COMPUTER SIMULATION OF TRANSPORT OF SMALL MOLECULES THROUGH A GAS CHANNEL EMBEDDED IN A PHOSPHOLIPID BILAYER
A series of molecular dynamics simulations are performed to study the transport of ammonia and carbon dioxide through a hydrated POPC (palmitoyloleoylphosphatidylcholine) bilayer and through bacterial ammonia transporter protein (AmtB) embedded in the lipid bilayer. The diffusion coefficients of the solutes in the two different systems are calculated to compare the rate of transport of the solutes through the different types of biological membranes. The solute molecules in the POPC bilayer system are allowed to diffuse from either the interior region of the lipid bilayer or the interface between the lipid bilayer and the bulk water phase. Diffusion coefficients of ammonia are on the order of 10^-5 cm2/s, while those of carbon dioxide are on the order of 10^-6 cm2/s, indicating the size dependency of the solute in transport through the hydrated lipid bilayer. Diffusion coefficients of ammonia and carbon dioxide through the AmtB channel protein are on the order of 10^-8 cm2/s. The retardation of the rate of transport through the channel is attributed to the restricted displacement of the solutes in the AmtB channel protein. The preferential association between the solutes and nitrogen atoms in the histidine residues of the AmtB channel protein is investigated by radial distribution function (RDF) analysis. The RDF results indicating strong association between ammonia and nitrogen atoms of the histidine residues supports evidence that the substrate for the AmtB protein is ammonia.
School:University of Cincinnati
School Location:USA - Ohio
Source Type:Master's Thesis
Keywords:molecular dynamics ammonia transporter phospholipid bilayer diffusion
Date of Publication:01/01/2005