Helix-coil transitions re-visited

Biophysical Chemistry

Volumn 101-102, Issue , 2002, Pages 255-265

  Scheraga, Harold A ^a   Vila, Jorge A ^b   Ripoll, Daniel R ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSIDAD NACIONAL DE SAN LUIS   (Argentina)

Author keywords

Equilibrium and kinetic treatment; Helix forming propensity; Helix probability profiles; Polyamino acids; Random copolymers; Role of hydration

Indexed keywords

ALANINE; COPOLYMER; GLUTAMINE; LYSINE; POLYMER; WATER; AMINO ACID; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CALCULATION; EQUILIBRIUM CONSTANT; KINETICS; MOLECULAR BIOLOGY; PRIORITY JOURNAL; SOLUBILITY; CHEMISTRY; MOLECULAR GENETICS; PROTEIN FOLDING;

AMINO ACID SEQUENCE; AMINO ACIDS; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; PROTEINS;

EID: 0037058898     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(02)00175-8     Document Type: Article

References (78)

1. Poland D., Scheraga H.A. Theory of Helix-Coil Transitions in Biopolymers. 1970;Academic Press, New York.
2. Hao M.-H., Scheraga H.A. Statistical thermodynamics of protein folding: sequence dependence. J. Phys. Chem. 98:1994;9882-9893.
3. Gō N., Gō M., Scheraga H.A. Molecular theory of the helix-coil transition in polyamino acids. I. Formulation. Proc. Natl. Acad. Sci. USA. 59:1968;1030-1037.
4. Gō M., Gō N., Scheraga H.A. Molecular theory of the helix-coil transition in polyamino acids. II. Numerical evaluation of s and σ for polyglycine and poly-L-alanine in the absence (for s and σ) and presence (for σ) of solvent. J. Chem. Phys. 52:1970;2060-2079.
5. Gō M., Gō N., Scheraga H.A. Molecular theory of the helix-coil transition in polyamino acids. III. Evaluation and analysis of s and σ for polyglycine and poly-L-alanine in water. J. Chem. Phys. 54:1971;4489-4503.
6. Gō M., Hesselink F.T., Gō N., Scheraga H.A. Molecular theory of the helix-coil transition in poly(amino acids). IV. Evaluation and analysis of s for poly(L-valine) in the absence and presence of water. Macromolecules. 7:1974;459-467.
7. Gō M., Scheraga H.A. Molecular theory of the helix-coil transition in polyamino acids. V. Explanation of the different conformational behavior of valine, isoleucine and leucine in aqueous solution. Biopolymers. 23:1984;1961-1977.
8. Pain R.H., Robson B. Analysis of the code relating sequence to secondary structure in proteins. Nature. 227:1970;62-63.
9. Lewis P.N., Scheraga H.A. Predictions of structural homologies in cytochrome c proteins. Arch. Biochem. Biophys. 144:1971;576-583.
10. Burgess A.W., Ponnuswamy P.K., Scheraga H.A. Analysis of conformations of amino acid residues and prediction of backbone topography in proteins. Israel J. Chem. 12:1974;239-286.
11. Robson B., Pain R.H. Analysis of the code relating sequence to conformation in globular proteins. Biochem. J. 141:1974;869-904.
12. Chou P.Y., Fasman G.D. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry. 13:1974;211-245.
13. Maxfield F.R., Scheraga H.A. Status of empirical methods for the prediction of protein backbone topography. Biochemistry. 15:1976;5138-5153.
14. Blout E.R., Karlson R.H. Polypeptides. III. The synthesis of high molecular weight poly-γ-benyl-L-glutamates. J. Am. Chem. Soc. 78:1956;941-946.
15. Doty P., Bradbury J.H., Holtzer A.M. Polypeptides. IV. The molecular weight, configuration and association of poly-γ-benyl-L-glutamate in various solvents. J. Am. Chem. Soc. 78:1956;947-954.
