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. 1996 Feb;70(2):693–702. doi: 10.1016/S0006-3495(96)79609-1

Water in channel-like cavities: structure and dynamics.

M S Sansom 1, I D Kerr 1, J Breed 1, R Sankararamakrishnan 1
PMCID: PMC1224969  PMID: 8789086

Abstract

Ion channels contain narrow columns of water molecules. It is of interest to compare the structure and dynamics of such intrapore water with those of the bulk solvent. Molecular dynamics simulations of modified TIP3P water molecules confined within channel-like cavities have been performed and the orientation and dynamics of the water molecules analyzed. Channels were modeled as cylindrical cavities with lengths ranging from 15 to 60 A and radii from 3 to 12 A. At the end of the molecular dynamics simulations water molecules were observed to be ordered into approximately concentric cylindrical shells. The waters of the outermost shell were oriented such that their dipoles were on average perpendicular to the normal of the wall of the cavity. Water dynamics were analyzed in terms of self-diffusion coefficients and rotational reorientation rates. For cavities of radii 3 and 6 A, water mobility was reduced relative to that of simulated bulk water. For 9- and 12-A radii confined water molecules exhibited mobilities comparable with that of the bulk solvent. If water molecules were confined within an hourglass-shaped cavity (with a central radius of 3 A increasing to 12 A at either end) a gradient of water mobility was observed along the cavity axis. Thus, water within simple models of transbilayer channels exhibits perturbations of structure and dynamics relative to bulk water. In particular the reduction of rotational reorientation rate is expected to alter the local dielectric constant within a transbilayer pore.

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Selected References

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

  1. Chiu S. W., Jakobsson E., Subramaniam S., McCammon J. A. Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. Biophys J. 1991 Jul;60(1):273–285. doi: 10.1016/S0006-3495(91)82049-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chiu S. W., Novotny J. A., Jakobsson E. The nature of ion and water barrier crossings in a simulated ion channel. Biophys J. 1993 Jan;64(1):98–109. doi: 10.1016/S0006-3495(93)81344-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cowan S. W., Schirmer T., Rummel G., Steiert M., Ghosh R., Pauptit R. A., Jansonius J. N., Rosenbusch J. P. Crystal structures explain functional properties of two E. coli porins. Nature. 1992 Aug 27;358(6389):727–733. doi: 10.1038/358727a0. [DOI] [PubMed] [Google Scholar]
  4. Daggett V., Levitt M. Realistic simulations of native-protein dynamics in solution and beyond. Annu Rev Biophys Biomol Struct. 1993;22:353–380. doi: 10.1146/annurev.bb.22.060193.002033. [DOI] [PubMed] [Google Scholar]
  5. Dani J. A., Levitt D. G. Diffusion and kinetic approaches to describe permeation in ionic channels. J Theor Biol. 1990 Oct 7;146(3):289–301. doi: 10.1016/s0022-5193(05)80740-4. [DOI] [PubMed] [Google Scholar]
  6. Granick S. Motions and relaxations of confined liquids. Science. 1991 Sep 20;253(5026):1374–1379. doi: 10.1126/science.253.5026.1374. [DOI] [PubMed] [Google Scholar]
  7. Karshikoff A., Spassov V., Cowan S. W., Ladenstein R., Schirmer T. Electrostatic properties of two porin channels from Escherichia coli. J Mol Biol. 1994 Jul 22;240(4):372–384. doi: 10.1006/jmbi.1994.1451. [DOI] [PubMed] [Google Scholar]
  8. Kerr I. D., Sankararamakrishnan R., Smart O. S., Sansom M. S. Parallel helix bundles and ion channels: molecular modeling via simulated annealing and restrained molecular dynamics. Biophys J. 1994 Oct;67(4):1501–1515. doi: 10.1016/S0006-3495(94)80624-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kreusch A., Schulz G. E. Refined structure of the porin from Rhodopseudomonas blastica. Comparison with the porin from Rhodobacter capsulatus. J Mol Biol. 1994 Nov 11;243(5):891–905. doi: 10.1006/jmbi.1994.1690. [DOI] [PubMed] [Google Scholar]
  10. Lear J. D., Wasserman Z. R., DeGrado W. F. Synthetic amphiphilic peptide models for protein ion channels. Science. 1988 May 27;240(4856):1177–1181. doi: 10.1126/science.2453923. [DOI] [PubMed] [Google Scholar]
  11. Sancho M., Partenskii M. B., Dorman V., Jordan P. C. Extended dipolar chain model for ion channels: electrostriction effects and the translocational energy barrier. Biophys J. 1995 Feb;68(2):427–433. doi: 10.1016/S0006-3495(95)80204-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Sansom M. S. Ion-channel gating. Twist to open. Curr Biol. 1995 Apr 1;5(4):373–375. doi: 10.1016/s0960-9822(95)00076-5. [DOI] [PubMed] [Google Scholar]
  13. Sansom M. S., Kerr I. D. Transbilayer pores formed by beta-barrels: molecular modeling of pore structures and properties. Biophys J. 1995 Oct;69(4):1334–1343. doi: 10.1016/S0006-3495(95)80000-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Sansom M. S., Sankararamakrishnan R., Kerr I. D. Modelling membrane proteins using structural restraints. Nat Struct Biol. 1995 Aug;2(8):624–631. doi: 10.1038/nsb0895-624. [DOI] [PubMed] [Google Scholar]
  15. Teeter M. M. Water-protein interactions: theory and experiment. Annu Rev Biophys Biophys Chem. 1991;20:577–600. doi: 10.1146/annurev.bb.20.060191.003045. [DOI] [PubMed] [Google Scholar]
  16. Unwin N. Acetylcholine receptor channel imaged in the open state. Nature. 1995 Jan 5;373(6509):37–43. doi: 10.1038/373037a0. [DOI] [PubMed] [Google Scholar]
  17. Unwin N. Nicotinic acetylcholine receptor at 9 A resolution. J Mol Biol. 1993 Feb 20;229(4):1101–1124. doi: 10.1006/jmbi.1993.1107. [DOI] [PubMed] [Google Scholar]
  18. Unwin N. The structure of ion channels in membranes of excitable cells. Neuron. 1989 Dec;3(6):665–676. doi: 10.1016/0896-6273(89)90235-3. [DOI] [PubMed] [Google Scholar]
  19. Weiss M. S., Schulz G. E. Structure of porin refined at 1.8 A resolution. J Mol Biol. 1992 Sep 20;227(2):493–509. doi: 10.1016/0022-2836(92)90903-w. [DOI] [PubMed] [Google Scholar]

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