• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of prosciprotein sciencecshl presssubscriptionsetoc alertsthe protein societyjournal home
Protein Sci. Oct 1992; 1(10): 1333–1342.
PMCID: PMC2142095

Differences in the amino acid distributions of 3(10)-helices and alpha-helices.

Abstract

Local determinants of 3(10)-helix stabilization have been ascertained from the analysis of the crystal structure data base. We have clustered all 5-length substructures from 51 nonhomologous proteins into classes based on the conformational similarity of their backbone dihedral angles. Several clusters, derived from 3(10)-helices and multiple-turn conformations, had strong amino acid sequence patterns not evident among alpha-helices. Aspartate occurred over twice as frequently in the N-cap position of 3(10)-helices as in the N-cap position of alpha-helices. Unlike alpha-helices, 3(10)-helices had few C-termini ending in a left-handed alpha conformation; most 3(10) C-caps adopted an extended conformation. Differences in the distribution of hydrophobic residues among 3(10)- and alpha-helices were also apparent, producing amphipathic 3(10)-helices. Local interactions that stabilize 3(10)-helices can be inferred both from the strong amino acid preferences found for these short helices, as well as from the existence of substructures in which tertiary interactions replace consensus local interactions. Because the folding and unfolding of alpha-helices have been postulated to proceed through reverse-turn and 3(10)-helix intermediates, sequence differences between 3(10)- and alpha-helices can also lend insight into factors influencing alpha-helix initiation and propagation.

Full Text

The Full Text of this article is available as a PDF (889K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Abad-Zapatero C, Griffith JP, Sussman JL, Rossmann MG. Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. J Mol Biol. 1987 Dec 5;198(3):445–467. [PubMed]
  • Aqvist J, Luecke H, Quiocho FA, Warshel A. Dipoles localized at helix termini of proteins stabilize charges. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):2026–2030. [PMC free article] [PubMed]
  • Baker EN, Hubbard RE. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol. 1984;44(2):97–179. [PubMed]
  • Barlow DJ, Thornton JM. Helix geometry in proteins. J Mol Biol. 1988 Jun 5;201(3):601–619. [PubMed]
  • Betzel C, Pal GP, Saenger W. Synchrotron X-ray data collection and restrained least-squares refinement of the crystal structure of proteinase K at 1.5 A resolution. Acta Crystallogr B. 1988 Apr 1;44(Pt 2):163–172. [PubMed]
  • Bode W, Epp O, Huber R, Laskowski M, Jr, Ardelt W. The crystal and molecular structure of the third domain of silver pheasant ovomucoid (OMSVP3). Eur J Biochem. 1985 Mar 1;147(2):387–395. [PubMed]
  • Chou KC, Maggiora GM, Némethy G, Scheraga HA. Energetics of the structure of the four-alpha-helix bundle in proteins. Proc Natl Acad Sci U S A. 1988 Jun;85(12):4295–4299. [PMC free article] [PubMed]
  • Donohue J. Hydrogen Bonded Helical Configurations of the Polypeptide Chain. Proc Natl Acad Sci U S A. 1953 Jun;39(6):470–478. [PMC free article] [PubMed]
  • Efimov AV. Structure of alpha-alpha-hairpins with short connections. Protein Eng. 1991 Feb;4(3):245–250. [PubMed]
  • Finzel BC, Poulos TL, Kraut J. Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution. J Biol Chem. 1984 Nov 10;259(21):13027–13036. [PubMed]
  • Guss JM, Freeman HC. Structure of oxidized poplar plastocyanin at 1.6 A resolution. J Mol Biol. 1983 Sep 15;169(2):521–563. [PubMed]
  • Hol WG, van Duijnen PT, Berendsen HJ. The alpha-helix dipole and the properties of proteins. Nature. 1978 Jun 8;273(5662):443–446. [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]
  • Kannan KK, Ramanadham M, Jones TA. Structure, refinement, and function of carbonic anhydrase isozymes: refinement of human carbonic anhydrase I. Ann N Y Acad Sci. 1984;429:49–60. [PubMed]
  • Karpen ME, de Haseth PL, Neet KE. Comparing short protein substructures by a method based on backbone torsion angles. Proteins. 1989;6(2):155–167. [PubMed]
  • Karpen ME, Neet KE, de Haseth PL. A common pentapeptide conformation occurs in viral acid proteases and other proteins. J Mol Biol. 1990 Nov 20;216(2):201–206. [PubMed]
  • Lindqvist Y. Refined structure of spinach glycolate oxidase at 2 A resolution. J Mol Biol. 1989 Sep 5;209(1):151–166. [PubMed]
  • Nicholson H, Becktel WJ, Matthews BW. Enhanced protein thermostability from designed mutations that interact with alpha-helix dipoles. Nature. 1988 Dec 15;336(6200):651–656. [PubMed]
  • Poulos TL, Finzel BC, Howard AJ. High-resolution crystal structure of cytochrome P450cam. J Mol Biol. 1987 Jun 5;195(3):687–700. [PubMed]
  • Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem. 1981;34:167–339. [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]
  • Schimmel PR, Flory PJ. Conformational energies and configurational statistics of copolypeptides containing L-proline. J Mol Biol. 1968 May 28;34(1):105–120. [PubMed]
  • Serrano L, Fersht AR. Capping and alpha-helix stability. Nature. 1989 Nov 16;342(6247):296–299. [PubMed]
  • Shoemaker KR, Kim PS, York EJ, Stewart JM, Baldwin RL. Tests of the helix dipole model for stabilization of alpha-helices. Nature. 1987 Apr 9;326(6113):563–567. [PubMed]
  • Suguna K, Bott RR, Padlan EA, Subramanian E, Sheriff S, Cohen GH, Davies DR. Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis. J Mol Biol. 1987 Aug 20;196(4):877–900. [PubMed]
  • Sundaralingam M, Sekharudu YC. Water-inserted alpha-helical segments implicate reverse turns as folding intermediates. Science. 1989 Jun 16;244(4910):1333–1337. [PubMed]
  • Tirado-Rives J, Jorgensen WL. Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water. Biochemistry. 1991 Apr 23;30(16):3864–3871. [PubMed]
  • Tobias DJ, Brooks CL., 3rd Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. Biochemistry. 1991 Jun 18;30(24):6059–6070. [PubMed]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Cited in Books
    Cited in Books
    PubMed Central articles cited in books
  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links