16. Katchalski E., Sela M. Synthesis and chemical properties of poly-α-amino acids. Adv. Protein Chem. 13:1958;243-492.
17. Matthews B.W. Structural basis of protein stability and DNA-protein interaction. Harvey Lect. 81:1987;33-51.
18. Scheraga H.A. The intrinsic tendency toward α-helix formation. Vijayan M., Yathindra N., Kolaskar A.S. Perspectives in Structure Biology. 1999;275-292 Indian Academy of Sciences, Bangalore.
19. Scheraga H.A. On the dominance of short-range interactions in polypeptides and proteins. Prague Symp., Pure Applied Chem. 36:1973;1-8.
20. Scheraga H.A. Use of random copolymers to determine the helix-coil stability constants of the naturally occurring amino acids. Pure Applied Chem. 50:1978;315-324.
21. Ramachandran G.N., Ramakrishnan C., Sasisekharan V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7:1963;95-99.
22. Schellman J.A. Thermodynamics of urea solutions and the heat of formation of the peptide hydrogen bond. Compt. Rend. Trav. Lab. Carlsberg Sér. Chim. 29:1955;223-259.
23. Zimm B.H., Bragg J.K. Theory of the phase transition between helix and random coil in polypeptide chains. J. Chem. Phys. 31:1959;526-535.
24. Lifson S., Roig A. On the theory of helix-coil transition in polypeptides. J. Chem. Phys. 34:1961;1963-1974.
25. Poland D.C., Scheraga H.A. Comparison of theories of the helix-coil transition in polypeptides. J. Chem. Phys. 43:1965;2071-2074.
26. Bixon M., Scheraga H.A., Lifson S. Effect of hydrophobic bonding on the stability of poly-L-alanine helices in water. Biopolymers. 1:1963;419-429.
27. Poland D.C., Scheraga H.A. Statistical mechanics of non-covalent bonds in polyamino acids. IV. Matrix treatment of hydrophobic bonds in the random coil and of the helix-coil transition for chains of arbitrary length. Biopolymers. 3:1965;315-334.
28. Poland D.C., Scheraga H.A. Statistical mechanics of non-covalent bonds in polyamino acids. III. Interhelical hydrophobic bonds in short chains. Biopolymers. 3:1965;305-313, 335-367.
29. Vásquez M., Scheraga H.A. Effect of sequence-specific interactions on the stability of helical conformations in polypeptides. Biopolymers. 27:1988;41-58.
30. Serrano L., Neira J.-L., Javier S., Fersht A.R. Effect of alanine versus glycine in α-helices on protein stability. Nature. 356:1992;453-455.
31. Doig A.J., Chakrabartty A., Klingler T.M., Baldwin R.L. Determination of free energies of N-capping in α-helices by modification of the Lifson-Roig helix-coil theory to include N- and C-capping. Biochemistry. 33:1994;3396-3403.
32. Cochran D.A.E., Doig A.J. Effect of the N2 residue on the stability of the α-helix for all 20 amino acids. Protein Sci. 10:2001;1305-1311.
33. Lewis P.N., Gō N., Gō M., Kotelchuck D., Scheraga H.A. Helix probability profiles of denatured proteins and their correlation with native structures. Proc. Natl. Acad. Sci. USA. 65:1970;810-815.
34. Gō N., Lewis P.N., Gō M., Scheraga H.A. A model for the helix-coil transition in specific-sequence copolymers of amino acids. Macromolecules. 4:1971;692-709.
35. Tanaka S., Scheraga H.A. Statistical mechanical treatment of protein conformation. 4. A four-state model for specific-sequence copolymers of amino acids. Macromolecules. 9:1976;142-182, 812-833 S., Tanaka, H.A. Scheraga, Statistical mechanical treatment of protein conformation. 6. Elimination of empirical rules for prediction by use of a high-order probability. Correlation between the amino acid sequences and conformations for homologous neurotoxin proteins. 10 (1977), 9-20, 305-316.
