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 present within and at the mouths of the central pore. The helix bundles were stabilized by networks of II-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 greater than or equal to 5 helices per bundle were open. Continuum electrostatics calculations suggested that the N=6 pore is cation-selective, whereas pores with N greater than or equal to 7 helices per bundle were predicted to be somewhat less ion-selective.