnick, T. R. (2003) J. Mol. Biol. 331, 693-711.
30. Garcia, A. E. (2004) Polymer 45, 669-676.
31. Mu, Y., Kosov, D. S. & Stock, G. (2003) J. Phys. Chem. B 107, 5064-5073.
32. Sorin, E. J. & Pande, V. S. (2005) Biophys. J. 88, 2472-2493.
33. Fitzkee, N. C. & Rose, G. D. (2004) Proc. Natl. Acad. Sci. USA 101, 12497-12502.
34. Doniach, S. (2001) Chem. Rev. 101, 1763-1778.
35. Pande, V. S., Baker, I., Chapman, J., Elmer, S. P., Khaliq, S., Larson, S. M., Rhee, Y. M., Shirts, M. R., Snow, C. D., Sorin, E. J. & Zagrovic, B. (2003) Biopolymers 68, 91-109.
36. Berendsen, H. J., van der Spoel, D. & Drunen, R. (1995) Comp. Phys. Comm. 91, 43-56.
37. Lindahl, E., Hess, B. & van der Spoel, D. (2001) J. Mol. Mod. 7, 306-317.
38. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. (1983) J. Chem. Phys. 79, 926-935.
39. 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. & Kollman, P. A. (1995) J. Am. Chem. Soc. 117, 5179-5197.
40. Kollman, P., Dixon, R., Cornell, W. D., Fox, T., Chipot, C. & Pohorille, A. (1997) in Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications, eds. van Gunsteren, W. F. & Weiner, P. K. (Escom, Dordrecht, The Netherlands), pp. 83-96.
41. Wang, J., Cieplak, P. & Kollman, P. (2000) J. Comp. Chem. 21, 1049-1074.
42. Garcia, A. E. & Sanbonmatsu, K. Y. (2002) Proc. Natl. Acad. Sci. USA 99, 2782-2787.
43. Nymeyer, H. & Garcia, A. E. (2003) Proc. Natl. Acad. Sci. USA 100, 13934-13939.
44. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. & Haak, J. R. (1984) J. Chem. Phys. 81, 3684-3690.
45. Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. (1997) J. Comp. Chem. 18, 1463-1472.
46. Oostenbrink, C., Villa, A., Mark, A. E. & van Gunsteren, W. F. (2004) J. Comp. Chem. 25, 1656-1676.
47. van Gunsteren, W. F., Billeter, S. R., Eising, A. A., Hunenberger, P. H., Kruger, P., Mark, A. E., Scott, W. R. P. & Tironi, I. G. (1996) Biomolecular Simulation: The GROMOS96 Manual and User Guide (Biomos, Zurich).
48. Scott, W. R. P., Hunenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, M., Torda, A. E., Huber, T., Krueger, P. & van Gunsteren, W. F. (1999) J. Phys. Chem. A 103, 3596-3607.
49. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F. & Hermans, J. (1981) in Intermodular Forces, ed. Pullman, B. (Reidel, Dordrecht, The Netherlands), pp. 331-342.
50. Ryckaert, J-P., Ciccotti, G. & Berendsen, H. J. C. (1977) J. Comp. Phys. 23, 327-341.
51. Svergun, D. I., Barberato, C. & Koch, M. H. J. (1995) J. Appl. Crystallogr. 28, 768-773.
52. Tiffany, M. L. & Krimm, S. (1968) Biopolymers 6, 1379-1382.
53. Tiffany, M. L. & Krimm, S. (1968) Biopolymers 6, 1767-1770.
54. Sreerama, N. & Woody, R. W. (1994) Biochemistry 33, 10022-10025.
55. Sorin, E. & Pande, V. S. (2005) J. Comp. Chem. 26, 682-690.
56. Chen, K., Liu, Z. & Kallenbach, N. R. (2004) Proc. Natl. Acad. Sci. USA 101, 15352-15357.
57. Flory, P. J. (1969) Statistical Mechanics of Chain Molecules (Interscience, New York).
58. Pappu, R. V., Srinivasan, R. & Rose, G. D. (2000) Proc. Natl. Acad. Sci. USA 97, 12565-12570.
59. Drozdov, A. N., Grossfield, A. & Pappu, R. V. (2004) J. Am. Chem. Soc. 126, 2574-2581.
60. Vuister, G. W. & Bax, A. (1993) J. Am. Chem. Soc. 115, 7772-7777.
61. Woutersen, S. & Hamm, P. (2005) J. Phys. Chem. B 104, 11316-11320.
62. Woutersen, S., Mu, Y., Stock, G. & Hamm, P. (2001) Proc. Natl. Acad. Sci. USA 98, 11254-11258.