Biology Reference
In-Depth Information
values are normally linked to lower areas per lipid and, generally, to higher mem-
brane packing. Such packing should in turn affect the average tilt angle of cholesterol
molecules with respect to the bilayer normal. For this reason, the distribution of cho-
lesterol tilt angles across the simulation is frequently used to assess membrane con-
densation and phase behavior (
De Joannis et al., 2011; Zhao et al., 2011
).
However, it should be emphasized that the structural behavior of any system is
ultimately described by the behavior of its particles. In statistical mechanics, one pa-
rameter called radial distribution function (RDF) is used to characterize the density
of molecules as a function of distance from a reference molecule. Thus, the RDF can
provide information on the probability of finding certain lipid species around a ref-
erence lipid drawing the radial symmetry of our system during the simulation. This
radial information can help in understanding the probability density of the different
coordination shells built around a certain molecule type. However, the standard RDF
parameter only gives density values in one dimension, namely, the distance from the
reference molecule (
Fig. 4.2
). By considering two or three variables to represent lipid
probability densities, one can visualize a more complete view of the symmetry or
solvation profile across the simulation. For example, the planar steroid ring of cho-
lesterol is defined by a smooth face (
a
-face) versus a rough face (
b
-face) that con-
tains off-plane methyl groups. Phospholipids do not interact indistinctly with both
cholesterol faces and we need more than positional information to characterize this
FIGURE 4.2
Radial distribution function, g (r), as a function of the distance to a reference molecule. The
plot shows the density of phospholipid tails around cholesterol molecules averaged over
500 ns of simulation for four different membranes. The x-axis represents the distance in nm
to the center of mass of each cholesterol molecule of the simulation. First and second
coordination shells show up around 0.6 and 0.85 nm, respectively.
