(775c) In Silico Model Escherichia Coli Membranes: Simulating a Lipid with a Cyclopropane Ring

            Bacterial
membranes are composed mostly of lipids with phosphoethanolamine (PE) and
phosphoglycerol (PG) head groups and a variety of fatty acid chains. A defining
characteristic of bacterial membranes is the presence of lipids with a
cyclic-containing chain. To our knowledge, a phospholipid with such a chain has
never been studied in a molecular dynamics simulation. Thus, novel force
field parameters to describe a cyclopropane moiety were developed using
parameters from the CHARMM36 (C36) general force field as a basis and
high-level quantum mechanical energies. Two simple membranes and one complex
membrane for use as realistic model Escherichia
coli (E. coli) cytoplasmic membranes were designed for future
work with secondary active transporters expressed in E. coli.
Compositions of the membranes were based on several different experimental
methods using an E. coli K12 strain grown on Luria broth.  One simple membrane consisted of 85 % PE
18:1/16:0 (POPE) and 15 % PG 18:1/16:0 (POPG), and the other of only PE cy17:0/16:0 (PMPE). The complex
membrane consisted of six different phospholipids, the most prevalent being the
cyclic-containing lipid, PMPE. NPT simulations were carried out at 310 K for 50
ns using the C36 lipid force field and the developed cyclopropane moiety force
field for each membrane. NMR deuterium order parameters (S_CD) and
density profiles are compared with experiment and other computational efforts
respectively. The complex model membrane will provide a basis to study membrane
bound proteins or other bound molecules expressed in E. coli with realistic molecular dynamic simulations.