Solvent dependence of PII conformation in model alanine peptides

Journal of the American Chemical Society

Volumn 126, Issue 46, 2004, Pages 15141-15150

  Liu, Zhigang ^a   Chen, Kang ^a   Ng, Angela ^a   Shi, Zhengshuang ^b   Woody, Robert W ^c   Kallenbach, Neville R ^a  

^a NEW YORK UNIVERSITY   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c Department of Environmental and Radiological Health Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; ETHANOL; HYDROGEN BONDS; METHANOL; MOLECULAR STRUCTURE; OLIGOMERS; ORGANIC SOLVENTS;

ALANINE PEPTIDES; ALIPHATIC ALCOHOLS; PENTAMERS; SOLVATION;

PROTEINS;

2 PROPANOL; ACETONITRILE; ACETYLGLYCYLGLYCYLALANYLGLYCYLGLYINAMIDE; ALANINE; DODECYL SULFATE SODIUM; GUANIDINE; METHANOL; OLIGOMER; ORGANIC SOLVENT; PENTAPEPTIDE; PROLINE; SOLVENT; TRIFLUOROETHANOL; UNCLASSIFIED DRUG; WATER;

ALPHA HELIX; ARTICLE; CIRCULAR DICHROISM; HYDRATION; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN CONFORMATION; PROTEIN FOLDING; SOLVATION;

CIRCULAR DICHROISM; HYDROGEN BONDING; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; OLIGOPEPTIDES; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; SOLVENTS; TRIFLUOROETHANOL;

EID: 9344251691     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja047594g     Document Type: Article

References (82)

