Favourable native-like helical local interactions can accelerate protein folding

Folding and Design

Volumn 2, Issue 1, 1997, Pages 23-33

  Viguera, Ana Rosa ^a   Villegas, Virtudes ^b   Avilés, Fxavier ^a   Serrano, Luis ^b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Kinetics; Mutants; Prediction; Protein stability; Thermoresistance; helix

Indexed keywords

BACTERIAL PROTEIN; MEMBRANE PROTEIN; METHYL ACCEPTING CHEMOTAXIS PROTEINS; METHYL-ACCEPTING CHEMOTAXIS PROTEINS; PRIMER DNA; SIGNAL TRANSDUCING ADAPTOR PROTEIN; TADA2L PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL MODEL; CHEMISTRY; CIRCULAR DICHROISM; GENETICS; HUMAN; KINETICS; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SITE DIRECTED MUTAGENESIS; TEMPERATURE; THERMODYNAMICS;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CIRCULAR DICHROISM; DNA PRIMERS; HUMANS; KINETICS; MEMBRANE PROTEINS; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; TEMPERATURE; THERMODYNAMICS; TRANSCRIPTION FACTORS;

EID: 0030623698     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(97)00003-5     Document Type: Article

References (48)

1. Biyngelson, J.D., Onuchic, J.N., Socci, N.D. & Wolynes, P.G. (1995). Funnels, pathways and the energy landscape of protein folding: a synthesis. Proteins 21, 167-195.
2. Karplus, M. & Šali, A. (1995). Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5,58-73.
3. Dill, K.A. (1994). Dominant forces in protein folding. Biochemistry 29, 7133-7155.
4. Munoz, V. & Serfano, L. (1995). Helix design, prediction and stability. Curr. Opin. Biotechnol. 6, 382-386.
5. Munoz, V. & Serrano, L (1996). Local versus nonlocal interactions in protein folding and stability - an experimentalist's point of view. Fold. Des. 1, R71-R77; 1359-0278-001-R0071.
6. Dyson, H.J. & Wright, P.E. (1993). Peptide conformation and protein folding. Curr. Opin. Struct. Biol. 3, 60-65.
7. Anfinsen, C.B. & Scheraga, H.A. (1975). Experimental and theoretical aspects of protein folding. Adv. Protein Chem. 29, 205-300.
8. Wetlaufer, D.B. (1973). Nucleation, rapid folding and globular intrachain regions in proteins. Proc. Nail. Acad. Sci. USA 70, 697-701.
9. Karplus, M. & Weaver, D.L (1976). Protein-folding dynamics. Nature 260,404-406.
10. Karplus, M. & Weaver, D.L. (1994). Protein folding dynamics. The diffusion-collision model and experimental data. Protein Sci. 3, 650-668.
11. Harrison, S.C. & Durbin, R. (1985). Is there a single pathway for the folding of a polypeptide chain? Proc. Natl. Acad. Sci. USA 82, 4028-4030.
12. Wright, P.E., Dyson, HJ. & Lerner, R.A. (1988). Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding. Biochemistry 27, 7167-7175.
13. Kim, P.S. & Baldwin, R.L. (1990). Intermediates in the folding reactions of small proteins. Annu. Rev. Biochem. 59, 631-660.
14. Dill, K.A., et al., & Chan H.S. (1995). Principles of protein folding. A perspective from simple exact models. Protein Sci. 4, 561-602.
15. Govindarajan, S. & Goldstein, R.A. (1995). Optimal local propensities for model proteins. Proteins 22,413-418.
16. Abkevich, V.l., Gutin, A.M. & Shakhnovich, E.I. (1995). Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. J. Mol. Biol. 252,460-471.
17. Unger, R. & Moult, J. (1996). Local interactions dominate folding in a simple protein model. J. Mol. Biol. 259, 988-994.
18. Shakhnovich, E.I & Gutin, A.M. (1990). Implications of thermodynamics of protein folding for evolution of primary sequences. Nature 346, 773-775.
19. Shakhnovich, EI. & Gutin, A.M. (1990). Enumeration of all compact conformations of copolymers with random sequence of links. J. Chem. Phys. 93,5967-5971.
20. Luthey-Schulten, Z., Ramirez, B.E. & Wolynes, P.G. (1995). Helix-coil, liquid crystal and spin glass transitions of a collapsed heteropolymer. J. Phys. Chem. 99, 2177-2185.
21. Saven, J.G. & Wolynes, P.G. (1996). Local conformational signals and the statistical thermodynamics of collapsed helical proteins. J. Mol. Biol. 257, 199-216.
22. Munoz, V., Cronet, P., López-Hernández, E. & Serrano, L (1996). Analysis of the effect of local interactions in protein stability. Fold. Des. 1, 167-178; 1359-0278-001-00167.
23. Villegas, V., Viguera, A.R., Avilés, F.X. & Serrano, L. (1996). Stabilization of proteins by rational design of a-helix stability using helix/coil transition theory. Fold. Des. 1, 29-34; 1359-0278-001-00029.
