Biology Reference
In-Depth Information
FIGURE 4.1
Electron density profiles of different membranes. This figure, reprinted with permission from
Sadiq et al. (2013
), shows the average electron density profile of five different membrane
systems simulated over 200 ns across the lipid bilayer (x-axis in
˚
). All systems contain the
cholesterol (1:3), POPC (1:3), plus the phospholipid under study, namely, DLPC, DMPC,
DPPC, DSPC, or SOPC (1:3). The center of the bilayer is located at 0 A
˚
. Membrane thickness
is normally measured as the “phosphate-to-phosphate” distance, that is, the distance in
˚
betweenmaximum peak values (normally at
15-25
˚
from the bilayer center). In contrast,
membrane interdigitation is assessed around the center of the bilayer. Both membrane
thickness and membrane interdigitation increase for longer chains; however, a subtle
interplay between chain length and degree of chain saturation exists. In this sense, despite
having the same carbon length, SOPC and DSPC chains display a different profile of
membrane interdigitation. DLPC, 1,2-dilauroyl phosphatidylcholine; DMPC, 1,2-dimyristoyl
phosphatidylcholine; DPPC, 1,2-dipalmitoyl phosphatidylcholine; DSPC, 1,2-distearoyl
phosphatidylcholine; POPC, 1-palmitoyl-2-oleoyl phosphatidylcholine; SOPC, 1-stearoyl-2-
oleoyl phosphatidylcholine.
as they have to inevitably accommodate the bottom part of their tails (
Fig. 4.1
). How-
ever, when dealing with protein-membrane systems, the local deformation of the
membrane around the protein needs to be taken into account when describing mem-
brane thickness. In this line,
Mondal, Khelashvili, Shan, Andersen, and Weinstein
(2011)
recently developed a tool to compute, among other things, the local deforma-
tion profile of GPCR-membrane simulations (see
Section 4.2.3
).
Yet, the structure of the membrane is ultimately determined by the conformation
of the individual lipid species within the bilayer. Therefore, the area per lipid is an
important parameter that holds information on the condensation degree of our system
and that can serve as a monitor of the equilibration state. This parameter is easily
