The relative order of helical propensity of amino acids changes with solvent environment

Proteins: Structure, Function and Genetics

Volumn 39, Issue 2, 2000, Pages 132-141

  Krittanai, Chartchai ^a   Johnson Jr , W Curtis ^a  

^a OREGON STATE UNIVERSITY   (United States)

Author keywords

Helical propensity; Peptides

Indexed keywords

SODIUM DIHYDROGEN PHOSPHATE;

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; CALCULATION; CONFORMATIONAL TRANSITION; PRIORITY JOURNAL; STATISTICAL MODEL; TITRIMETRY;

AMINO ACID SEQUENCE; AMINO ACIDS; CIRCULAR DICHROISM; METHANOL; MOLECULAR SEQUENCE DATA; OLIGOPEPTIDES; PROTEIN STRUCTURE, SECONDARY; REPRODUCIBILITY OF RESULTS; SOLVENTS; THERMODYNAMICS; TITRIMETRY; WATER;

EID: 0034192637     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000501)39:2<132::AID-PROT3>3.0.CO;2-2     Document Type: Article

References (72)

1. Anfinsen CB, Haber E, Sela M, White FH. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc Natl Acad Sci USA 1961;47:1309-1314.
2. Pongor S, Szaley AA. Prediction of homology and divergence in the secondary structure of polypeptides. Proc Natl Acad Sci USA 1985;82:366-370.
3. Sweet RM. Evolutionary similarity among peptide segments is a basis for prediction of protein folding. Biopolymers 1986;25:1565-1577.
4. Nishikawa K, Ooi T. Amino acid sequence homolog applied to the prediction of protein secondary structure, and joint prediction with existing methods. Biochim Biophys Acta 1986;871:45-54.
5. Levin JM, Robson B, Garnier J. An algorithm for secondary structure determination in proteins based on sequence simulation. FASEB Lett 1986;205:303-308.
6. Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJE. Prediction of protein secondary structure and active sites using alignment of homologous sequence. J Mol Biol 1987;194:957-961.
7. Edelman J, White SH. Linear optimization of predictors for secondary structure application to transbilayer segments of membrane proteins. J Mol Biol 1989;210:195-209.
8. Qian N, Sejnowski TJ. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 1988; 202:865-884.
9. Holley LH, Karplus M. Protein secondary structure prediction with a neural network. Proc Natl Acad Sci USA 1989;86:152-156.
10. Stolorz P, Lapedes A, Xia Y. Predicting protein secondary structure using neural net and statistical methods. J Mol Biol 1992;225: 363-377
11. Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
12. Lim VI. Structural principles of the globular organization of protein chains: a stereochemical theory of globular protein secondary structure. J Mol Biol 1974;88:857-872.
13. Lim VI. Algorithms for prediction of α-helices and β-structural regions in globular proteins. J Mol Biol 1974;88:873-894.
14. Burgess AW, Ponnuswanvy PK, Scheraga HA. Analysis of conformations of amino acid residues and prediction of backbone topography in proteins. Israel J Chem 1974;12:239-286.
15. Chou PY, Fasman GD. Conformational parameters for amino acids in helical β-sheets, and random coil regions calculated from proteins. Biochemistry 1974;13:211-222.
16. Chou PY, Fasman GD. Prediction of protein conformation. Biochemistry 1974;13:222-245.
17. Chou PY, Fasman GD. β-Turns in proteins. J Mol Biol 1977;115: 135-175.
18. Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence Adv Enzymol 1978;47:45-148.
19. Chou PY, Fasman GD. Empirical predictions of protein conformation. Ann Rev Biochem 1978;47:251-276.
20. Chou PY, Fasman GD. Prediction of β-turns. Biophys J 1979;26: 367-400.
21. Gamier J, Osguthorpe DJ, Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978;120:97-120.
