Sugar–membrane interactions are believed to be
responsible
for cell preservation during desiccation and freezing, but the molecular
mechanism by which they achieve this is still not well understood.
The associated decrease of the main phase transition temperature of
phospholipid bilayers is explained by two opposing views on the matter:
the direct sugar–phospholipid interaction at the bilayer interface
(water replacement hypothesis) and an entropy-driven phase transition
with sugar molecules concentrating away from the lipid interface (hydration
forces explanation). Both mechanisms are supported by experiments
but molecular dynamics (MD) simulations have overwhelmingly shown
the occurrence of direct sugar–phospholipid interactions. We
have performed MD simulations of 1,2-dioleoyl-sn-glycero-3-phosphocholine
(DOPC) bilayers at different water and sucrose contents. The behavior
of sucrose was found to depend on both the sucrose and water contents:
at high sucrose concentration and at low hydration, it is best described
by the hydration forces explanation model, whereas at low sucrose
concentration, it is consistent with the water replacement hypothesis
model. These simulations reveal that at low concentration, sucrose
molecules preferentially interact directly with the membrane interface
while at high concentration, they preferentially accumulate in the
intermembrane solution. The transition between the two modes of interaction
is revealed for the first time as being governed by the saturation
of the lipid bilayer interface with sucrose molecules, and this occurs
more rapidly as the level of hydration decreases.
We present a new version of the program package nMoldyn, which has been originally developed for a neutron-scattering oriented analysis of molecular dynamics simulations of macromolecular systems (Kneller et al., Comput. Phys. Commun. 1995, 91, 191) and was later rewritten to include in-depth time series analyses and a graphical user interface (Rog et al., J. Comput. Chem. 2003, 24, 657). The main improvement in this new version and the focus of this article are the parallelization of all the analysis algorithms for use on multicore desktop computers as well as distributed-memory computing clusters. The parallelization is based on a task farming approach which maintains a simple program structure permitting easy modification and extension of the code to integrate new analysis methods.
Biophysical studies of model cell
membranes at full and low hydration
are usually carried out using scattering measurements on multi-bilayer
systems. Molecular simulations of lipid bilayers aimed at reproducing
those experimental conditions are usually conducted using single bilayers
with different amounts of water. These simulation conditions may lead
to artifacts arising from size effects and self-interactions because
of periodic boundary conditions. We have tested the influence of the
size and number of bilayers on membrane properties using the Lipid14
force field for lipids in molecular dynamics simulations of 1,2-dioleoyl-sn-glycero-3-phosphocholine bilayers at full hydration (44
water molecules per lipid), low hydration (18 water molecules per
lipid), and dehydration (9 water molecules per lipid). A number of
additional simulations were conducted with the Slipids force field
for comparison. We have found that the average area per lipid (APL),
thickness, mass density profiles, and acyl tail order parameters are
insensitive to the size and the number of bilayers for all hydration
states. The Lipid14 force field can also successfully reproduce the
experimentally observed decrease in APL and corresponding increase
in bilayer thickness upon dehydration, reflecting the increase in
ordering as the system becomes more gel-like. Additionally, decreasing
hydration levels were associated with a trend away from normal lateral
diffusion and toward more subdiffusive regimes across both force fields.
In summary, at least for the Lipid14 force field, the use of a single
bilayer with 128 phospholipid molecules provides an adequate representation
of multi-bilayer systems at varying levels of hydration.
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