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Biophys J. Oct 1998; 75(4): 1935–1944.
PMCID: PMC1299864

Geometrical and sequence characteristics of alpha-helices in globular proteins.

Abstract

Understanding the sequence-structure relationships in globular proteins is important for reliable protein structure prediction and de novo design. Using a database of 1131 alpha-helices with nonidentical sequences from 205 nonhomologous globular protein chains, we have analyzed structural and sequence characteristics of alpha-helices. We find that geometries of more than 99% of all the alpha-helices can be simply characterised as being linear, curved, or kinked. Only a small number of alpha-helices ( approximately 4%) show sharp localized bends in their middle regions, and thus are classified as kinked. Approximately three-fourths (approximately 73%) of the alpha-helices in globular proteins show varying degrees of smooth curvature, with a mean radius of curvature of 65 +/- 33 A; longer helices are less curved. Computation of helix accessibility to the solvent indicates that nearly two-thirds of the helices ( approximately 66%) are largely buried in the protein core, and the length and geometry of the helices are not correlated with their location in the protein globule. However, the amino acid compositions and propensities of individual amino acids to occur in alpha-helices vary with their location in the protein globule, their geometries, and their lengths. In particular, Gln, Glu, Lys, and Arg are found more often in helices near the surface of globular proteins. Interestingly, kinks often seem to occur in regions where amino acids with low helix propensities (e.g., beta-branched and aromatic residues) cluster together, in addition to those associated with the occurrence of proline residues. Hence the propensities of individual amino acids to occur in a given secondary structure depend not only on conformation but also on its length, geometry, and location in the protein globule.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Argos P, Palau J. Amino acid distribution in protein secondary structures. Int J Pept Protein Res. 1982 Apr;19(4):380–393. [PubMed]
  • Banner DW, Kokkinidis M, Tsernoglou D. Structure of the ColE1 rop protein at 1.7 A resolution. J Mol Biol. 1987 Aug 5;196(3):657–675. [PubMed]
  • Barlow DJ, Thornton JM. Helix geometry in proteins. J Mol Biol. 1988 Jun 5;201(3):601–619. [PubMed]
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. [PubMed]
  • Blundell T, Barlow D, Borkakoti N, Thornton J. Solvent-induced distortions and the curvature of alpha-helices. Nature. 1983 Nov 17;306(5940):281–283. [PubMed]
  • Blundell TL, Zhu ZY. The alpha-helix as seen from the protein tertiary structure: a 3-D structural classification. Biophys Chem. 1995 Jun-Jul;55(1-2):167–184. [PubMed]
  • Chakrabarti P, Bernard M, Rees DC. Peptide-bond distortions and the curvature of alpha-helices. Biopolymers. 1986 Jun;25(6):1087–1093. [PubMed]
  • Chakrabartty A, Schellman JA, Baldwin RL. Large differences in the helix propensities of alanine and glycine. Nature. 1991 Jun 13;351(6327):586–588. [PubMed]
  • Chou KC, Zhang CT. Prediction of protein structural classes. Crit Rev Biochem Mol Biol. 1995;30(4):275–349. [PubMed]
  • Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci. 1994 Mar;3(3):522–524. [PMC free article] [PubMed]
  • Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Protein Sci. 1992 Mar;1(3):409–417. [PMC free article] [PubMed]
  • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. [PubMed]
  • KENDREW JC, BODO G, DINTZIS HM, PARRISH RG, WYCKOFF H, PHILLIPS DC. A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature. 1958 Mar 8;181(4610):662–666. [PubMed]
  • Kumar S, Bansal M. Structural and sequence characteristics of long alpha helices in globular proteins. Biophys J. 1996 Sep;71(3):1574–1586. [PMC free article] [PubMed]
  • Kumar S, Bansal M. Dissecting alpha-helices: position-specific analysis of alpha-helices in globular proteins. Proteins. 1998 Jun 1;31(4):460–476. [PubMed]
  • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971 Feb 14;55(3):379–400. [PubMed]
  • PAULING L, COREY RB, BRANSON HR. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A. 1951 Apr;37(4):205–211. [PMC free article] [PubMed]
  • Presta LG, Rose GD. Helix signals in proteins. Science. 1988 Jun 17;240(4859):1632–1641. [PubMed]
  • Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of alpha helices. Science. 1988 Jun 17;240(4859):1648–1652. [PubMed]
  • Sankararamakrishnan R, Vishveshwara S. Geometry of proline-containing alpha-helices in proteins. Int J Pept Protein Res. 1992 Apr;39(4):356–363. [PubMed]
  • Serrano L, Fersht AR. Capping and alpha-helix stability. Nature. 1989 Nov 16;342(6247):296–299. [PubMed]
  • Serrano L, Neira JL, Sancho J, Fersht AR. Effect of alanine versus glycine in alpha-helices on protein stability. Nature. 1992 Apr 2;356(6368):453–455. [PubMed]
  • Srinivasan R. Helical length distribution from protein crystallographic data. Indian J Biochem Biophys. 1976 Jun;13(2):192–193. [PubMed]
  • von Heijne G. Proline kinks in transmembrane alpha-helices. J Mol Biol. 1991 Apr 5;218(3):499–503. [PubMed]
  • Vorobjev YN, Hermans J. SIMS: computation of a smooth invariant molecular surface. Biophys J. 1997 Aug;73(2):722–732. [PMC free article] [PubMed]
  • Williams RW, Chang A, Juretić D, Loughran S. Secondary structure predictions and medium range interactions. Biochim Biophys Acta. 1987 Nov 26;916(2):200–204. [PubMed]
  • Woolfson DN, Williams DH. The influence of proline residues on alpha-helical structure. FEBS Lett. 1990 Dec 17;277(1-2):185–188. [PubMed]
  • Zhu ZY, Blundell TL. The use of amino acid patterns of classified helices and strands in secondary structure prediction. J Mol Biol. 1996 Jul 12;260(2):261–276. [PubMed]

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