Dissecting α-helices: Position-specific analysis of α-helices in globular proteins

Proteins: Structure, Function and Genetics

Volumn 31, Issue 4, 1998, Pages 460-476

  Kumar, Sandeep ^a   Bansal, Manju ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

helix; Amino acid; Database; Secondary structure; Sequence; Structure

Indexed keywords

GLOBULAR PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY;

EID: 0032101291     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980601)31:4<460::AID-PROT12>3.0.CO;2-D     Document Type: Article

References (55)

1. Presta, L.G., Rose, G.D. Helix signals in proteins. Science 240:1632-1641, 1988.
2. Hol, W.G.J., Van Duijnen, P.T., Brendsen, H.J.C. The α-helix dipole and properties of proteins. Nature 273:443-446, 1978.
3. Hol, W.G.J., Hail, L.M., Sander, C. Dipoles of the α-helix and β-sheet: Their role in protein folding. Nature 294:532-536, 1981.
4. Hol, W.G. Effect of the α-helix dipole upon the functioning and structure of proteins and peptides. Adv. Biophys. 19:133-165, 1985.
5. Hol, W.G. The role of the α-helix dipole in protein function and structure. Prog. Biophys. Mol. Biol. 45:149-195, 1985.
6. Blagdon, D.E., Goodman, M. Mechanism of protein and polypeptide helix initiation. Biopolymers 14:241-245, 1975.
7. Wada, A., Nakamura, H. Nature of charge distribution in proteins. Nature, 293:757-758, 1981.
8. Warwicker, J., Watson, H.C. Calculation of the electric potential in the active-site cleft due to α-helix dipoles. J. Mol. Biol. 157:671-679, 1982.
9. Argos, P., Palau, J. Amino acid distribution in protein secondary structures. Int. J. Prot. Pept. Res. 19:380-393, 1982.
10. Richardson, J.S., Richardson, D.C. Amino acid preferences for specific locations at the ends of α-helices. Science 240:1648-1652, 1988.
11. Serrano, L., Fersht, A.R. Capping and α-helix stability. Nature 342:296-299, 1989.
12. Serrano, L., Neira, J.L., Sancho, J., Fersht, A.R. Effect of alanine versus glycine in α-helices on protein stability. Nature 256:453-456, 1992.
13. Lecomte, J.T.J., Moore, C.D. Helix formation in Apocytochrome-B5: The role of neutral histidine at the N-cap position. J. Am. Chem. Soc. 113:9663-9665, 1991.
14. Bell, J.A., Becktel, W.J., Sauer, C., Baase, W.A., Matthews, B.W. Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of 6 amino acid substitutions at Thr 59. Biochemistry 31:3590-3596, 1992.
15. Chakrabartty, A., Doig, A.J., Baldwin, R.L. Helix capping propensities in peptides parallel those in proteins. Proc. Natl. Acad. Sci. U.S.A. 90:11332-11336, 1993
16. Farood, B., Feliciano, E.J., Nambiar, K.P. Stabilisation of α-helical structures in short peptides via end capping. Pro. Natl. Acad. Sci. U.S.A. 90:838-842, 1993.
17. Lyu, P.C., Wemmer, D.E., Zhou, H.X., Pinker, R.J., Kallenbach, N.R. Capping interactions in isolated α-helices: Position-dependent substitution effects and structure of a serine-capped helix. Biochemistry 32:421-425, 1993.
18. Yumoto, N., Murase, S., Hattori, T., Yamamoto, H., Tatsu, Y., Yoshikawa, S. Stabilisation of α-helix in C-terminal fragments of neuropeptide-Y. Biochem. Biophys. Res. Commun. 196:1490-1495, 1993.
19. Doig, A.J., Chakrabartty, A., Kingler, T.M., Baldwin, R.L. Determination of free energies of N-capping in α-helices by modification of Lifson-Roig helix-coil theory to include N- and C-capping. Biochemistry 33:3396-3403, 1994.
20. Doig, A.J., Baldwin, R.L. N- and C-capping preferences for all 20 amino acids in α helical peptides. Protein Sci. 4:2247-2251, 1995.
21. Petukhov, M., Yumoto, N., Murase, S., Onmura, R., Yashikawa, S. Factors that affect the stabilisation of α-helices in short peptides by a capping box. Biochemistry, 35:387-397, 1996.
22. Harper, E.T., Rose, G.D. Helix stop signals in proteins and peptides: The capping box. Biochemistry 32:7605-7609, 1993.
23. Dasgupta, S., Bell, J.A. Design of helix ends: Amino acid preferences, hydrogen bonding and electrostatic interactions. Int. J. Pept. Prot. Res. 41:499-511, 1993.
24. Aurora, R., Srinivasan, R., Rose, G.D. Rules for alpha-helix termination by glycine. Science 264:1126-1130, 1994.
25. Zhou, H.X., Lyu, P.C., Wemmer, D.E., Kallenbach, N.R. α-helix capping in synthetic model peptides by reciprocal sidechain-mainchain interactions : Evidence for an N-terminal "Capping Box". Proteins 18:1-7, 1994.
