A small tripeptide AFA undergoes two state cooperative conformational transitions: Implications for conformational biases in unfolded states

Protein and Peptide Letters

Volumn 14, Issue 6, 2007, Pages 581-589

  Patel, Sunita ^a   Taimni, Richa ^a   Sasidhar, Yellamraju U ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

GROMACS; Molecular dynamics; Protein folding; Tripeptide; Two state transitions; Unfolded state

Indexed keywords

EID: 34447260484     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986607780989886     Document Type: Article

References (49)

1. Bai, Y., Chung, J., Dyson, H.J. and Wright, P.E. (2001) Protein Sci., 10, 1056-1066.
2. Klein-Seetharaman, J., Oikawa, M., Grimshaw, S.B., Wirmer, J., Duchardt, E., Ueda, T., Imoto, T., Smith, L.J., Dobson, C.M. and Schwalbe, H. (2002) Science, 295, 1719-1722.
3. Religa, T.L., Markson, J.S., Mayor, U., Freund, S.M. and Fersht, A.R. (2005) Nature, 437, 1053-1056.
4. Moglich, A., Joder, K. and Kiefhaber, T. (2006) Proc. Natl. Acad. Sci. U. S. A., 103, 12394-12399.
5. Dyson, H.J. and Wright, P.E. (2004) Chem. Rev., 104, 3607-3622.
6. Tang, Y., Goger, M.J. and Raleigh, D.P. (2006) Biochemistry, 45, 6940-6946.
7. Eaton, W.A., Thompson, P.A., Chan, C.K., Hage, S.J. and Hofrichter, J. (1996) Structure, 4, 1133-1139.
8. Bachmann, A., Segel, D. and Kiefhaber, T. (2002) Biophys. Chem., 96, 141-151.
9. Roder, H., Maki, K., Latypov, R.F., Cheng, H. and Shastry, M.C.R. (2005) in Protein Folding Handbook. (Buchner, J.&.K., T., Ed). pp. 491-535. Wiley-VCH, Weinheim, Germany.
10. Flory, P.J. (1969) Statistical Mechanics of Chain Molecules. p. 252. Wiley, New York,
11. 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. (2004) Proc. Natl. Acad. Sci. U. S. A., 101, 12491-12496.
12. Tanford, C. (1968) Adv. Protein Chem., 23, 121-282.
13. Fitzkee, N.C. and Rose, G.D. (2004) Proc. Natl. Acad. Sci. U. S. A., 101, 12497-12502.
14. Pappu, R.V., Srinivasan, R. and Rose, G.D. (2000) Proc. Natl. Acad. Sci. U. S. A., 97, 12565-12570.
15. Fitzkee, N.C. and Rose, G.D. (2005) J. Mol. Biol., 353, 873-887.
16. Tang, Y., Rigotti, D.J., Fairman, R. and Raleigh, D.P. (2004) Biochemistry, 43, 3264-3272.
17. Segel, D.J., Bachmann, A., Hofrichter, J., Hodgson, K.O., Doniach, S. and Kiefhaber, T. (1999) J. Mol. Biol., 288, 489-499.
18. Roder, H., Maki, K. and Cheng, H. (2006) Chem. Rev., 106, 1836-1861.
19. Welker, E., Maki, K., Shastry, M.C., Juminaga, D., Bhat, R., Scheraga, H.A. and Roder, H. (2004) Proc. Natl. Acad. Sci. U. S. A., 101, 17681-17686.
20. Sosnick, T.R., Shtilerman, M.D., Mayne, L. and Englander, S.W. (1997) Proc. Natl. Acad. Sci. U. S. A., 94, 8545-8550.
21. Qi, P.X., Sosnick, T.R. and Englander, S.W. (1998) Nat. Struct. Biol., 5, 882-884.
