5,934 research outputs found
Molecular Electroporation and the Transduction of Oligoarginines
Certain short polycations, such as TAT and polyarginine, rapidly pass through
the plasma membranes of mammalian cells by an unknown mechanism called
transduction as well as by endocytosis and macropinocytosis. These
cell-penetrating peptides (CPPs) promise to be medically useful when fused to
biologically active peptides. I offer a simple model in which one or more CPPs
and the phosphatidylserines of the inner leaflet form a kind of capacitor with
a voltage in excess of 180 mV, high enough to create a molecular electropore.
The model is consistent with an empirical upper limit on the cargo peptide of
40--60 amino acids and with experimental data on how the transduction of a
polyarginine-fluorophore into mouse C2C12 myoblasts depends on the number of
arginines in the CPP and on the CPP concentration. The model makes three
testable predictions.Comment: 15 pages, 5 figure
Melting of Branched RNA Molecules
Stability of the branching structure of an RNA molecule is an important
condition for its function. In this letter we show that the melting
thermodynamics of RNA molecules is very sensitive to their branching geometry
for the case of a molecule whose groundstate has the branching geometry of a
Cayley Tree and whose pairing interactions are described by the Go model.
Whereas RNA molecules with a linear geometry melt via a conventional continuous
phase transition with classical exponents, molecules with a Cayley Tree
geometry are found to have a free energy that seems smooth, at least within our
precision. Yet, we show analytically that this free energy in fact has a
mathematical singularity at the stability limit of the ordered structure. The
correlation length appears to diverge on the high-temperature side of this
singularity.Comment: 4 pages, 3 figure
Anomalously Slow Domain Growth in Fluid Membranes with Asymmetric Transbilayer Lipid Distribution
The effect of asymmetry in the transbilayer lipid distribution on the
dynamics of phase separation in fluid vesicles is investigated numerically for
the first time. This asymmetry is shown to set a spontaneous curvature for the
domains that alter the morphology and dynamics considerably. For moderate
tension, the domains are capped and the spontaneous curvature leads to
anomalously slow dynamics, as compared to the case of symmetric bilayers. In
contrast, in the limiting cases of high and low tensions, the dynamics proceeds
towards full phase separation.Comment: 4 pages, 5 figure
Efficiency at maximum power of interacting molecular machines
We investigate the efficiency of systems of molecular motors operating at
maximum power. We consider two models of kinesin motors on a microtubule: for
both the simplified and the detailed model, we find that the many-body
exclusion effect enhances the efficiency at maximum power of the many-motor
system, with respect to the single motor case. Remarkably, we find that this
effect occurs in a limited region of the system parameters, compatible with the
biologically relevant range.Comment: To appear in Phys. Rev. Let
Macroscopic loop formation in circular DNA denaturation
The statistical mechanics of DNA denaturation under fixed linking number is
qualitatively different from that of the unconstrained DNA. Quantitatively
different melting scenarios are reached from two alternative assumptions,
namely, that the denatured loops are formed in expense of 1) overtwist, 2)
supercoils. Recent work has shown that the supercoiling mechanism results in a
BEC-like picture where a macroscopic loop appears at Tc and grows steadily with
temperature, while the nature of the denatured phase for the overtwisting case
has not been studied. By extending an earlier result, we show here that a
macroscopic loop appears in the overtwisting scenario as well. We calculate its
size as a function of temperature and show that the fraction of the total sum
of microscopic loops decreases above Tc, with a cusp at the critical point.Comment: 5 pages, 3 figures, submitted for publicatio
Phase Transitions in Multicomponent String Model
We propose a one-dimensional model of a string decorated with adhesion
molecules (stickers) to mimic multicomponent membranes in restricted
geometries. The string is bounded by two parallel walls and it interacts with
one of them by short range attractive forces while the stickers are attracted
by the other wall. The exact solution of the model in the case of infinite wall
separation predicts both continuous and discontinuous transitions between
phases characterised by low and high concentration of stickers on the string.
Our model exhibits also coexistence of these two phases, similarly to models of
multicomponent membranes.Comment: letter, 8 pages, 3 figure
Ribosome recycling induces optimal translation rate at low ribosomal availability
Funding statement The authors thank BBSRC (BB/F00513/X1, BB/I020926/1 and DTG) and SULSA for funding. Acknowledgement The authors thank R. Allen, L. Ciandrini, B. Gorgoni and P. Greulich for very helpful discussions and careful reading of the manuscript.Peer reviewedPublisher PD
Mean encounter times for cell adhesion in hydrodynamic flow: analytical progress by dimensional reduction
For a cell moving in hydrodynamic flow above a wall, translational and
rotational degrees of freedom are coupled by the Stokes equation. In addition,
there is a close coupling of convection and diffusion due to the
position-dependent mobility. These couplings render calculation of the mean
encounter time between cell surface receptors and ligands on the substrate very
difficult. Here we show for a two-dimensional model system how analytical
progress can be achieved by treating motion in the vertical direction by an
effective reaction term in the mean first passage time equation for the
rotational degree of freedom. The strength of this reaction term can either be
estimated from equilibrium considerations or used as a fit parameter. Our
analytical results are confirmed by computer simulations and allow to assess
the relative roles of convection and diffusion for different scaling regimes of
interest.Comment: Reftex, postscript figures include
Domain Growth, Budding, and Fission in Phase Separating Self-Assembled Fluid Bilayers
A systematic investigation of the phase separation dynamics in self-assembled
multi-component bilayer fluid vesicles and open membranes is presented. We use
large-scale dissipative particle dynamics to explicitly account for solvent,
thereby allowing for numerical investigation of the effects of hydrodynamics
and area-to-volume constraints. In the case of asymmetric lipid composition, we
observed regimes corresponding to coalescence of flat patches, budding,
vesiculation and coalescence of caps. The area-to-volume constraint and
hydrodynamics have a strong influence on these regimes and the crossovers
between them. In the case of symmetric mixtures, irrespective of the
area-to-volume ratio, we observed a growth regime with an exponent of 1/2. The
same exponent is also found in the case of open membranes with symmetric
composition
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