Secondary structure provides a template for the folding of nearby polypeptides

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

Volumn 103, Issue 47, 2006, Pages 17765-17770

  Kameda, Tomoshi ^a,b   Takada, Shoji ^a,c  

^a KOBE UNIVERSITY   (Japan)

^b Japan Biological Information Research Center   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Energy landscape; Generalized born; Polyproline II; Protein folding; Replica exchange

Indexed keywords

ALANINE; POLYPEPTIDE; PROLINE; SOLVENT;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BETA CHAIN; DIELECTRIC CONSTANT; ENERGY TRANSFER; ENTROPY; HYDROGEN BOND; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; SIMULATION;

COMPUTER SIMULATION; MODELS, MOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SOFTWARE;

EID: 33845213187     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0602632103     Document Type: Article

References (52)

1. Onuchic JN, Luthey-Schulten Z, Wolynes PG (1997) Annu Rev Phys Chem 48:545-600.
2. Yang S, Cho SS, Levy Y, Cheung MS, Levine H, Wolynes PG, Onuchic JN (2004) Proc Natl Acad Sci USA 101:13786-13791.
3. Dobson CM (2003) Nature 426:884-890.
4. Minton AP (2000) Curr Opin Struct Biol 10:34-39.
5. Spek EJ, Olson CA, Shi ZS, Kallenbach NR (1999) J Am Chem Soc 121:5571-5572.
6. Marqusee S, Robbins VH, Baldwin RL (1989) Proc Natl Acad Sci USA 86:5286-5290.
7. Scholtz JM, York EJ, Stewart JM, Baldwin RL (1991) J Am Chem Soc 113:5102-5104.
8. Chou PY, Fasman GD (1978) Adv Enzymol Relat Areas Mol Biol 47:45-148.
9. Gasset M, Baldwin MA, Lloyd DH, Gabriel JM, Holtzman DM, Cohen F, Fletterick R, Prusiner SB (1992) Proc Natl Acad Sci USA 89:10940-10944.
10. Forood B, Perez-Paya E, Houghten RA, Blondelle SE (1995) Biochem Biophys Res Commun 211:7-13.
11. Ingwall RT, Scheraga HA, Lotan N, Berger A, Katchalski E (1968) Biopolymers 6:331-368.
12. Shi Z, Olson CA, Rose GD, Baldwin RL, Kallenbach NR (2002) Proc Natl Acad Sci USA 99:9190-9195.
13. Han WG, Jalkanen KJ, Elstner M, Suhai S (1998) J Phys Chem B 102:2587-2602.
14. Eker F, Cao XL, Nafie L, Huang Q, Schweitzer-Stenner R (2003) J Phys Chem B 107:358-365.
15. Poon CD, Samulski ET, Weise CF, Weisshaar JC (2000) J Am Chem Soc 122:5642-5643.
16. Woutersen S, Hamm P (2001) J Chem Phys 114:2727-2737.
17. Garcia AE (2004) Polymer 45:669-676.
18. Kentsis A, Mezei M, Gindin T, Osman R (2004) Proteins 55:493-501.
19. Zagrovic B, Lipfert J, Sorin EJ, Millett IS, van Gunsteren WF, Doniach S, Pande VS (2005) Proc Natl Acad Sci USA 102:11698-11703.
20. Pappu RV, Rose GD (2002) Protein Sci 11:2437-2455.
21. Ding L, Chen K, Santini PA, Shi ZS, Kallenbach NR (2003) J Am Chem Soc 125:8092-8093.
22. Sugita Y, Okamoto Y (1999) Chem Phys Lett 314:141-151.
23. Neria E, Fischer S, Karplus M (1996) J Chem Phys 105:1902-1921.
24. Dominy BN, Brooks CL (1999) J Phys Chem B 103:3765-3773.
25. Weise CF, Weisshaar JC (2003) J Phys Chem B 107:3265-3277.
26. Hu H, Elstner M, Hermans J (2003) Proteins 50:451-463.
27. Sreerama N, Woody RW (1999) Proteins 36:400-406.
28. Liu ZG, Chen K, Ng A, Shi ZS, Woody RW, Kallenbach NR (2004) J Am Chem Soc 126:15141-15150.
29. Makowska J, Rodziewicz-Motowidlo S, Baginska K, Vila JA, Liwo A, Chmurzynski L, Scheraga HA (2006) Proc Natl Acad Sci USA 103:1744-1749.
30. Ikeda K, Galzitskaya OV, Nakamura H, Higo J (2003) J Comput Chem 24:310-318.
31. Kitao A, Hayward S, Go N (1998) Proteins 33:496-517.
32. Garcia AE (1992) Phys Rev Lett 68:2696-2699.
33. Mu YG, Stock G (2002) J Phys Chem B 106:5294-5301.
34. Bai YW, Karimi A, Dyson HJ, Wright PE (1997) Protein Sci 6:1449-1457.
35. Meisner WK, Sosnick TR (2004) Proc Natl Acad Sci USA 101:13478-13482.
36. Daggett V, Fersht AR (2003) Trends Biochem Sci 28:18-25.
37. Kimura T, Uzawa T, Ishimori K, Morishima I, Takahashi S, Konno T, Akiyama S, Fujisawa T (2005) Proc Natl Acad Sci USA 102:2748-2753.
38. Shiraki K, Nishikawa K, Goto Y (1995) J Mol Biol 245:180-194.
39. Uversky VN, Narizhneva NV, Kirschstein SO, Winter S, Lober G (1997) Folding Des 2:163-172.
40. Luo PZ, Baldwin RL (1997) Biochemistry 36:8413-8421.
41. Hong DP, Hoshino M, Kuboi R, Goto Y (1999) J Am Chem Soc 121:8427-8433.
42. Vila JA, Ripoll DR, Scheraga HA (2000) Proc Natl Acad Sci USA 97:13075-13079.
43. Richardson JS, Richardson DC (2002) Proc Natl Acad Sci USA 99:2754-2759.
44. Hukushima K, Nemoto K (1996) J Phys Soc Jpn 65:1604-1608.
45. Chothia C, Levitt M, Richardson D (1981) J Mol Biol 145:215-250.
46. Bursulaya BD, Brooks CL (2000) J Phys Chem B 104:12378-12383.
47. Pitera JW, Swope W (2003) Proc Natl Acad Sci USA 100:7587-7592.
48. Hoover WG (1985) Phys Rev A At Mol Opt Phys 31:1695-1697.
49. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) J Comput Chem 23:327-341.
50. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comput Chem 4:187-217.
51. Lifson S, Roig A (1961) J Chem Phys 34:1963-1974.
52. Kabsch W, Sander C (1983) Biopolymers 22:2577-2637.