22. Sosnick, T.R., Mayne, L. and Englander, S.W. (1996) Proteins, 24, 413-426.
23. Eker, F., Cao, X., Nafie, L. and Schweitzer-Stenner, R. (2002) J. Am. Chem. Soc., 124, 14330-14341.
24. Eker, F., Cao, X., Nafie, L., Huang, Q. and Schweitzer-Stenner, R. (2003) J. Phys. Chem. B, 107, 358-365.
25. Eker, F., Griebenow, K. and Schweitzer-Stenner, R. (2003) J. Am. Chem. Soc., 125, 8178-8185.
26. Mu, Y. and Stock, G. (2002) J. Phys. Chem. B, 106, 5294-5301.
27. Graf, J., Nguyen, P.H., Stock, G. and Schwalbe, H. (2007) J. Am. Chem. Soc., 129, 1179-1189.
28. Eker, F., Griebenow, K., Cao, X., Nafie, L.A. and Schweitzer-Stenner, R. (2004) Proc. Natl. Acad. Sci. U. S. A., 101, 10054-10059.
29. Motta, A., Reches, M., Pappalardo, L., Andreotti, G. and Gazit, E. (2005) Biochemistry, 44, 14170-14178.
30. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F. and Hermans, J. (1981) Interaction models for water in relation to protein hydration. In: Inter molecular Forces (Pullman, B., Ed). pp. 331-342. Reidel Publishing Company, Dordrecht, The Netherlands.
31. Lindahl, E., Hess, B. and van der Spoel, D. (2001) J. Mol. Mod., 7, 306-317.
32. Jorgensen, W.L. and Tirado-Rives, J. (1988) J. Am. Chem. Soc., 110, 1657-1666.
33. Essmann, U., Perera, L., Berkowitz, M., Darden, T., Lee, H. and Pedersen, L. (1995) J. Chem. Phys., 103, 8577-8593.
34. Darden, T., York, D. and Pedersen, L. (1993) J. Chem. Phys., 98, 10089-10092.
35. Hess, B., Bekker, H., Berendsen, H.J.C. and Fraaije, J.G.E.M. (1997) J. Comp. Chem., 18, 1463-1472.
36. Berendsen, H., Postma, J., DiNola, A. and Haak, J. (1984) J. Chem. Phys., 81, 3684-3690.
37. Humphrey, W., Dalke, A. and Schulten, K. (1996) J. Mol. Graph., 14, 33-8, 27-8.
38. Amadei, A., Linssen, A.B. and Berendsen, H.J. (1993) Proteins, 17, 412-425.
39. de Groot, B.L., Amadei, A., Scheek, R.M., van Nuland, N.A. and Berendsen, H.J. (1996) Proteins, 26, 314-22.
40. Daidone, I., Amadei, A. and Di Nola, A. (2005) Proteins, 59, 510-518.
41. Schulz, G.E. and Schirmer, R.H. (1978) Principles of Protein Structure. (Cantor, R.C., Ed). pp. 1-314. Springer, New York.
42. Karplus, P.A. (1996) Protein Sci., 5, 1406-1420.
43. Mandel, N., Mandel, G., Trus, B.L., Rosenberg, J., Carlson, G. and Dickerson, R.E. (1977) J. Biol. Chem., 252, 4619-4636.
44. Drozdov, A.N., Grossfield, A. and Pappu, R.V. (2004) J. Am. Chem. Soc., 126, 2574-2581.
45. Beglov, D. and Roux, B. (1995) Biopolymers, 35, 171-178.
46. Park, C., Carlson, M.J. and Goddard, W.A.III. (2000) J. Phys. Chem. A, 104, 2498-2503.
47. Dyson, H.J. and Wright, P.E. (1995) FASEB J., 9, 37-42.
48. Deschamps, J.R. (2005) AAPS J., 7, E813-9.
49. Zhao, B., Helms, L.R., DesJarlais, R.L., Abdel-Meguid, S.S. and Wetzel, R. (1995) Nat. Struct. Biol., 2, 1131-1137.