22. Garnier J, Levin JM, Gibrat JF, Biou V. Secondary structure prediction and protein design. Biochem Soc Symp 1994;57:11-24.
23. Salzberg S, Cost S. Predicting protein secondary structure with a nearest-neighbor algorithm. J Mol Biol 1992;227:371-374.
24. Yi T-M, Lander ES. Protein secondary structure prediction using nearest-neighbor methods. J Mol Biol 1993;232:1117-1129.
25. Hayward S, Collins JF. Limits on α-helix prediction with neural network models. Proteins 1992;14:372-381.
26. Wojcik J, Altmann KH, Scheraga HA. 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 1990;30:121-134.
27. Merutka G, Lipton W, Shalongo W, Park S-H, Stellwagen E. Effect of central-residue replacements on the helical stability of a monomeric peptide. Biochemistry 1990;29:7511-7515.
28. Lyu PC, Liff MI, Marky LA, Kallenbach NE. Side chain contributions to the stability of α-helical structure in peptides. Science 1990;250:669-673.
29. Park S-H, Shalongo W, Stellwagen E. Residue helix parameters obtained from dichroic analysis of peptides of defined sequence. Biochemistry 1993;32:7048-7053.
30. Park S-H, Shalongo W, Stellwagen E. Modulation of the helical stability of a model peptide by ionic residues. Biochemistry 1993;32:12901-12905.
31. Munoz V, Serrano L. Elucidating the folding problem of helical peptides using empirical parameters. Nat Struct Biol 1994;6:399-409.
32. Chakrabartty A, Kortemme T, Baldwin RL. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 1994;3:843-852.
33. Rohl CA, Chakrabartty A, Baldwin RL. Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol. Protein Sci 1996;5: 2623-2637.
34. Myers JK, Pace CN, Scholtz JM. A direct comparison of helix propensity in proteins and peptides. Proc Natl Acad Sci USA 1997;94:2833-2837.
35. Myers JK, Pace CN, Seholtz JM. Helix propensities are identical in proteins and peptides. Biochemistry 1997;36:10923-10929.
36. Pace, C.N., Scholtz, J.M. A helix propensity scale based on experimental studies of peptides and proteins. Biophys J 1998;75: 422-427.
37. Yang J, Spek EJ, Gong Y, Zhou H, Kallenbach NR. The role of context on α-helix stabilization: host-guest analysis in a mixed background peptide model. Protein Sci 1997;6:1264-1272.
38. 1. Protein Sci 1998;7:383-388.
39. O'Neil KT, DeGrado WF. A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids. Science 1990,250:646-652.
40. Horovitz A, Matthews JM, Fersht AR. α-Helix stability in proteins. II. Factors that influence stability at an internal position. J Mol Biol 1992;227:560-568.
41. Blaber M, Zhang X, Matthews BW. Structural basis of amino acid α-helix propensity. Science 1993;260:1637-1640.
42. Blaber M, Zhang X, Lindstrom JD, Pepiot SD, Baase WA, Matthews BW. Determination of α-helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme. J Mol Biol 1994;235:600-624.
43. Li S-C, Deber CM. Peptide environment specifies conformation. J Biol Chem 1993;268:22975-22978.
44. Li S-C, Deber CM. A measure of helical propensity for amino acids in membrane environments. Nat Struct Biol 1994;1:368-373.
45. Zhong L, Johnson WC Jr. Environmental affects of amino acid preference for secondary structure. Proc Natl Acad Sci USA 1992;89:4462-4465.
46. Waterhous DV, Johnson WC Jr. Importance of environment in determining secondary structure in proteins. Biochemistry 1994; 33:2121-2128.
47. Avbelj F, Moult J. Role of electrostatic screening in determining protein main chain conformational preferences. Biochemistry 1995;34:755-764.
48. Hol WGJ The role of the α-helix dipole in protein function and structure. Prog Biophys Mol Biol 1987;45:149-195.
