Morphology of Voids in Molecular Systems.
A Voronoi-Delaunay Analysis of a Simulated DMPC Membrane
Abstract:
A generalized version of the Voronoi-Delaunay method
is used to the study relatively large intermolecular
voids in a model of the hydrated DMPC bilayer,
obtained from all-atom Monte Carlo simulation. Application
of the original version of the method for molecular systems
has been hampered by the fact that these systems
geometrically represent ensembles of partially overlapping spheres
of different radii. The generalized version
of the method is based on using the additively weighed Voronoi diagram,
representing the locus of spatial points being equally far from
the surface rather than the center of the corresponding pair of atoms.
This version of the Voronoi-Delaunay method can be readily used
to reveal and analyze voids accessible for probes of different radii
even in rather complex molecular systems.
When the properties of the voids present in the simulated DMPC membrane
are investigated, their shape, size, and orientation
have been analyzed in detail in the different regions of the membrane
located at different depths along the membrane normal axis.
The characteristics of the voids are found to be different
in different regions
of the bilayer, namely (i) at the
middle of the membrane, in the region of the hydrophobic lipid tails,
(ii) in the region of the hydrophilic
zwitterionic headgroups, and
(iii) in the region of the bulklike water adjacent
to the bilayer. The largest and
oblong voids are found in the middle of the membrane,
with a preferred orientation that is parallel to the
bilayer normal axis.
A clear correlation between the orientation of the voids
and the orientation of the lipid
chains is observed.
In the bulk water region the fraction of the empty space is
even higher than at the middle
of the membrane; however, here the voids are distributed more uniformly.
Finally, in the high-density region
of the hydrophilic headgroups the voids are found, on average,
smaller than in the other parts of the system.