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PMID: 7508762 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The pore dimensions of gramicidin A.

Biophysical journal ·Vol. 65 ·No. 6 ·1993-12-00 ·Pages 2455-60

Smart OS, Goodfellow JM, Wallace BA

Abstract

The ion channel forming peptide gramicidin A adopts a number of distinct conformations in different environments. We have developed a new method to analyze and display the pore dimensions of ion channels. The procedure is applied to two x-ray crystal structures of gramicidin that adopt distinct antiparallel double helical dimer conformations and a nuclear magnetic resonance (NMR) structure for the beta6.3 NH2-terminal to NH2-terminal dimer. The results are discussed with reference to ion conductance properties and dependence of pore dimensions on the environment.

MeSH Terms
Amino Acid Sequence Crystallography, X-Ray/methods Gramicidin/chemistry Ion Channels Magnetic Resonance Spectroscopy/methods Mathematics Models, Biological Models, Molecular Molecular Sequence Data Protein Structure, Secondary
Chemicals
Ion Channels Gramicidin
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Smart O S
Department of Crystallography, Birkbeck College, University of London, England.
Goodfellow J M
Wallace B A
References (31)
31 references, click to expand
  1. Ion-bond forms of the gramicidin a transmembrane channel.
    Biophys J. 1984 Jan;45(1):114-6 PMID: 19431532
  2. X-ray analysis and protein structure.
    Cold Spring Harb Symp Quant Biol. 1950;14:65-78 PMID: 15442899
  3. DNA-supercoiling is affected in vitro by the peptide antibiotics tyrocidine and gramicidin.
    Eur J Biochem. 1986 Nov 3;160(3):587-91 PMID: 2430800
  4. Conformation of peptide chains containing both L- & D-residues. I. Helical structures with alternating L- & D-residues with special reference to the LD-ribbon & the LD-helices.
    Indian J Biochem Biophys. 1972 Mar;9(1):1-11 PMID: 4642355
  5. Molecular dynamics computations and solid state nuclear magnetic resonance of the gramicidin cation channel.
    Biophys J. 1991 Oct;60(4):974-8 PMID: 1720680
  6. Effect of linear gramicidin on sporulation and intracellular ATP pools of Bacillus brevis.
    Arch Microbiol. 1985 Dec;143(3):248-52 PMID: 2420301
  7. Three-dimensional structure at 0.86 A of the uncomplexed form of the transmembrane ion channel peptide gramicidin A.
    Science. 1988 Jul 8;241(4862):188-91 PMID: 2455345
  8. Solvent-accessible surfaces of proteins and nucleic acids.
    Science. 1983 Aug 19;221(4612):709-13 PMID: 6879170
  9. POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids.
    J Mol Graph. 1992 Dec;10(4):229-34 PMID: 1476996
  10. Conformation of the gramicidin A transmembrane channel: A 13C nuclear magnetic resonance study of 13C-enriched gramicidin in phosphatidylcholine vesicles.
    J Mol Biol. 1980 Oct 15;143(1):1-19 PMID: 6160255
  11. Gramicidin channels.
    Annu Rev Physiol. 1984;46:531-48 PMID: 6201133
  12. Cavity search: an algorithm for the isolation and display of cavity-like binding regions.
    J Comput Aided Mol Des. 1990 Dec;4(4):337-54 PMID: 2092080
  13. An interaction between gramicidin and the sigma subunit of RNA polymerase.
    Proc Natl Acad Sci U S A. 1982 Feb;79(4):1045-8 PMID: 6175958
  14. Ion-water and ion-polypeptide correlations in a gramicidin-like channel. A molecular dynamics study.
    Biophys J. 1990 Nov;58(5):1133-56 PMID: 1705448
  15. Comparison of the effect of linear gramicidin analogues on bacterial sporulation, membrane permeability, and ribonucleic acid polymerase.
    Biochemistry. 1979 Oct 16;18(21):4532-6 PMID: 91382
  16. The Protein Data Bank: a computer-based archival file for macromolecular structures.
    J Mol Biol. 1977 May 25;112(3):535-42 PMID: 875032
  17. Optimization by simulated annealing.
    Science. 1983 May 13;220(4598):671-80 PMID: 17813860
  18. The gramicidin pore: crystal structure of a cesium complex.
    Science. 1988 Jul 8;241(4862):182-7 PMID: 2455344
  19. The gramicidin A transmembrane channel: a proposed pi(L,D) helix.
    Proc Natl Acad Sci U S A. 1971 Mar;68(3):672-6 PMID: 5276779
  20. GRAMICIDIN A. V. THE STRUCTURE OF VALINE- AND ISOLEUCINE-GRAMICIDIN A.
    J Am Chem Soc. 1965 May 5;87:2011-20 PMID: 14290276
  21. The conformation of gramicidin A.
    Biochemistry. 1974 Dec 17;13(26):5249-56 PMID: 4139971
  22. 1H-NMR study of gramicidin A transmembrane ion channel. Head-to-head right-handed, single-stranded helices.
    FEBS Lett. 1985 Jul 8;186(2):168-74 PMID: 2408920
  23. Gramicidin, valinomycin, and cation permeability of Streptococcus faecalis.
    J Bacteriol. 1967 Jul;94(1):53-60 PMID: 4961416
  24. Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A.
    Biophys J. 1989 Jul;56(1):171-82 PMID: 2473789
  25. Ion transfer across lipid membranes in the presence of gramicidin A. II. The ion selectivity.
    Biochim Biophys Acta. 1972 Aug 9;274(2):313-22 PMID: 5049000
  26. The dimeric nature of the gramicidin A transmembrane channel: conductance and fluorescence energy transfer studies of hybrid channels.
    J Mol Biol. 1977 Jun 15;113(1):89-102 PMID: 69713
  27. Gramicidin channel selectivity. Molecular mechanics calculations for formamidinium, guanidinium, and acetamidinium.
    Biophys J. 1992 Jul;63(1):152-61 PMID: 1384733
  28. Monoclinic uncomplexed double-stranded, antiparallel, left-handed beta 5.6-helix (increases decreases beta 5.6) structure of gramicidin A: alternate patterns of helical association and deformation.
    Proc Natl Acad Sci U S A. 1991 Jun 15;88(12):5345-9 PMID: 1711230
  29. The permeation properties of small organic cations in gramicidin A channels.
    Biophys J. 1993 Apr;64(4):1017-28 PMID: 7684267
  30. Function of peptide antibiotics in sporulation.
    Nat New Biol. 1972 Oct 25;239(95):228-30 PMID: 4507802
  31. On the supramolecular organization of gramicidin channels. The elementary conducting unit is a dimer.
    Biophys J. 1992 Jan;61(1):189-203 PMID: 1371703
Article Info
Journal
Biophysical journal
Abbr.
Biophys J
ISSN
0006-3495
DOI
10.1016/S0006-3495(93)81293-1
Published
1993-12-00
Pages
2455-60
Language
English
Region
United States
NLM ID
0370626
PMCID
PMC1225986
Subset
IM
External Links
PubMed source DOI: 10.1016/S0006-3495(93)81293-1 PMC Full Text View journal details
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