Skip to main content
NCBI home page
Biophysical Journal logoLink to Biophysical Journal
. 1989 Aug;56(2):253–261. doi: 10.1016/S0006-3495(89)82671-2

Water and polypeptide conformations in the gramicidin channel. A molecular dynamics study.

S W Chiu 1, S Subramaniam 1, E Jakobsson 1, J A McCammon 1
PMCID: PMC1280474  PMID: 2476188

Abstract

Theoretical studies of ion channels address several important questions. The mechanism of ion transport, the role of water structure, the fluctuations of the protein channel itself, and the influence of structural changes are accessible from these studies. In this paper, we have carried out a 70-ps molecular dynamics simulation on a model structure of gramicidin A with channel waters. The backbone of the protein has been analyzed with respect to the orientation of the carbonyl and the amide groups. The results are in conformity with the experimental NMR data. The structure of water and the hydrogen bonding network are also investigated. It is found that the water molecules inside the channel act as a collective chain; whereas the conformation in which all the waters are oriented with the dipoles pointing along the axis of the channel is a preferred one, others are also accessed during the dynamics simulation. A collective coordinate involving the channel waters and some of the hydrogen bonding peptide partners is required to describe the transition of waters from one configuration to the other.

Full text

PDF
253

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Andersen O. S. Gramicidin channels. Annu Rev Physiol. 1984;46:531–548. doi: 10.1146/annurev.ph.46.030184.002531. [DOI] [PubMed] [Google Scholar]
  2. Elber R., Karplus M. Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. Science. 1987 Jan 16;235(4786):318–321. doi: 10.1126/science.3798113. [DOI] [PubMed] [Google Scholar]
  3. Fields G. B., Fields C. G., Petefish J., Van Wart H. E., Cross T. A. Solid-phase peptide synthesis and solid-state NMR spectroscopy of [Ala3-15N][Val1]gramicidin A. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1384–1388. doi: 10.1073/pnas.85.5.1384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Kim K. S., Vercauteren D. P., Welti M., Chin S., Clementi E. Interaction of K+ ion with the solvated gramicidin A transmembrane channel. Biophys J. 1985 Mar;47(3):327–335. doi: 10.1016/S0006-3495(85)83923-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Lee W. K., Jordan P. C. Molecular dynamics simulation of cation motion in water-filled gramicidinlike pores. Biophys J. 1984 Dec;46(6):805–819. doi: 10.1016/S0006-3495(84)84079-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Mackay D. H., Berens P. H., Wilson K. R., Hagler A. T. Structure and dynamics of ion transport through gramicidin A. Biophys J. 1984 Aug;46(2):229–248. doi: 10.1016/S0006-3495(84)84016-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Mackay D. H., Wilson K. R. Possible allosteric significance of water structures in proteins. J Biomol Struct Dyn. 1986 Dec;4(3):491–500. doi: 10.1080/07391102.1986.10506364. [DOI] [PubMed] [Google Scholar]
  8. Myers V. B., Haydon D. A. Ion transfer across lipid membranes in the presence of gramicidin A. II. The ion selectivity. Biochim Biophys Acta. 1972 Aug 9;274(2):313–322. doi: 10.1016/0005-2736(72)90179-4. [DOI] [PubMed] [Google Scholar]
  9. Roux B., Karplus M. The normal modes of the gramicidin-A dimer channel. Biophys J. 1988 Mar;53(3):297–309. doi: 10.1016/S0006-3495(88)83107-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Skerra A., Brickmann J. Simulation of voltage-driven hydrated cation transport through narrow transmembrane channels. Biophys J. 1987 Jun;51(6):977–983. doi: 10.1016/S0006-3495(87)83425-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Skerra A., Brickmann J. Structure and dynamics of one-dimensional ionic solutions in biological transmembrane channels. Biophys J. 1987 Jun;51(6):969–976. doi: 10.1016/S0006-3495(87)83424-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Stillinger F. H., Weber T. A. Packing structures and transitions in liquids and solids. Science. 1984 Sep 7;225(4666):983–989. doi: 10.1126/science.225.4666.983. [DOI] [PubMed] [Google Scholar]
  13. Sung S. S., Jordan P. C. Why is gramicidin valence selective? A theoretical study. Biophys J. 1987 Apr;51(4):661–672. doi: 10.1016/S0006-3495(87)83391-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Wallace B. A. Structure of gramicidin A. Biophys J. 1986 Jan;49(1):295–306. doi: 10.1016/S0006-3495(86)83642-6. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES