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Literature DB >> 10096876

An alamethicin channel in a lipid bilayer: molecular dynamics simulations.

D P Tieleman¹, H J Berendsen, M S Sansom.

Abstract

We present the results of 2-ns molecular dynamics (MD) simulations of a hexameric bundle of Alm helices in a 1-palmitoyl-2-oleoylphosphatidylcholine bilayer. These simulations explore the dynamic properties of a model of a helix bundle channel in a complete phospholipid bilayer in an aqueous environment. We explore the stability and conformational dynamics of the bundle in a phospholipid bilayer. We also investigate the effect on bundle stability of the ionization state of the ring of Glu18 side chains. If all of the Glu18 side chains are ionised, the bundle is unstable; if none of the Glu18 side chains are ionized, the bundle is stable. pKA calculations suggest that either zero or one ionized Glu18 is present at neutral pH, correlating with the stable form of the helix bundle. The structural and dynamic properties of water in this model channel were examined. As in earlier in vacuo simulations (Breed et al., 1996 .Biophys. J. 70:1643-1661), the dipole moments of water molecules within the pore were aligned antiparallel to the helix dipoles. This contributes to the stability of the helix bundle.

Entities: Chemical Disease

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Year: 1999 PMID： 10096876 PMCID： PMC1300154 DOI： 10.1016/s0006-3495(99)77337-6

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

53 in total

An alamethicin channel in a lipid bilayer: molecular dynamics simulations.

Review 1. The biophysics of peptide models of ion channels.

2. Ion transport in a model gramicidin channel. Structure and thermodynamics.

3. A molecular model of membrane excitability.

4. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

5. A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5-A resolution.

6. Molecular dynamics simulation of a synthetic ion channel.

7. Proline residues in transmembrane helices of channel and transport proteins: a molecular modelling study.

Review 8. Model ion channels: gramicidin and alamethicin.

9. Synthetic amphiphilic peptide models for protein ion channels.

Review 10. Alamethicin and related membrane channel forming polypeptides.

1. Statistical mechanical equilibrium theory of selective ion channels.

2. Protonation of lysine residues inverts cation/anion selectivity in a model channel.

3. Homology modeling and molecular dynamics simulation studies of an inward rectifier potassium channel.

4. Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane.

5. Structure and dynamics of K channel pore-lining helices: a comparative simulation study.

6. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels.

7. Molecular dynamics simulations of wild-type and mutant forms of the Mycobacterium tuberculosis MscL channel.

8. Size distribution of barrel-stave aggregates of membrane peptides: influence of the bilayer lateral pressure profile.

9. Filter flexibility in a mammalian K channel: models and simulations of Kir6.2 mutants.

10. Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer.