Molecular structure of the outer bacterial membrane of Pseudomonas aeruginosa via classical simulation.
A detailed structural analysis has been performed of the outer bacterial membrane of Pseudomonas aeruginosa using a parameterized classical simulation model (R. D. Lins and T. P. Straatsma, Biophysical Journal, 2001, Vol. 81, pp. 1037-1046) with modest modifications. The structural analysis of the membrane is presented and newly discovered characteristics of the membrane are discussed. Simulations indicate that the relative contribution of different ligands to calcium ion coordination varies across the membrane, while maintaining a constant average coordination number of 6.1. Water penetrates the surface of the membrane to a depth of about 30 A. The hydration of ions and phosphate groups is shown to depend on location within the membrane. A measure of saccharide residue orientation is defined and average orientations are presented. Saccharide residues possess varying degrees of motion with a trend of greater mobility at the membrane surface. However, their motion is limited and even in the membrane outer core region the average structure appears fairly rigid over a period of 1 ns.
Shroll
Robert M
RM
Computational Biochemistry, Biophysics, and Biology Group, Pacific Northwest National Laboratory Richland, WA 99352, USA.
Straatsma
T P
TP
D002118:Calcium / Q000378:metabolism; D002462:Cell Membrane / Q000737:chemistry* / Q000378:metabolism; D019295:Computational Biology; D006860:Hydrogen Bonding; D008070:Lipopolysaccharides / Q000737:chemistry; D008956:Models, Chemical; D010710:Phosphates / Q000378:metabolism; D011550:Pseudomonas aeruginosa / Q000737:chemistry* / Q000378:metabolism
D008070:Lipopolysaccharides; D010710:Phosphates; D002118:Calcium