1. Baldwin, R. L. Adv. Protein Chem. 2002, 62, 361-367.
2. Tanford, C. Adv. Protein Chem. 1968, 23, 121-282.
3. Millett, I. S.; Doniach, S.; Plaxco, K. W. Adv. Protein Chem. 2002, 62, 241-262.
4. Eaton, W. A.; Munoz, V.; Hagen, S. J.; Jas, G. S.; Lapidus, L. J.; Henry, E. R.; Hofrichter, J. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 327-359.
5. Englander, S. W. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 213-238.
6. Plaxco, K. W.; Simons, K. T.; Ruczinski, I.; Baker, D. Biochemistry 2000, 39, 11177-11183.
7. Baldwin, R. L.; Rose, G. D. Trends Biochem Sci. 1999, 24, 77-83.
8. Rose, G. D. Adv Protein Chem. 2002, 62, xv-xxi.
9. Fitzkee, N. C.; Rose, G. D. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 12497-12502.
10. Shortle, D. R. Curr. Opin. Struct. Biol. 1996, 6, 24-30.
11. Shortle, D.; Ackerman, M. S. Science 2001, 293, 487-489.
12. Shi, Z.; Woody, R. W.; Kallenbach, N. R. Adv. Protein Chem. 2002, 62, 163-240.
13. Swindells, M. B.; MacArthur, M. W.; Thornton, J. M. Nat. Struct. Biol. 1995, 2, 596-603.
14. Jha, A.; Colubri, A.; Zaman, M. H.; Sosnick, T. R.; Freed, K. F. Science, submitted.
15. Marqusee, S.; Baldwin, R. L. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 8898-8902.
16. Scholtz, J. M.; Baldwin, R. L. Annu. Rev. Biophys. Biomol. Struct. 1992, 21, 95-118.
17. Rohl, C. A.; Chakrabartty, A.; Baldwin, R. L. Protein Sci. 1996, 5, 2623-2637.
18. Kallenbach, N. R.; Lyu, P. C.; Zhou, H. X. In Circular Dichroism and the Conformational Analysis of Biomolecules; Fasman, G. D., Ed.; Plenum Press: New York, 1996; pp 202-260.
19. Scholtz, J. M.; Qian, H.; York, E. J.; Stewart, J. M.; Baldwin, R. L. Biopolymers 1991, 31, 1463-1470.
20. Spek, E. J.; Olson, C. A.; Shi, Z.; Kallenbach, N. R. J. Am. Chem. Soc. 1999, 121, 5571-5572.
21. Madison, V.; Kopple, K. D. J. Am. Chem. Soc. 1980, 102, 4855-4863.
22. Man, W. G.; Jalkanen, K. J.; Elstner, M.; Suhai, S. J. Phys. Chem. B 1998, 102, 2587-2602.
23. Poon, C. D.; Samulski, E. T.; Weise, C. F.; Weisshaar, J. C. J. Am. Chem. Soc. 2000, 122, 5642-5643.
24. Woutersen, S.; Mu, Y.; Stock, G.; Hamm, P. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11254-11258.
25. Eker, F.; Cao, X.; Nafie, L.; Schweitzer-Stenner, R. J. Am. Chem. Soc. 2002, 124, 14330-14341.
26. Eker, F.; Cao, X.; Nafie, L.; Huang, Q.; Schweitzer-Stenner, R. J. Phys. Chem. B 2003, 107, 358-365.
27. Weise, C. F.; Weisshaar, J. C. J. Phys. Chem. B 2003, 107, 3265-3277.
28. Ding, L.; Chen, K.; Santini, P. A.; Shi, Z.; Kallenbach, N. R. J. Am. Chem. Soc. 2003, 125, 8092-8093.
29. Shi, Z.; Olson, C. A.; Rose, G. D.; Baldwin, R. L.; Kallenbach, N. R. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 9190-9195.
30. Adzhubei, A. A.; Sternberg, M. J. J. Mol. Biol. 1993, 229, 472-493.
31. Adzhubei, A. A.; Sternberg, M. J. Protein Sci. 1994, 3, 2395-2410.
32. Creamer, T. P. Proteins 1998, 33, 218-226.
33. Stapley, B. J.; Creamer, T. P. Protein Sci. 1999, 8, 587-595.
34. Sreerama, N.; Woody, R. W. Proteins 1999, 36, 400-406.
35. Pappu, R. V.; Rose, G. D. Protein Sci. 2002, 11, 2437-2455.
36. Takekiyo, T.; Imai, T.; Kato, M.; Taniguchi, Y. Biopolymers 2004, 73, 283-290.
37. Garcia, A. E. Polymer 2004, 45, 669-676.
38. Pitto, M.; Sandek, V.; Sklenar, V. A. J. Biomol. NMR 1992, 2, 611-665.
39. Bax, A.; Davis, D. G. J. Magn. Reson. 1985, 65, 355-360.