36. Wako H., Saitô N., Scheraga H.A. Statistical mechanical treatment of α-helices and extended structures in proteins with inclusion of short- and medium-range interactions. J. Protein Chem. 2:1983;221-249.
37. Marqusee S., Robbins V.H., Baldwin R.L. Unusually stable helix formation in short alanine-based peptides. Proc. Natl. Acad. Sci. USA. 86:1989;5286-5290.
38. O'Neil K.T., De Grado W.F. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science. 250:1990;646-651.
39. Lyu P.C., Liff M.I., Marky L.A., Kallenbach N.R. Side chain contributions to the stability of α-helical structure in peptides. Science. 250:1990;669-673.
40. Merutka G., Lifton W., Shalongo W., Park S.H., Stellwagen E. Effect of central-residue replacements on the helical stability of a monomeric peptide. Biochemistry. 29:1990;7511-7515.
41. Padmanabhan S., Marqusee S., Ridgeway T., Laue T.M., Baldwin R.L. Relative helix-forming tendencies of non-polar amino acids. Nature. 344:1990;268-270.
42. Vila J., Williams R.L., Grant J.A., Wojcik J., Scheraga H.A. The intrinsic helix-forming tendency of L-alanine. Proc. Natl. Acad. Sci. USA. 89:1992;7821-7825.
43. Williams L., Kather K., Kemp D.S. High helicities of Lys-containing, Ala-rich peptides are primarily attributable to a large, context-dependent Lys stabilization. J. Am. Chem. Soc. 120:1998;11033-11043.
44. Lewis P.N., Scheraga H.A. Prediction of structural homology between bovine α-lactalbumin and hen egg white lysozyme. Arch. Biochem. Biophys. 144:1971;584-588.
45. Scholtz J.M., York E.J., Stewart J.M., Baldwin R.L. A neutral water-soluble, α-helical peptide: the effect of ionic strength on the helix-coil equilibrium. J. Am. Chem. Soc. 113:1991;5102-5104.
46. Ingwall R.T., Scheraga H.A., Lotan N., Berger A., Katchalski E. Conformational studies of poly-L-alanine in water. Biopolymers. 6:1968;331-368.
47. Scheraga H.A. Effect of side chain-backbone electrostatic interactions on the stability of α-helices. Proc. Natl. Acad. Sci. USA. 82:1985;5585-5587.
48. Lehman G.W., McTague J.P. Melting of DNA. J. Chem. Phys. 49:1968;3170-3179.
49. Poland D., Scheraga H.A. The Lifson-Allegra theories of the helix-coil transition for random copolymers: comparison with exact results and extension. Biopolymers. 7:1969;887-908.
50. Lifson S. Theory of the helix-coil transition in DNA considered as a copolymer. Biopolymers. 1:1963;25-32.
51. Allegra G. The calculation of average functions of local conformations for a non-interacting copolymer system with neighbor interactions. J. Polymer Sci. C16:1967;2815-2824.
52. Von Dreele P.H., Poland D., Scheraga H.A. Helix-coil stability constants for the naturally occurring amino acids in water. I. Properties of copolymers and approximate theories. Macromolecules. 4:1971;396-407.
53. Schwarz G. Zur kinetik der helix-coil-umwandlung von polypeptiden in lösung. Ber. Bunsenges. Physik. Chem. 68:1964;843-850.
54. Schwarz G. On the kinetics of the helix-coil transition of polypeptides in solution. J. Mol. Biol. 11:1965;64-77.
55. McQuarrie D.A., McTague J.P., Reiss H. Kinetics of polypeptide denaturation. Biopolymers. 3:1965;657-663.
56. Poland D., Scheraga H.A. Kinetics of the helix-coil transition in polyamino acids. J. Chem. Phys. 45:1966;2071-2090.
