Loop length, intramolecular diffusion and protein folding

Nature Structural Biology

Volumn 4, Issue 11, 1997, Pages 939-946

  Viguera, Ana Rosa ^a   Serrano, Luis ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

FODRIN; GLYCINE;

ARTICLE; ESCHERICHIA COLI; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE;

AMINO ACID SEQUENCE; DIFFUSION; GLYCINE; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SPECTRIN; SRC HOMOLOGY DOMAINS; THERMODYNAMICS;

ESCHERICHIA COLI;

EID: 0030663205     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb1197-939     Document Type: Article

References (40)

1. Jackson, S.E. & Fersht, A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30, 10428-10435 (1991).
2. Alexander, P., Orban, J. & Bryan, P. Kinetic analysis of folding and unfolding of the 56 amino acid IgG-binding domain of Streptococcal protein G. Biochemistry 31, 7243-7248 (1992).
3. Sosnick, T.R., Mayne, L., Miller, R. & Englander, S.W. The barriers in protein folding. Nature Struct. Biol. 1, 149-156 (1992).
4. Viguera, A.R., Martínez, J.C., Filimonov, V.V., Mateo, P.L. and Serrano, L. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry 33, 2142-2150 (1994).
5. Schindler, T., Herrler, M., Marahiel, M.A. & Schmid, F.X. Extremely rapid protein folding in the absence of intermediates. Nature Struct. Biol. 2, 663-673 (1995).
6. Huang, G.S. & Oas, T.G. Submillisecond folding of monomeric λ repressor. Proc. Nat. Acad. Sci. USA. 92, 6878-6882 (1995).
7. Villegas, V. et al. Evidence for a two-state transition in the folding process of the activation domain of human procarboxypeptidase A2. Biochemistry 34, 15105-15110 (1995).
8. Kragelund, B.B., et al. Fast and one-step folding of closely and distantly related homologous proteins of a four-helix bundle family. J. Mol. Biol. 256, 187-200 (1996).
9. Fersht, A.R. Characterizing transition states in protein folding: an essential step in the puzzle. Curr. Opin. Struct. Biol. 5, 79-84 (1995).
10. Lopez-Hernandez, E. & Serrano, L. Structure of the transition state for folding of the 129aa protein, CheY, resembles that of a smaller protein, Cl-2. Folding & Design, 1, 43-55 (1996).
11. Muñoz, V. & Serrano, L. Local vs non-local interactions in protein folding and stability. An experimentalist point of view. Folding & Design 1, R71-R77 (1996).
12. Itzhaki, L.S., Otzen, D.E. & Fersht, A.R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260-288 (1995).
13. Viguera, A.R., Wilmanns, M. & Serrano, L. Different folding transition states could result in the some native structure. Nature Struct. Biol. 3, 874-880 (1996).
14. Abkevich, V.I., Gutin, A.M. & and Shakhnovich, E.I. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 33, 10026-10036 (1994)
15. Viguera, A.R., Villegas, V., Aviles, F.X. & Serrano, L. Favourable native-like helical local interactions can accelerate protein folding. Folding & Design 2, 23-3-. (1997).
16. Virtudes, V., Viguera, A.R., Aviles, F.X. & Serrano, L. Stabilisation of proteins by rational design of α-helix stability using helix/coil transition theory. Folding & Design 1,29-34 (1996).
17. Itzhaki, L.S., Otzen, D.E. & Fersht, A.R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260-288 (1995).
18. Viguera, A.R., Jimenez, M.A., Rico, M. & Serrano, L. Conformational analysis of peptides corresponding to β-hairpins and a β-sheet that represent the entire sequence of α-spectrin SH3-domain. J. Mol. Biol. 255, 507-521 (1995).
19. Sibanda, B.L. & Thornton, J.M. Accomodating sequence changes in β-hairpins in proteins. J. Mol. Biol. 229, 428-447 (1993).
20. Musacchio, A., M. E. M. Noble, M. E. M, Pautit, R. Wierenga, R. & Saraste, M. Crystal structure of a Src-homology 3 (SH3) domain. Nature 359, 851-855 (1992).
21. 15N-NMR assignment and solution structure of the SH3 domain of spectrin. Comparison with the crystal structure. J. of Biomol. NMR. (1997) in the press.
22. Viguera, A.R., Martinez, J.C., Filimonov, V.V., Mateo, P.L. & Serrano, L. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state transition. Biochemistry 33, 2142-2150 (1994).
23. Viguera, A.R., Blanco, F.J. & Serrano, L. The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics. J. Mol. Biol. 247, 670-681 (1995).
24. Chan, H.S. & Dill, K.A. Intrachain loops in polymers. J.. Chem. Phys. 90, 492-509 (1988)
25. Nagi, D.A. & Regan L. An inverse correlation between loop length and stability in a four-helix bundle protein. Folding & Design 2, 67-76 (1997).
26. Onuchic, J.N., Socci, N.D., Luthey-Schulten, Z. & Wolynes, P.G. Protein folding funnels: the nature of the transition state ensemble. Folding & Design 1, 441-450 (1996).
27. Karplus,M & Weaver, D.L. Protein folding dynamics: the diffusion-collision model and experimental data. Protein-Sci. 3, 650-668 (1994).
28. Sosnick, T.R., Mayne L. & Englander S.W. Molecular Collapse: The rate-limiting step in two-state cytochrome-c folding Proteins 24, 413-426 (1996).
29. Fersht, A.R., Itzhaki, L.S., elMasry, N., Matthews, J.M. & Otzen, D.E. . Single versus parallel pathways of protein folding and fractional formation of structure in the transition state. Proc. Natl. Acad. Sci. USA. 91, 10426-10429 (1994).
30. Kunkel, T.A. Rapid and efficient site-directed mutagenesis without phenotypic selection. Proc. Natl. Acad. Sci. U.S.A. 82, 488-492 (1985).
31. Gill S.C. & von Hippel. P.H. Calculation of protein extinction coefficients from amino acid sequence data. Anal. Biochem. 182, 319-326 (1989).
32. Marion, D. & Wüthrich, K. Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurement of proton-proton spin-spin coupling constants. Biochem. Biophys. Res. Comm. 113, 967-974 (1983).
33. Aue, W.P., Bartholdi, E. & Ernst, R.R. Two dimensional spectroscopy. Application to nuclear magnetic resonance. J. Chem. Phys. 64, 2229-2246 (1976).
34. Piantini, U., Sørensen, O. W., & Ernst, R. R. Multiple quantum filters for elucidating NMR coupling networks. J. Amer. Chem. Soc. 104, 6800-6801 (1982).
35. Kumar, A., Ernst, R.R. & Wüthrich, K. A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Comm, 95, 1-6 (1980)
36. Bax, A., & Davis, D. G. MLEV-17 based two-dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson. 65, 355-360 (1985).
37. Wüthrich, K. In NMR of proteins and nucleic acids (John Wiley & sons. New York; 1986).
38. Prieto, J., Wilmanns, M., Jimenez, M.A., Rico, M. & Serrano, L. Non-native interactions in protein folding and stability: Introducing a helical tendency in the all β-sheet α-spectrin SH3 domain. J. Mol. Biol. 268, 760-778 (1997).
39. Johnson, C.M. & Fersht, A.R. Protein stability as a function of denaturant concentration: The thermal stability of barnase in the presence of urea. Biochemistry 34, 6795-6804 (1995).
40. Pace, C.N. Determination and analysis of urea and guanidium hydrochloride denaturation curves. Meth. Enz. 131, 266-280 (1986).