4,606 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
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
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
Bidirectional transport on a dynamic lattice
Bidirectional variants of stochastic many particle models for transport by
molecular motors show a strong tendency to form macroscopic clusters on static
lattices. Inspired by the fact that the microscopic tracks for molecular motors
are dynamical, we study the influence of different types of lattice dynamics on
stochastic bidirectional transport. We observe a transition toward efficient
transport (corresponding to the dissolution of large clusters) controlled by
the lattice dynamics.Comment: 5 pages, 5 figure
Model for the unidirectional motion of a dynein molecule
Cytoplasmic dyneins transport cellular organelles by moving on a microtubule
filament. It has been found recently that depending on the applied force and
the concentration of the adenosine triphosphate (ATP) molecules, dynein's step
size varies. Based on these studies, we propose a simple model for dynein's
unidirectional motion taking into account the variations in its step size. We
study how the average velocity and the relative dispersion in the displacement
vary with the applied load. The model is amenable to further extensions by
inclusion of details associated with the structure and the processivity of the
molecule.Comment: 10 pages, 5 figure
Microtubule length distributions in the presence of protein-induced severing
Microtubules are highly regulated dynamic elements of the cytoskeleton of
eukaryotic cells. One of the regulation mechanisms observed in living cells is
the severing by the proteins katanin and spastin. We introduce a model for the
dynamics of microtubules in the presence of randomly occurring severing events.
Under the biologically motivated assumption that the newly created plus end
undergoes a catastrophe, we investigate the steady state length distribution.
We show that the presence of severing does not affect the number of
microtubules, regardless of the distribution of severing events. In the special
case in which the microtubules cannot recover from the depolymerizing state (no
rescue events) we derive an analytical expression for the length distribution.
In the general case we transform the problem into a single ODE that is solved
numerically.Comment: 9 pages, 4 figure
Rheology of Active Filament Solutions
We study the viscoelasticity of an active solution of polar biofilaments and
motor proteins. Using a molecular model, we derive the constitutive equations
for the stress tensor in the isotropic phase and in phases with liquid
crystalline order. The stress relaxation in the various phases is discussed.
Contractile activity is responsible for a spectacular difference in the
viscoelastic properties on opposite sides of the order-disorder transition.Comment: 4 pages, 1 figur
How does torsional rigidity affect the wrapping transition of a semiflexible chain around a spherical core?
We investigated the effect of torsional rigidity of a semiflexible chain on
the wrapping transition around a spherical core, as a model of nucleosome, the
fundamental unit of chromatin. Through molecular dynamics simulation, we show
that the torsional effect has a crucial effect on the chain wrapping around the
core under the topological constraints. In particular, the torsional stress (i)
induces the wrapping/unwrapping transition, and (ii) leads to a unique complex
structure with an antagonistic wrapping direction which never appears without
the topological constraints. We further examine the effect of the stretching
stress for the nucleosome model, in relation to the unique characteristic
effect of the torsional stress on the manner of wrapping
Insight into Resonant Activation in Discrete Systems
The resonant activation phenomenon (RAP) in a discrete system is studied
using the master equation formalism. We show that the RAP corresponds to a
non-monotonic behavior of the frequency dependent first passage time
probability density function (pdf). An analytical expression for the resonant
frequency is introduced, which, together with numerical results, helps
understand the RAP behavior in the space spanned by the transition rates for
the case of reflecting and absorbing boundary conditions. The limited range of
system parameters for which the RAP occurs is discussed. We show that a minimum
and a maximum in the mean first passage time (MFPT) can be obtained when both
boundaries are absorbing. Relationships to some biological systems are
suggested.Comment: 5 pages, 5 figures, Phys. Rev. E., in pres
Helicase activity on DNA as a propagating front
We develop a propagating front analysis, in terms of a local probability of
zipping, for the helicase activity of opening up a double stranded DNA (dsDNA).
In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front
separates the zipped and unzipped phases of a dsDNA and a drive acts locally
around the front. Bounds from variational analysis and numerical estimates for
the speed of a helicase are obtained. Different types of helicase behaviours
can be distinguished by the nature of the drive.Comment: 5 pages, 5 eps figures; replaced by the published versio
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