40. Bothner-by, A. A.; Stephens, R. L.; Lee, J. M.; Warren, C. D.; Jeanloz, R. W. J. Am. Chem. Soc. 1984, 106, 811-813.
41. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Bax, A. J. Biomol. NMR 1995, 6, 277-293.
42. Goddard, T. D.; Kneller, D. G. SPARKY 3; University of California, San Francisco, 2003.
43. Schmidt, J. M.; Blumel, M.; Lohr, F.; Rüterjans, H. J. Biomol. NMR 1999, 14, 1-12.
44. Karplus, M. J. Chem. Phys. 1959, 30, 11-15.
45. Bax, A.; Davis, D. G. J. Magn. Reson. 1985, 63, 207-360.
46. Nilges, M.; Macias, M. J.; O'donoghue, S. I.; Oschkinat, H. J. Mol. Biol. 1997, 269, 408-422.
47. Bayley, P. M.; Nielsen, E. B.; Schellman, J. A. J. Phys. Chem. 1969, 73, 228-243.
48. Hirst, J. D.; Colella, K.; Gilbert, A. T. J. Phys Chem. B 2003, 107, 11813-11819.
49. Sreerama, N.; Woody, R. W. Methods Enzymol. 2004, 383, 318-351.
50. Woody, R. W.; Sreerama, N. J. Chem. Phys. 1999, 111, 2844-2845.
51. Chin, D.-H.; Woody, R. W.; Rohl, C. A.; Baldwin, R. A. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 15416-15421.
52. Clark, L. B. J. Am. Chem. Soc. 1995, 117, 7974-7986.
53. Peterson, D. L.; Simpson, W. T. J. Am. Chem. Soc. 1957, 79, 2375-2382.
54. Serrano-Andrés, L.; Fülscher, M. P. J. Am. Chem. Soc. 1996, 118, 12190-12199.
55. Hirst, J. D.; Hirst, D. M.; Brooks. C. L. J. Phys. Chem. A 1997,101, 4821-4827.
56. Smith, J. A.; Pease, L. G. Crit. Rev. Biochem. 1980, 8, 315-399.
57. Tinoco, I., Jr. Adv. Chem. Phys. 1962, 4, 113-160.
58. Woody, R. W.; Tinoco, I., Jr. J. Chem. Phys. 1967, 46, 4927-4945.
59. Zubkov, V. A.; Vol'kenshtein, M. V. Mol. Biol. (Engl. transl. of Molekul. Biol.) 1970, 4, 598-606.
60. Garmer, D. R.; Stevens, W. J. J. Phys. Chem. 1989, 93, 8263-8270.
61. Woody, R. W., to be submitted.
62. Ooi, T.; Scott, R. A.; Vanderkooi, G.; Scheraga, H. A. J. Chem Phys. 1967, 46, 4410-4426.
63. McGuire, R. F.; Vanderkooi, G.; Momany, F. A.; Ingwall, R. T.; Crippen, G. M.; Lotan, N.; Tuttle, R. W.; Kashuba, K.I.; Scheraga, H. A. Macromolecules 1971, 4, 112-124.
64. Rose, G. D.; Gierasch, L. M.; Smith, J. A. Adv. Protein Chem. 1985, 1-109.
65. Venkatachalam, C. M. Biopolymers 1968, 6, 1425-1436.
66. Madison, V.; Schellman, J. Biopolymers 1972, 11, 1041-1076.
67. Tterlikkis, L.; Loxsom, F. M.; Rhodes, W. Biopolymers 1973, 12, 675-684.
68. Woody, R. W. Biophys. J. 2004, 86, 617a.
69. Reichardt, C. Chem. Rev. 1994, 94, 2319-2358.
70. Snyder, L. R. J. Chromatogr. Sci. 1978, 16, 223-34.
71. Hong, D.; Hoshino, M.; Kuboi, R.; Goto, Y. J. Am. Chem. Soc. 1999, 121, 8427-8433.
72. Manning, M. C.; Woody, R. W. Biopolymers 1991, 31, 569-586.
73. Tiffany, M. L.; Krimm, S. Biopolymers 1973, 12, 575-587.
74. Hu, H.; Elstner, M.; Hermans, J. Proteins: Struct., Fund., Genet. 2003, 50, 451-463.
75. Drozdov, A. N.; Grossfield, A.; Pappu, R. V. J. Am. Chem. Soc. 2004, 126, 2574-2581.
76. Mezei, M.; Fleming, P. J.; Srinivasan, R.; Rose, G. D. Proteins 2004, 55, 502-507.
77. Nelson, J. W.; Kallenbach, N. R. Proteins 1986, 1, 211-217.
78. Luo, P.; Baldwin, R. L. Biochemistry 1997, 36, 8413-8421.
79. Luo, P.; Baldwin, R. L. J. Mol. Biol. 1998, 279, 49-57.
80. Kentsis, A.; Sosnick, T. R. Biochemistry 1998, 37, 14613-14622.
81. Plaxco, K. W.; Morton, C. J.; Grimshaw, S. B.; Jones, J. A.; Pitkeathly, M.; Campbell, I. D.; Dobson, C. M. J. Biomol NMR 1997, 10, 221-230.
82. Garcia, A. E.; Onuchic, J. N. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13898-13903.