26. Seale, J.W., Srinivasan, R., Rose, G.D. Sequence determinants of the capping box, a stabilising motif at the N-termini of alpha-helices. Protein Sci. 3:1741-1745, 1994.
27. Munoz, V., Serrano, L. Analysis of i, i + 5 and i, i + 8 hydrophobic interactions in α-helical model peptide bearing hydrophobic staple motif. Biochemistry 34:15301-15306, 1995.
28. Munoz, V., Blanco, F.J., Serrano, L. The hydrophobic staple motif and a role for loop-residues in alpha-helix stability and protein folding. Nat. Struct. Biol. 2:380-385, 1995.
29. Doig, A.J., MacArthur, M.W., Stapely, B.J., Thornton, J.M. Structures of N-termini of helices in proteins. Protein Sci. 6:147-155, 1997.
30. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., et al. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
31. Hobohm, U., Scharf, M., Schneider, R., Sander, C. Selection of representative protein data sets. Protein Sci. 1:409-417, 1992.
32. Hobohm, U., Sander, C. Enlarged representative set of protein structures. Protein Sci. 3:522-524, 1994.
33. Kabsch, W., Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
34. Kumar, S., Bansal, M. Structural and sequence characteristics of long alpha-helices in globular proteins. Biophys. J. 71:1574-1586, 1996.
35. Williams, R.W., Chang, A., Juretic, D., Loughran, S. Secondary-structure prediction and medium-range interactions. Biochim. Biophys. Acta 916:200-204, 1987
36. Chou, K.C., Zhang, C.T. Prediction of protein structural classes. Crit. Rev. Bioch. Mol. Biol. 30:275-349, 1995.
37. Medhi, J. "Statistical Methods: An Introductory Text." New Delhi: Wiley Eastern Limited, 1992.
38. Arnott, S., Dover, S.D. Refinement of bond angles of an α-helix. J. Mol. Biol. 30:209-212, 1967.
39. Gray, T.M., Mathews, B.W. Intrahelical hydrogen bonding of serine, threonine and cysteine residues within α-helices and its relevance to membrane-bound proteins. J. Mol. Biol. 175:75-81, 1984.
40. Bordo, D., Argos, P. The role of sidechain hydrogen bonds in the formation and stabilisation of secondary structures in soluble proteins. J. Mol. Biol. 243:504-519, 1994.
41. Woolfson, D.N., Williams, D.H. The influence of proline residues on alpha-helical structure. FEBS Lett. 277:185-188, 1990.
42. Schimmel, P.R., Flory, P.J. Conformational energies and configurational statistics of copolypeptides containing L-Proline. J. Mol. Biol. 34:105-120, 1968.
43. L conformation at the ends of helices. In: "Protein Folding." Jaenicke, R. (ed.). Amsterdam: Elsvier, 1980:53-61.
44. Preißner, R., Bork, P. On α-helices terminated by glycine. 1. Identification of common structural features. Biochem. Biophys. Res. Comm. 180:660-665, 1991.
45. Bork, P., Preißner, R. On α-helices terminated by glycine. 2. Recognition by sequence patterns. Biochem. Biophys. Res. Comm. 180:666-672, 1991.
46. Atschular, E.L., Lades, M. Possible exceptions to rules of α-helix termination by Glycine. Science 269:1451-1452, 1995.
47. Chakrabartty, A., Baldwin, R.L. Stability of α-helices. Adv. Prot. Chem. 46:141-176, 1995
48. Chou, P.Y., Fasman, G.D. Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins. Biochemistry 13:211-221, 1974.
49. Levitt, M. Conformational preferences of amino acids in globular proteins. Biochemistry 17:4277-4285, 1978.
50. Altmann, K.-H., Wojcik, J., Vasuez, M., Scheraga, H.A. Helix-coil stability for the naturally occurring amino acids in water. XXIII. Proline parameters from random poly(hydroxybutylgulatame-co-L-proline). Biopolymers 30:107-120, 1990.
51. Wojcik, J., Altmann, K.-H., Scheraga, H.A. Helix-coil stability for naturally occurring amino acids in water. XXIV. Half-cystine parameters from random poly(hydroxybutyl-glutamate-co-S-methylthio-L-cysteine). Biopolymers 30: 121-134, 1990.
52. O'Neil, K.T., DeGrado, W.F. A thermodynamic scale for helix-forming tendencies of the commonly occurring amino acids. Science 250:646-650, 1990.
53. Betz, S., Fairman, R., O'Neil, K., Lear, J., DeGrado, W.F. Design of two-stranded and three-stranded coiled coil peptides. Phil. Trans. R. Soc. London. B348:81-88, 1995.
54. Horovitz, A., Matthews, J., Fersht, A.R. α-helix stability in proteins. II. Factors that influence stability at an internal position. J. Mol. Biol. 227:560-568, 1992
55. Blaber, M., Zhang, X., Matthews, B. Structural basis of amino acid helix propensity. Science 260:1637-1640, 1993.