Interactions between a helical residue and tertiary structures: Helix propensities in small peptides and in native proteins

Journal of Molecular Biology

Volumn 261, Issue 2, 1996, Pages 279-288

  Qian, Hong ^a,b   Chan, Sunney I ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Helix stability; Hydrogen exchange; Local fluctuation; Minimal frustration; Protein folding

Indexed keywords

AMINO ACID; AMPHOPHILE; PROTEIN; SYNTHETIC PEPTIDE;

ARTICLE; ENTHALPY; ENTROPY; HYDROGEN BOND; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS;

EID: 0030590219     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0459     Document Type: Article

References (39)

1. Bai, Y., Milne, J. S., Mayne, L. & Englander, S. W. (1994). Protein stability parameters measured by hydrogen exchange. Proteins: Struct. Funct. Genet. 20, 1-14.
2. Ben-Naim, A. (1991). The role of hydrogen bonds in protein association. J. Phys. Chem. 95, 1437-1444.
3. Bierzynski, A., Kim, P. S. & Baldwin, R. L. (1982). A salt bridge stabilizes the helix formed by isolated C-peptide of RNAse A. Proc. Natl Acad. Sci. USA, 79, 2470-2474.
4. Blaber, M., Zhang, X. J. & Matthews, B. W. (1993). Structural basis of amino acid α helix propensity. Science, 260, 1637-1640.
5. Blaber, M., Zhang, X. J., Lindstrom, J. D., Pepiot, S. D., Baase, W. A. & Matthews, B. W. (1994). Determination of α-helix propensity within the context of a folded protein: sites 44 and 131 in bacteriophage T4 lysozyme. J. Mol. Biol. 235, 600-624.
6. Bryngelson, J. D. & Wolynes, P. G. (1987). Spin glasses and the statistical mechanics of protein folding. Proc. Natl Acad. Sci. USA, 84, 7524-7528.
7. Chakrabartty, A. & Baldwin, R. L. (1995). Stability of α-helices. Advan. Protein Chem. 46, 141-176.
8. Chakrabartty, A., Schellman, J. A. & Baldwin, R. L. (1991). Large differences in the helix propensities of alanine and glycine. Nature, 351, 586-588.
9. Chakrabartty, A., Kortemme, T. & Baldwin, R. L. (1994). Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interaction. Protein Sci. 3, 843-852.
10. Connelly, P. R., Varadarajan, R., Sturtevant, J. M. & Richards, F. M. (1990). Thermodynamics of protein-peptide interactions in the ribonuclease S system studied by titration calorimetry. Biochemistry, 29, 6108-6114.
11. Connelly, P. R., Aldape, R. A., Bruzzese, F. J., Chambers, S. P., Fitzgibbon, M. J., Flemming, M. A., Itoh, S., Livingston, D. J., Navia, M. A., Thompson, J. A. & Wilson, K. P. (1994). Enthalpy of hydrogen bond formation in a protein-ligand binding reaction. Proc. Natl Acad. Sci. USA, 91, 1964-1968.
12. Creamer, T. P. & Rose, G. D. (1992). Side-chain entropy opposes α-helix formation but rationalizes experimentally determined helix-forming propensities. Proc. Natl Acad. Sci. USA, 89, 5937-5941.
13. Creamer, T. P. & Rose, G. D. (1994). α-Helix-forming propensities in peptides and proteins. Proteins: Struct. Funct. Genet. 19, 85-97.
14. Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133-7155.
15. Dill, K. A. & Shortle, D. (1991). Denatured states of proteins. Annu. Rev. Biochem. 60, 795-825.
16. Eberhardt, E. S. & Raines, R. T. (1994). Amide-amide and amide-water hydrogen bonds: implications for protein folding and stability. J. Am. Chem. Soc. 116, 2149-2150.
17. Editorial (1994). The nature of the α-helix. Nature Struct. Biol. 1, 343-344.
18. Eisenberg, D., Weiss, R. M. & Terwilliger, T. C. (1984). The hydrophobic moment detects periodicity in protein hydrophobicity. Proc. Natl Acad. Sci. USA, 81, 140-144.
19. Englander, S. W. & Kallenbach, N. R. (1983). Hydrogen exchange and structural dynamics of proteins and nucleic acids. Quart. Rev. Biophys. 16, 521-655.
20. Goodman, E. M. & Kim, P. S. (1991). Periodicity of amide proton exchange rates in a coiled-coil zipper peptide. Biochemistry, 30, 11615-11620.
21. Kuwajima, K., Semisotnov, G. V., Finkelstein, A. V., Sugai, S. & Ptitsin, O. B. (1993). Secondary structure of global proteins at the early stages in protein folding. FEBS Letters, 334, 265-268.
22. Lifson, S. & Roig, A. (1961). On the theory of helix-coil transition in polypeptides. J. Chem. Phys. 34, 1963-1974.
23. Lim, W. A. & Sauer, R. T. (1989). Alternative packing arrangements in the hydrophobic core of λ repressor. Nature, 339, 31-36.
24. Lockhart, D. J. & Kim, P. S. (1992). Internal Stark effect measurements of the electric field at the amino terminus of an α-helix. Science, 257, 947-951.
25. Lockhart, D. J. & Kim, P. S. (1993). Electrostatic screening of charge and dipole interactions with the helix backbone. Science, 260, 198-202.
26. Lumry, R., Biltonen, R. & Brandts, J. F. (1966). Validity of the "two-state" hypothesis for conformational transitions of proteins. Biopolymers, 4, 917-944.
27. + salt bridges in short peptides of de novo design. Proc. Natl Acad. Sci. USA, 84, 8898-8902.
28. Marqusee, S. & Sauer, R. T. (1994). Contributions of hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in λ repressor. Protein Sci. 3, 2217-2225.
29. O'Neil, K. T. & Degrado, W. F. (1990). A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science, 250, 646-651.
30. Qian, H. (1993). Single-residue substitution in homopolypeptides: perturbative helix-coil theory at a single site. Biopolymers, 33, 1605-1616.
31. Qian, H. (1994). A thermodynamic model for helix-coil transition coupled to dimerization of short coiled-coil peptides. Biophys. J. 67, 349-355.
32. Qian, H. (1996). Prediction of α-helices in proteins based on thermodynamic parameters from solution chemistry. J. Mol. Biol. 256, 663-666.
33. Qian, H. & Hopfield J. J. (1996). Entropy-enthalpy compensation: perturbation and relaxation in thermodynamic systems. J. Chem. Phys. In the press.
34. Qian, H. & Schellman, J. A. (1992). Helix-coil theories: a comparative study for finite length polypeptides. J. Phys. Chem. 96, 3987-3994.
35. Qian, H., Mayo, S. L. & Morton, A. (1994). Protein hydrogen exchange: quantitative analysis by a two-process model. Biochemistry, 33, 8167-8171.
36. 15N-labeled helical peptides measured by isotope-edited NMR. Biochemistry, 33, 7760-7767.
37. Schellman, J. A. (1958). The factors affecting the stability of hydrogen-bonded polypeptide structures in solution. J. Phys. Chem. 62, 1485-1494.
38. Scholz, J. M., Qian, H., Robbins, V. H. & Baldwin, R. L. (1993). The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide. Biochemistry, 32, 9668-9676.
39. Woodward, C., Simon, I. & Tüchsen, (1982). Hydrogen exchange and the dynamics structure of proteins. Mol. Cell Biochem. 48, 135-160.