49. Sali D, Bycroft M, Fersht AR. Stabilization of protein structure by interactions of α-helix dipole with a charged side-chain. Nature 1988;335:740-743.
50. Serrano L, Fersht AR. Capping and α-helix stability. Nature 1989;342:296-299.
51. Armstrong KM, Baldwin RL. Charged histidine affects α-helix stability at all positions in the helix by interacting with the backbone charges. Proc Natl Acad Sci USA 1993;90:11337-11340.
52. Padmanabhan S, Baldwin RL. Straight-chain nonpolar amino acids are good helix-formers in water. J Mol Biol 1991;219:135-137.
53. Creamer TP, Rose GD. α-helix-forming propensities in peptides and proteins. Proteins 1994;19:85-97.
54. Lee KH, Xie D, Freire E, Amzel LM. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins 1994;20:68-84.
55. Wang J, Purisima EO. Analysis of thermodynamic determinants in helix propensities of nonpolar amino acids through a novel free energy calculation. J Am Chem Soc 1996;118:995-1001.
56. Padmanabhan S, York EJ, Stewart JM, Baldwin RL. Helix propensities of basic amino acids increase with the length of the side-chain. J Mol Biol 1996;257:726-734.
57. Stapley BJ, Doig AJ. Free energies of amino acid side-chain rotamers in α-helices, β-sheets and α-helix N-caps. J Mol Biol 1997;272:456-464.
58. Hermans J, Anderson AG, Yun RH. Differential helix propensity of small apolar side chains studied by molecular dynamics simulations. Biochemistry 1992;31:5646-5653.
59. Luque I, Mayorga OL, Freire E. Structure-based thermodynamic scale of α-helix propensities in amino acids. Biochemistry 1996;35: 13681-13688.
60. Atherton E, Sheppard RC. Solid phase peptide synthesis. Oxford, UK: IRL Press at Oxford University Press; 1989.
61. Chen GC, Yang JT. Two point calibration of circular dichrometer with d-10-camphorsulfonic acid. Anal Lett 1977;10:1195-1207.
62. Elwell ML. Stability of phage T4 lysozymes. Ph.D. thesis, Department of Chemistry, University of Oregon, 1976.
63. Chakrabartty A, Kortemme T, Padmanabhan S, Baldwin RL. Aromatic side-chain contributions to far-ultraviolet circular dichroism of helical peptides and its effect on measurement of helix propensities. Biochemistry 1993;32:5560-5565.
64. Woody RW. Aromatic side-chain contributions to the far ultraviolet circular dichroism of peptides and proteins. Biopolymers 1978;17:1451-1467.
65. Krittanai C, Johnson WC, Jr. Correcting the circular dichroism spectra of peptides for contributions of absorbing side chains. Anal Biochem 1997;253:57-64.
66. Johnson WC, Jr. Analysis of circular dichroism spectra. In: Brand L, Johnson ML, editors. Methods in enzymology. San Diego, CA: Academic Press; 1992. p 426-447.
67. Henry ER, Hofrichter J. Singular value decomposition: application to analysis of experimental data. In: Brand L, Johnson ML, editors. Methods in enzymology. San Diego, CA: Academic Press; 1992. p 129-191.
68. Qian H, Schellman JA. Helix-coil theories: a comparative study for finite length polypeptides. J Phys Chem 1992;96:3987-3994.
69. Lifson S, Roig A. On the theory of helix-coil transition in polypeptides. J Chem Phys 1961;34:1963-1974.
70. Chou PY. Prediction of protein structural classes from amino acid compositions. In: Fasman GD, editor. Prediction of protein structure and the principles of protein conformation. New York and London: Plenum Press; 1989. p 549-565.
71. Williams RW, Chang A, Juretic D, Loughran S. Secondary structure predictions and medium range interactions. Biochim Biophys Acta 1987;916:200-204.
72. Karplus PA. Hydrophobicity regained. Protein Sci 1997;6:1302-1307.