05年的AMBER肽膜作用文章

Phosphatidylethanolamine-Phosphatidylglycerol Bilayer as a Model of the Inner Bacterial Membrane

ABSTRACT:
Phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) are the main lipid components of the inner bacterial membrane. A computer model for such a membrane was built of palmitoyloleoyl PE (POPE) and palmitoyloleoyl PG (POPG) in the proportion 3:1, and sodium ions (Na1) to neutralize the net negative charge on each POPG (POPE-POPG bilayer). The bilayer was simulated for 25 ns. A final 10-ns trajectory fragment was used for analyses. In the bilayer interfacial region, POPEs and POPGs interact readily with one another via intermolecular hydrogen (H) bonds and water bridges. POPE is the main H-bond donor in either PE...PE or PE...PG H-bonds; PG...PG H-bonds are rarely formed. Almost all POPEs are H-bonded and/or water bridged to either POPE or POPG but PE-PG links are favored. In effect, the atom packing in the nearthe-interface regions of the bilayer core is tight. Na1 does not bind readily to lipids, and interlipid links via Na1 are not numerous. Although POPG and POPE comprise one bilayer, their bilayer properties differ. The average surface area per POPG is larger and the average vertical location of the POPG phosphate group is lower than those of POPE. Also, the alkyl chains of POPG are more ordered and less densely packed than the POPE chains. The main conclusion of this study is that in the PE-PG bilayer PE interacts more strongly with PG than with PE. This is a likely molecular-level event behind a regulating mechanism developed by the bacteria to control its membrane permeability and stability consisting in changes of the relative PG/PE concentration in the membrane.

先用AMBER 4.0作了14ns的模拟，再用AMBER 5.0跑了14ns，一共25ns。膜POPE：POPG=3：1，主要模拟带负电荷的原核生物（细菌）细胞膜。

[ 本帖最后由 geffery 于 2008-8-29 18:47 编辑 ]