3 research outputs found
Atomistic Model for Nearly Quantitative Simulations of Langmuir Monolayers
Lung
surfactant and a tear film lipid layer are examples of biologically
relevant macromolecular structures found at the air–water interface.
Because of their complexity, they are often studied in terms of simplified
lipid layers, the simplest example being a Langmuir monolayer. Given
the profound biological significance of these lipid assemblies, there
is a need to understand their structure and dynamics on the nanoscale,
yet there are not many techniques able to provide this information.
Atomistic molecular dynamics simulations would be a tool fit for this
purpose; however, the simulation models suggested until now have been
qualitative instead of quantitative. This limitation has mainly stemmed
from the challenge to correctly describe the surface tension of water
with simulation parameters compatible with other biomolecules. In
this work, we show that this limitation can be overcome by using the
recently introduced four-point OPC water model, whose surface tension
for water is demonstrated to be quantitatively consistent with experimental
data and which is also shown to be compatible with the commonly employed
lipid models. We further establish that the approach of combining
the OPC four-point water model with the CHARMM36 lipid force field
provides nearly quantitative agreement with experiments for the surface
pressure–area isotherm for POPC and DPPC monolayers, also including
the experimentally observed phase coexistence in a DPPC monolayer.
The simulation models reported in this work pave the way for nearly
quantitative atomistic studies of lipid-rich biological structures
at air–water interfaces
Calcium Sensing by Recoverin: Effect of Protein Conformation on Ion Affinity
The
detailed functional mechanism of recoverin, which acts as a
myristoyl switch at the rod outer-segment disk membrane, is elucidated
by direct and replica-exchange molecular dynamics. In accord with
NMR structural evidence and calcium binding assays, simulations point
to the key role of enhanced calcium binding to the EF3 loop of the
semiopen state of recoverin as compared to the closed state. This
2–4-order decrease in calcium dissociation constant stabilizes
the semiopen state in response to the increase of cytosolic calcium
concentration in the vicinity of recoverin. A second calcium ion then
binds to the EF2 loop and, consequently, the structure of the protein
changes from the semiopen to the open state. The latter has the myristoyl
chain extruded to the cytosol, ready to act as a membrane anchor of
recoverin
nmrlipids.blogspot.fi — on October 25th 2015
<p>Snapshot of the blog nmrlipids.blogspot.fi on October 25th 2015.</p>
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<p>The NMRlipids project is an open scientific collaboration to understand the atomistic resolution structures of lipid bilayers through classical molecular dynamics simulations. The project is progressed through the comments in the blog and using the GitHub organization (see links). The main results are also published in traditional peer reviewed scientific journals.</p