Literature DB >> 6206901

Structure and dynamics of ion transport through gramicidin A.

D H Mackay, P H Berens, K R Wilson, A T Hagler.   

Abstract

Molecular dynamics calculations in which all atoms were allowed to move were performed on a water-filled ion channel of the polypeptide dimer gramicidin A (approximately 600 atoms total) in the head-to-head Urry model conformation. Comparisons were made among nine simulations in which four different ions (lithium, sodium, potassium, and cesium) were each placed at two different locations in the channel as well as a reference simulation with only water present. Each simulation lasted for 5 ps and was carried out at approximately 300 K. The structure and dynamics of the peptide and interior waters were found to depend strongly on the ion tested and upon its location along the pore. Speculations on the solution and diffusion of ions in gramicidin are offered based on the observations in our model that smaller ions tended to lie off axis and to distort the positions of the carbonyl oxygens more to achieve proper solvation and that the monomer-monomer junction was more distortable than the center of the monomer. With the potential energy surface used, the unique properties of the linear chain of interior water molecules were found to be important for optimal solvation of the various ions. Strongly correlated motions persisting over 25 A among the waters in the interior single-file column were observed.

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Year:  1984        PMID: 6206901      PMCID: PMC1435037          DOI: 10.1016/S0006-3495(84)84016-3

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  37 in total

1.  Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals.

Authors:  A T Hagler; E Huler; S Lifson
Journal:  J Am Chem Soc       Date:  1974-08-21       Impact factor: 15.419

2.  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.

Authors:  G N Ramachnandran; R Chandrasekaran
Journal:  Indian J Biochem Biophys       Date:  1972-03       Impact factor: 1.918

Review 3.  Gramicidin as an example of a single-filing ionic channel.

Authors:  G Eisenman; B Enos; J Hägglund; J Sandblom
Journal:  Ann N Y Acad Sci       Date:  1980       Impact factor: 5.691

4.  Conformation of the gramicidin A transmembrane channel: A 13C nuclear magnetic resonance study of 13C-enriched gramicidin in phosphatidylcholine vesicles.

Authors:  S Weinstein; B A Wallace; J S Morrow; W R Veatch
Journal:  J Mol Biol       Date:  1980-10-15       Impact factor: 5.469

5.  Molecular dynamics study of ion transport in transmembrane protein channels.

Authors:  W Fischer; J Brickmann; P Läuger
Journal:  Biophys Chem       Date:  1981-04       Impact factor: 2.352

Review 6.  Hydrogen bonded chain mechanisms for proton conduction and proton pumping.

Authors:  J F Nagle; S Tristram-Nagle
Journal:  J Membr Biol       Date:  1983       Impact factor: 1.843

7.  Interaction of cation fluxes in gramicidin A channels in lipid bilayer membranes.

Authors:  L V Schagina; A E Grinfeldt; A A Lev
Journal:  Nature       Date:  1978-05-18       Impact factor: 49.962

8.  Location of monovalent cation binding sites in the gramicidin channel.

Authors:  D W Urry; K U Prasad; T L Trapane
Journal:  Proc Natl Acad Sci U S A       Date:  1982-01       Impact factor: 11.205

9.  Ion channels formed by chemical analogs of gramicidin A.

Authors:  E Bamberg; H J Apell; H Alpes; E Gross; J L Morell; J F Harbaugh; K Janko; P Läuger
Journal:  Fed Proc       Date:  1978-10

10.  Influence of membrane thickness and ion concentration on the properties of the gramicidin a channel. Autocorrelation, spectral power density, relaxation and single-channel studies.

Authors:  H A Kolb; E Bamberg
Journal:  Biochim Biophys Acta       Date:  1977-01-04
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  59 in total

1.  Statistical mechanical equilibrium theory of selective ion channels.

Authors:  B Roux
Journal:  Biophys J       Date:  1999-07       Impact factor: 4.033

2.  Energetics of ion conduction through the gramicidin channel.

Authors:  Toby W Allen; Olaf S Andersen; Benoît Roux
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-22       Impact factor: 11.205

3.  The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents.

Authors:  Artem B Mamonov; Rob D Coalson; Abraham Nitzan; Maria G Kurnikova
Journal:  Biophys J       Date:  2003-06       Impact factor: 4.033

4.  Shaking stack model of ion conduction through the Ca(2+)-activated K+ channel.

Authors:  M F Schumaker
Journal:  Biophys J       Date:  1992-10       Impact factor: 4.033

5.  Ionic permeation free energy in gramicidin: a semimicroscopic perspective.

Authors:  Vladimir L Dorman; Peter C Jordan
Journal:  Biophys J       Date:  2004-06       Impact factor: 4.033

6.  Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields.

Authors:  Toby W Allen; Olaf S Andersen; Benoit Roux
Journal:  Biophys J       Date:  2006-02-24       Impact factor: 4.033

7.  Open channel noise. V. Fluctuating barriers to ion entry in gramicidin A channels.

Authors:  S H Heinemann; F J Sigworth
Journal:  Biophys J       Date:  1990-03       Impact factor: 4.033

8.  Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels.

Authors:  Mitsunori Kato; Arieh Warshel
Journal:  J Phys Chem B       Date:  2005-10-20       Impact factor: 2.991

9.  Molecular dynamics computations and solid state nuclear magnetic resonance of the gramicidin cation channel.

Authors:  S W Chiu; L K Nicholson; M T Brenneman; S Subramaniam; Q Teng; J A McCammon; T A Cross; E Jakobsson
Journal:  Biophys J       Date:  1991-10       Impact factor: 4.033

10.  On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation.

Authors:  Toby W Allen; O S Andersen; Benoit Roux
Journal:  J Gen Physiol       Date:  2004-12       Impact factor: 4.086

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