5 research outputs found
Effect of the Southeast Asian Ovalocytosis Deletion on the Conformational Dynamics of Signal-Anchor Transmembrane Segment 1 of Red Cell Anion Exchanger 1 (AE1, Band 3, or SLC4A1)
The
first transmembrane (TM1) helix in the red cell anion exchanger
(AE1, Band 3, or SLC4A1) acts as an internal signal anchor that binds
the signal recognition particle and directs the nascent polypeptide
chain to the endoplasmic reticulum (ER) membrane where it moves from
the translocon laterally into the lipid bilayer. The sequence N-terminal
to TM1 forms an amphipathic helix that lies at the membrane interface
and
is connected to TM1 by a bend at Pro403. Southeast Asian ovalocytosis
(SAO) is a red cell abnormality caused by a nine-amino acid deletion
(Ala400–Ala408) at the N-terminus of TM1. Here we demonstrate,
by extensive (∼4.5 μs) molecular dynamics simulations
of TM1 in a model 1-palmitoyl-2-oleoyl-<i>sn</i>-glycero-3-phosphocholine
membrane, that the isolated TM1 peptide is highly dynamic and samples
the structure of TM1 seen in the crystal structure of the membrane
domain of AE1. The SAO deletion not only removes the proline-induced
bend but also causes a “pulling in” of the part of the
amphipathic helix into the hydrophobic phase of the bilayer, as well
as the C-terminal of the peptide. The dynamics of the SAO peptide
very infrequently resembles the structure of TM1 in AE1, demonstrating
the disruptive effect the SAO deletion has on AE1 folding. These results
provide a precise molecular view of the disposition and dynamics of
wild-type and SAO TM1 in a lipid bilayer, an important early biosynthetic
intermediate in the insertion of AE1 into the ER membrane, and extend
earlier results of cell-free translation experiments
Roles of Interleaflet Coupling and Hydrophobic Mismatch in Lipid Membrane Phase-Separation Kinetics
Characterizing
the nanoscale dynamic organization within lipid
bilayer
membranes is central
to our understanding of cell membranes at a molecular level. We investigate
phase separation and communication across leaflets in ternary lipid
bilayers, including saturated lipids with between 12 and 20 carbons
per tail. Coarse-grained molecular dynamics simulations reveal a novel
two-step kinetics due to hydrophobic mismatch, in which the initial
response of the apposed leaflets upon quenching is to increase local
asymmetry (antiregistration), followed by dominance of symmetry (registration)
as the bilayer equilibrates. Antiregistration can become thermodynamically
preferred if domain size is restricted below ∼20 nm, with implications
for the symmetry of rafts and nanoclusters in cell membranes, which
have similar reported sizes. We relate our findings to theory derived
from a semimicroscopic model in which the leaflets experience a “direct”
area-dependent coupling, and an “indirect” coupling
that arises from hydrophobic mismatch and is most important at domain
boundaries. Registered phases differ in composition from antiregistered
phases, consistent with a direct coupling between the leaflets. Increased
hydrophobic mismatch purifies the phases, suggesting that it contributes
to the molecule-level lipid immiscibility. Our results demonstrate
an interplay of competing interleaflet couplings that affect phase
compositions and kinetics, and lead to a length scale that
can influence lateral and transverse bilayer organization within cells
Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane
The cytoskeleton underlying cell
membranes may influence the dynamic
organization of proteins and lipids within the bilayer by immobilizing
certain transmembrane (TM) proteins and forming corrals within the
membrane. Here, we present coarse-grained resolution simulations of
a biologically realistic membrane model of asymmetrically organized
lipids and TM proteins. We determine the effects of a model of cytoskeletal
immobilization of selected membrane proteins using long time scale
coarse-grained molecular dynamics simulations. By introducing compartments
with varying degrees of restraints within the membrane models, we
are able to reveal how compartmentalization caused by cytoskeletal
immobilization leads to reduced and anomalous diffusional mobility
of both proteins and lipids. This in turn results in a reduced rate
of protein dimerization within the membrane and of hopping of membrane
proteins between compartments. These simulations provide a molecular
realization of hierarchical models often invoked to explain single-molecule
imaging studies of membrane proteins
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
A necessary
step prior to starting any membrane protein computer
simulation is the creation of a well-packed configuration of protein(s)
and lipids. Here, we demonstrate a method, <i>alchembed</i>, that can simultaneously and rapidly embed multiple proteins into
arrangements of lipids described using either atomistic or coarse-grained
force fields. During a short simulation, the interactions between
the protein(s) and lipids are gradually switched on using a soft-core
van der Waals potential. We validate the method on a range of membrane
proteins and determine the optimal soft-core parameters required to
insert membrane proteins. Since all of the major biomolecular codes
include soft-core van der Waals potentials, no additional code is
required to apply this method. A tutorial is included in the Supporting Information
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
A necessary
step prior to starting any membrane protein computer
simulation is the creation of a well-packed configuration of protein(s)
and lipids. Here, we demonstrate a method, <i>alchembed</i>, that can simultaneously and rapidly embed multiple proteins into
arrangements of lipids described using either atomistic or coarse-grained
force fields. During a short simulation, the interactions between
the protein(s) and lipids are gradually switched on using a soft-core
van der Waals potential. We validate the method on a range of membrane
proteins and determine the optimal soft-core parameters required to
insert membrane proteins. Since all of the major biomolecular codes
include soft-core van der Waals potentials, no additional code is
required to apply this method. A tutorial is included in the Supporting Information