57. Buchete N.-V., Straub J.E. Mean first-passage time calculations for the coil-to-helix transition: the active helix Ising model. J. Phys. Chem. B. 105:2001;6684-6697.
58. Brooks C.L. III. Helix-coil kinetics: folding time scales for helical peptides from a sequential kinetic model. J. Phys. Chem. 100:1996;2546-2549.
59. Klimov D.K., Betancourt M.R., Thirumalai D. Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics. Folding Design. 3:1998;481-496.
60. Thompson P.A., Eaton W.A., Hofrichter J. Laser temperature jump study of the helix⇔coil kinetics of an alanine peptide interpreted with a 'kinetic zipper' model. Biochemistry. 36:1997;9200-9210.
61. Ooi T., Scott R.A., Vanderkooi G., Scheraga H.A. Conformational analysis of macromolecules. IV. Helical structures of poly-L-alanine, poly-L-valine, poly-β-methyl-L-aspartate, poly-γ-methyl-L-glutamate, and poly-L-tyrosine. J. Chem. Phys. 46:1967;4410-4426.
62. Némethy G., Gibson K.D., Palmer K.A., et al. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96:1992;6472-6484.
63. Wojcik J., Altmann K.H., Scheraga H.A. Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random Poly(hydroxybutylglutamine-co-S-methylthio-L-cysteine). Biopolymers. 30:1990;121-134.
64. Platzer K.E.B., Ananthanarayanan V.S., Andreatta R.H., Scheraga H.A. Helix-coil stability constants for the naturally occurring amino acids in water. IV. Alanine parameters from random poly(hydroxypropyl-glutamine-co-L-alanine). Macromolecules. 5:1972;177-187.
65. Vila J.A., Ripoll D.R., Scheraga H.A. Physical reasons for the unusual α-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc. Natl. Acad. Sci. USA. 97:2000;13075-13079.
66. Vila J.A., Ripoll D.R., Scheraga H.A. Influence of lysine content and pH on the stability of alanine-based co-polypeptides. Biopolymers. 58:2001;235-246.
67. Garcia A.E., Sanbonmatsu K.Y. Alpha helical stabilization by side chain shielding of backbone hydrogen bonds. Proc. Natl. Acad. Sci. USA. 99:2002;2782-2787.
68. Vila J., Williams R.L., Vasquez M., Scheraga H.A. Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor. Proteins: Struct. Funct. Genet. 10:1991;199-218.
69. Ripoll D.R., Vorobjev Y.N., Liwo A., Vila J.A., Scheraga H.A. Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides. J. Mol. Biol. 264:1996;770-783.
70. Ripoll D.R., Vila J.A., Villegas M.E., Scheraga H.A. On the pH-conformational dependence of the unblocked SYPYD peptide. J. Mol. Biol. 292:1999;431-440.
71. Ripoll D.R., Liwo A., Scheraga H.A. New developments of the electrostatically driven Monte Carlo method: test on the membrane-bound portion of melittin. Biopolymers. 46:1998;117-126.
72. HNα, in a globular protein. J. Mol. Biol. 180:1984;741-751.
73. Karplus M. Contact electron-spin coupling of nuclear magnetic moments. J. Chem. Phys. 30:1959;11-15.
74. Karplus M. Vicinal proton coupling in nuclear magnetic resonance. J. Am. Chem. Soc. 85:1963;2870-2871.
75. HNα coupling constants. J. Biomol. NMR. 7:1996;331-334.
76. 3amide. J. Am. Chem. Soc. 116:1994;8288-8293.
77. Shirley W.A., Brooks C.L. III. Curious structure in 'canonical' alanine-based peptides. Proteins: Struct. Funct. Genet. 28:1997;59-71.
78. Werner J.H., Dyer R.B., Fesinmeyer R.M., Andersen N.H. Dynamics of the primary processes of protein folding: helix nucleation. J. Phys. Chem. B 106:2002;487-494.