24. Villegas, V., et al., & Serrano, L. (1995). Evidence for a two-state transition in the folding process of the activation domain of human procarboxypeptidase A2. Biochemistry 34, 15105-15110.
25. Munoz, V. & Serrano, L. (1994). Elucidating the folding problem of helical peptides using empirical parameters. Wat Struct. Biol. 1, 399-409.
26. Munoz, V. & Serrano, L. (1995). Elucidating the folding problem of helical peptides using empirical parameters II. Helix macro dipole effects and rational modification of the helical content of natural peptides. J. Mol. Biol. 245, 275-296.
27. Munoz, V. & Serrano, L. (1996). Development of the multiple sequence approximation with the AGADIR model of α-helix formation. Comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers in press.
28. Vendrell, J., Billeter, M., Wider, G., Avilés, F.X. & Wütrich, K. (1991). The NMR structure of the activation domain isolated from procarboxypeptidase B. EMBO J. 10,11-15.
29. Guasch, A., Coll, M., Avilés, F.X. & Huber, R. (1992). Three dimensional structure of porcine pancreatic procarboxypeptidase A. A comparison of the A and B zymogens and their determinants for inhibition and activation. J. Mol. Biol. 224, 141-157.
30. Flimonov, V.V., Prieto, J., Mateo, P.L & Serrano, L. (1993). Thermodynamic analysis of the chemotactic protein from £. coli, CheY. Biochemistry 32, 12906-12921.
31. Muñoz, V., Lôpez, E. & Serrano, L. (1994). Kinetic characterization of the chemotactic protein from E. coli CheY. Kinetic analysis of the inverse hydrophobic effect. Biochemistry 33, 5858-5866.
32. López-Hernandez, E., Cronet, P., Serrano, L. & Mufioz, V. (1997). Folding kinetics of CheY mutants with enhanced native α-helix propensities. J. Mol. Biol. in press.
33. Fersht, A.R. (1995). Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl. Acad. Sci. USA 92,10869-10873.
34. Kragelund, B.B., et al., & Poulsen, F.M. (1996). Fast and one-step folding of closely and distantly related homologous proteins of a fourhelix bundle family. J. Mol. Biol. 256,187-200.
35. Böhm, G. & Jaenicke, R. (1994). Relevance of sequence statistics for the properties of extremophilic proteins. Int. J. Pept. Protein Res. 43, 97-106.
36. Querol, E., Perez-Pons, J.A. & Mozo-Villarias, A. (1996). Analysis of protein conformational characteristics related to thermostability. Protein Eng. 9, 265-271.
37. Pace, C.N. (1986). Determination and analysis of urea and guanidium hydrochloride denaturation curves. Methods Enzymol. 131, 226-280.
38. Serrano, L, Day, T. & Fersht, A.R. (1993). The step-wise mutation of barnase to binase and a procedure for engineering increased stability of proteins: an experimental analysis of the evolution of protein stability. J. Mol. Biol. 233,305-312.
39. Clakson, T., Gussow, D. & Jones, P.T. (1991). PCR: A Practical Approach. (McPerson, M.J., Quirke, P. & Taylor, G.R., eds). IRL Press, Oxford.
40. Sarkar, G. & Sommer, S.S. (1990). The "megaprimer" method of sitedirected mutagenesis. Biotechniques 8,404-407.
41. 15N-NMR assignment and solution structure of the chemotactic Escherichia coli Che Y protein. Eur. J. Biochem. 215, 573-585.
42. Gill, S.C. & Von Hippel, P.H. (1989). Calculation of protein extinction coefficients from amino acid sequence data. Analyt. Biochem. 182, 319-326.
43. Schindler, T., Herrler, M., Marahiel, M.A. & Schmid, F.X. (1995). Extremely rapid protein folding in the absence of intermediates. Nat. Struct. Biol. 2, 663-673.
44. Viguera, A.R., Martinez, J.C., Filimonov, V.V., Mateo, P.L. & Serrano, L. (1994). Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry 33, 2142-2150.
45. Jackson, S.E. & Fersht, A.R. (1991). Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30, 10428-10435.
46. Alexander, P., Orban, J. & Bryan, P. (1992). Kinetic analysis of folding and unfolding of the 56 amino acid IgG-binding domain of streptococcal protein G. Biochemistry 31, 7243-7248.
47. Sosnick, T.R., Mayne, L, Miller, R. & Englander, S.W. (1992). The barriers in protein folding. Wat Struct. Biol. 1, 149-156.
48. Huang, G.S. & Oas, T.G. (1995). Submillisecond folding of monomeric X. represser. Proc. Natl. Acad. Sci. USA 92, 6878-6882.