Alamethicin channels – modelling via restrained molecular dynamics simulations

Alamethicin channels have been modelled as approximately parallel bundles of transbilayer helices containing between N=4 and 8 helices per bundle. Initial models were generated by in vacuo restrained molecular dynamics (MD) simulations, and were refined by 60 ps MD simulations with water molecules p...

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Bibliographic Details
Published in:Biochimica et biophysica acta 1997-04, Vol.1325 (2), p.235-249
Main Authors: Breed, J, Biggin, P.C, Kerr, I.D, Smart, O.S, Sansom, M.S.P
Format: Article
Language:English
Subjects:
Alamethicin
Alamethicin - chemistry
Amino Acid Sequence
Channel-forming peptide
Computer Simulation
Electrostatics
Ion channel
Ion Channels - chemistry
Ionophores - chemistry
Models, Molecular
Molecular Sequence Data
Molecular Structure
Peptaibol
Static Electricity
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Summary:Alamethicin channels have been modelled as approximately parallel bundles of transbilayer helices containing between N=4 and 8 helices per bundle. Initial models were generated by in vacuo restrained molecular dynamics (MD) simulations, and were refined by 60 ps MD simulations with water molecules present within and at the mouths of the central pore. The helix bundles were stabilized by networks of H-bonds between intra-pore water molecules and Gln-7 side-chains. Channel conductances were predicted on the basis of pore radius profiles, and suggested that the N=4 bundle formed an occluded pore, whereas pores with N≥5 helices per bundle were open. Continuum electrostatics calculations suggested that the N=6 pore is cation-selective, whereas pores with N≥7 helices per bundle were predicted to be somewhat less ion-selective.
ISSN:0005-2736
0006-3002
1879-2642
DOI:10.1016/S0005-2736(96)00262-3