A PDZ domain recapitulates a unifying mechanism for protein folding

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

Volumn 104, Issue 1, 2007, Pages 128-133

  Gianni, Stefano ^a   Geierhaas, Christian D ^b   Calosci, Nicoletta ^a   Jemth, Per ^c   Vuister, Geerten W ^d   Travaglini Allocatelli, Carlo ^a   Vendruscolo, Michele ^b   Brunori, Maurizio ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c UPPSALA UNIVERSITY   (Sweden)

^d RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

Author keywords

Molecular dynamics; Protein engineering; Transition state

Indexed keywords

GLOBULAR PROTEIN; PDZ PROTEIN; POLYPEPTIDE;

ARTICLE; DIFFUSION; MOLECULAR DYNAMICS; MOLECULAR MODEL; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STRUCTURE;

PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS;

EID: 33846115692     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0602770104     Document Type: Article

References (47)

1. Daggett V, Fersht AR (2003) Trends Biochem Sci 28:18-25.
2. Karplus M, Weaver DL (1994) Protein Sci 3:650-668.
3. Kim PS, Baldwin RL (1990) Annu Rev Biochem 59:631-660.
4. Baker D (2000) Nature 405:39-42.
5. Onuchic JN, Wolynes PG (2004) Curr Opin Struct Biol 14:70-75.
6. Wong KB, Clarke J, Bond CJ, Neira JL, Freund SM, Fersht AR, Daggett V (2000) J Mol Biol 296:1257-1282.
7. Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, Jas GS, Freund SMV, Alonso DOV, Daggett V, Fersht AR (2003) Nature 421:863-867.
8. Yang WY, Gruebele M (2003) Nature 423:193-197.
9. Myers JK, Oas TG (1999) Biochemistry 38:6761-6768.
10. Islam SA, Karplus M, Weaver DL (2004) Structure (London) 12:1833-1845.
11. Itzhaki LS, Otzen DE, Fersht AR (1995) J Mol Biol 254:260-288.
12. Fersht AR (1995) Proc Natl Acad Sci USA 92:10869-10873.
13. Gianni S, Guydosh NR, Khan F, Caldas TD, Mayor TJ, White GW, DeMarco ML, Daggett V, Fersht AR (2003) Proc Natl Acad Sci USA 100:13286-13291.
14. White GW, Gianni S, Grossmann JG, Jemth P, Fersht AR, Daggett V (2005) J Mol Biol 350:757-775.
15. Fersht AR, Matouschek A, Serrano L (1992) J Mol Biol 224:771-782.
16. Vendruscolo M, Paci E, Dobson CM, Karplus M (2001) Nature 409:641-645.
17. Wüthrich K (1989) Science 243:45-50.
18. Gianni S, Calosci N, Aelen JM, Vuister GW, Brunori M, Travaglini-Allocatelli C (2005) Prot Eng Des Sci 18:389-395.
19. Fersht AR, Sato S (2004) Proc Natl Acad Sci USA 101:7976-7981.
20. Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG (1996) Fold Des 1:441-450.
21. Onuchic JN, Luthey-Schulten Z, Wolynes PG (1997) Annu Rev Phys Chem 48:545-600.
22. Plaxco KW, Simons KT, Baker D (1998) J Mol Biol 277:985-994.
23. Sanchez IE, Kiefhaber T (2003) J Mol Biol 325:367-376.
24. Fersht AR (1999) Structure and Mechanism in Protein Science (Freeman, New York).
25. Jemth P, Day R, Gianni S, Khan F, Allen M, Daggett V, Fersht AR (2005) J Mol Biol 350:363-378.
26. Khan F, Chuang JI, Gianni S, Fersht AR (2003) J Mol Biol 333:169-186.
27. Ternstrom T, Mayor U, Akke M, Oliveberg M (1999) Proc Natl Acad Sci USA 96:14854-14859.
28. Scott KA, Randles LG, Clarke J (2004) J Mol Biol 344:207-211.
29. Kamagata K, Kuwajima K (2006) J Mol Biol 357:1647-1654.
30. Silow M, Oliveberg M (1997) Proc Natl Acad Sci USA 94:6084-6086.
31. Santoro MM, Bolen DW (1988) Biochemistry 27:8063-8068.
32. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comput Chem 4:187-217.
33. Lazaridis T, Karplus M (1999) Proteins 35:133-152.
34. Schaftenaar G, Noordik JH (2000) J Comput Aided Mol Des 14:123-134.
35. Vendruscolo M, Dobson CM (2005) Philos Trans R Soc A 363:433-452.
36. Lindorff-Larsen K, Vendruscolo M, Paci E, Dobson CM (2004) Nat Struct Mol Biol 11:443-449.
37. Carter P, Andersen CA, Rost B (2003) Nucleic Acids Res 31:3293-3295.
38. Paci E, Vendruscolo M, Dobson CM, Karplus M (2002) J Mol Biol 324:151-163.
39. Jemth P, Gianni S, Day R, Li B, Johnson CM, Daggett V, Fersht AR (2004) Proc Natl Acad Sci USA 101:6450-6455.
40. Travaglini-Allocatelli C, Gianni S, Morea V, Tramontano A, Soulimane T, Brunori M (2003) J Biol Chem 278:41136-41140.
41. Travaglini-Allocatelli C, Gianni S, Dubey VK, Borgia A, Di Matteo A, Bonivento D, Cutruzzola F, Bren KL, Brunori M (2005) J Biol Chem 280:25729-25734.
42. Capaldi AP, Shastry MC, Kleanthous C, Roder H, Radford SE (2001) Nat Struct Biol 8:68-72.
43. Teilum K, Maki K, Kragelund BB, Poulsen FM, Roder H (2002) Proc Natl Acad Sci USA 99:9807-9812.
44. Parker MJ, Spencer J, Clarke AR (1995) J Mol Biol 253:771-786.
45. Park SH, Shastry MC, Roder H (1999) Nat Struct Biol 6:943-947.
46. Bai Y (1999) Proc Natl Acad Sci USA 96:477-480.
47. Borgia A, Bonivento D, Travaglini-Allocatelli C, Di Matteo A, Brunori M (2006) J Biol Chem 281:9331-9336.