title: Analysis and evaluation of channel models: simulations of alamethicin.
abstract: Alamethicin is an antimicrobial peptide that forms stable channels with well-defined conductance levels. We have used extended molecular dynamics simulations of alamethicin bundles consisting of 4, 5, 6, 7, and 8 helices in a palmitoyl-oleolyl-phosphatidylcholine bilayer to evaluate and analyze channel models and to link the models to the experimentally measured conductance levels. Our results suggest that four helices do not form a stable water-filled channel and might not even form a stable intermediate. The lowest measurable conductance level is likely to correspond to the pentamer. At higher aggregation numbers the bundles become less symmetrical. Water properties inside the different-sized bundles are similar. The hexamer is the most stable model with a stability comparable with simulations based on crystal structures. The simulation was extended from 4 to 20 ns or several times the mean passage time of an ion. Essential dynamics analyses were used to test the hypothesis that correlated motions of the helical bundles account for high-frequency noise observed in open channel measurements. In a 20-ns simulation of a hexameric alamethicin bundle, the main motions are those of individual helices, not of the bundle as a whole. A detailed comparison of simulations using different methods to treat long-range electrostatic interactions (a twin range cutoff, Particle Mesh Ewald, and a twin range cutoff combined with a reaction field correction) shows that water orientation inside the alamethicin channels is sensitive to the algorithms used. In all cases, water ordering due to the protein structure is strong, although the exact profile changes somewhat. Adding an extra 4-nm layer of water only changes the water ordering slightly in the case of particle mesh Ewald, suggesting that periodicity artifacts for this system are not serious.
authors.affiliation: Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada. tieleman@ucalgary.ca
authors.forename: D Peter
authors.initials: DP
authors.lastname: Tieleman
authors.forename: Berk
authors.initials: B
authors.lastname: Hess
authors.forename: Mark S P
authors.initials: MS
authors.lastname: Sansom
mesh_terms: D000408:Alamethicin / Q000737:chemistry*; D000465:Algorithms; D000890:Anti-Infective Agents / Q000737:chemistry / Q000494:pharmacology*; D055592:Biophysical Phenomena; D001703:Biophysics; D002118:Calcium / Q000378:metabolism; D015220:Calcium Channels / Q000737:chemistry; D003198:Computer Simulation; D006863:Hydrogen-Ion Concentration; D008051:Lipid Bilayers / Q000737:chemistry; D008564:Membrane Potentials; D010455:Peptides / Q000737:chemistry; D010713:Phosphatidylcholines / Q000737:chemistry; D011189:Potassium Chloride / Q000737:chemistry; D011312:Pressure; D017433:Protein Structure, Secondary; D055672:Static Electricity; D013696:Temperature; D013997:Time Factors
chemical_list: D000890:Anti-Infective Agents; D015220:Calcium Channels; D008051:Lipid Bilayers; D010455:Peptides; D010713:Phosphatidylcholines; D000408:Alamethicin; D011189:Potassium Chloride; D002118:Calcium