564 research outputs found
Unwrapping of DNA-protein complexes under external stretching
A DNA-protein complex modelled by a semiflexible chain and an attractive
spherical core is studied in the situation when an external stretching force is
acting on one end monomer of the chain while the other end monomer is kept
fixed in space. Without stretching force, the chain is wrapped around the core.
By applying an external stretching force, unwrapping of the complex is induced.
We study the statics and the dynamics of the unwrapping process by computer
simulation and simple phenomenological theory. We find two different scenarios
depending on the chain stiffness: For a flexible chain, the extension of the
complex scales linearly with the external force applied. The sphere-chain
complex is disordered, i.e. there is no clear winding of the chain around the
sphere. For a stiff chain, on the other hand, the complex structure is ordered,
which is reminiscent to nucleosome. There is a clear winding number and the
unwrapping process under external stretching is discontinuous with jumps of the
distance-force curve. This is associated to discrete unwinding processes of the
complex. Our predictions are of relevance for experiments, which measure
force-extension curves of DNA-protein complexes, such as nucleosome, using
optical tweezers.Comment: 8 pages, 7 figure
The two-angle model and the phase diagram for Chromatin
We have studied the phase diagram for chromatin within the framework of the
two-angle model. Rather than improving existing models with finer details our
main focus of the work is getting mathematically rigorous results on the
structure, especially on the excluded volume effects and the effects on the
energy due to the long-range forces and their screening. Thus we present a
phase diagram for the allowed conformations and the Coulomb energies
Intrinsic Low Temperature Paramagnetism in B-DNA
We present experimental study of magnetization in -DNA in
conjunction with structural measurements. The results show the surprising
interplay between the molecular structures and their magnetic property. In the
B-DNA state, -DNA exhibits paramagnetic behaviour below 20 K that is
non-linear in applied magnetic field whereas in the A-DNA state, remains
diamagnetic down to 2 K. We propose orbital paramagnetism as the origin of the
observed phenomena and discuss its relation to the existence of long range
coherent transport in B-DNA at low temperature.Comment: 5 pages, 4 figures, submitted to Physical Review Letters October 200
Organized condensation of worm-like chains
We present results relevant to the equilibrium organization of DNA strands of
arbitrary length interacting with a spherical organizing center, suggestive of
DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in
which a wrapping state is transformed into a complex multi-leafed, rosette
structure as the adhesion energy is reduced. The statistical mechanics of the
"melting" of a rosette can be mapped into an exactly soluble one-dimensional
many-body problem.Comment: 15 pages, 2 figures in a pdf fil
Hierarchical Chain Model of Spider Capture Silk Elasticity
Spider capture silk is a biomaterial with both high strength and high
elasticity, but the structural design principle underlying these remarkable
properties is still unknown. It was revealed recently by atomic force
microscopy that, an exponential force--extension relationship holds both for
capture silk mesostructures and for intact capture silk fibers [N. Becker et
al., Nature Materials 2, 278 (2003)]. In this Letter a simple hierarchical
chain model was proposed to understand and reproduce this striking observation.
In the hierarchical chain model, a polymer is composed of many structural
motifs which organize into structural modules and supra-modules in a
hierarchical manner. Each module in this hierarchy has its own characteristic
force. The repetitive patterns in the amino acid sequence of the major
flagelliform protein of spider capture silk is in support of this model.Comment: 4 pages, 3 figures. Will be formally published in PR
Kinetics of the helix-coil transition
Based on the Zimm-Bragg model we study cooperative helix-coil transition
driven by a finite-speed change of temperature. There is an asymmetry between
the coil-to-helix and helix-to-coil transition: the latter is displayed already
for finite speeds, and takes shorter time than the former. This hysteresis
effect has been observed experimentally, and it is explained here via
quantifying system's stability in the vicinity of the critical temperature. A
finite-speed cooling induces a non-equilibrium helical phase with the
correlation length larger than in equilibrium. In this phase the characteristic
length of the coiled domain and the non-equilibrium specific heat can display
an anomalous response to temperature changes. Several pertinent experimental
results on the kinetics helical biopolymers are discussed in detail.Comment: 6 pages, 8 figure
Chromatin: a tunable spring at work inside chromosomes
This paper focuses on mechanical aspects of chromatin biological functioning.
Within a basic geometric modeling of the chromatin assembly, we give for the
first time the complete set of elastic constants (twist and bend persistence
lengths, stretch modulus and twist-stretch coupling constant) of the so-called
30-nm chromatin fiber, in terms of DNA elastic properties and geometric
properties of the fiber assembly. The computation naturally embeds the fiber
within a current analytical model known as the ``extensible worm-like rope'',
allowing a straightforward prediction of the force-extension curves. We show
that these elastic constants are strongly sensitive to the linker length, up to
1 bp, or equivalently to its twist, and might locally reach very low values,
yielding a highly flexible and extensible domain in the fiber. In particular,
the twist-stretch coupling constant, reflecting the chirality of the chromatin
fiber, exhibits steep variations and sign changes when the linker length is
varied.
We argue that this tunable elasticity might be a key feature for chromatin
function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure
Constraints, Histones, and the 30 Nanometer Spiral
We investigate the mechanical stability of a segment of DNA wrapped around a
histone in the nucleosome configuration. The assumption underlying this
investigation is that the proper model for this packaging arrangement is that
of an elastic rod that is free to twist and that writhes subject to mechanical
constraints. We find that the number of constraints required to stabilize the
nuclesome configuration is determined by the length of the segment, the number
of times the DNA wraps around the histone spool, and the specific constraints
utilized. While it can be shown that four constraints suffice, in principle, to
insure stability of the nucleosome, a proper choice must be made to guarantee
the effectiveness of this minimal number. The optimal choice of constraints
appears to bear a relation to the existence of a spiral ridge on the surface of
the histone octamer. The particular configuration that we investigate is
related to the 30 nanometer spiral, a higher-order organization of DNA in
chromatin.Comment: ReVTeX, 15 pages, 18 figure
Force-dependent binding constants
Life is an emergent property of transient interactions between biomolecules and other organic and inorganic molecules that somehow leads to harmony and order. Measurement and quantitation of these biological interactions is of value to scientists, and is a major goal of biochemistry, as affinities provide insight into biological processes. In an organism these interactions occur in the context of forces and the need for a consideration of binding affinities in the context of a changing mechanical landscape necessitates a new way to consider the biochemistry of protein-protein interactions. In the last few decades the field of Mechanobiology has exploded, as both the appreciation, and the technical advances required to facilitate the study, of how forces impact on biological processes has become evident. The aim of this review is to introduce the concept of force-dependence of biomolecular interactions, and the requirement to be able to measure force-dependent binding constants. The focus of this discussion will be on the mechanotransduction that occurs at the integrin-mediated adhesions with the extracellular matrix, and the major mechanosensors talin and vinculin. However, the approaches that the cell uses to sense and respond to forces are applicable to other systems, and therefore provides a general discussion of the force-dependence of biomolecule interactions
Statistical-mechanical lattice models for protein-DNA binding in chromatin
Statistical-mechanical lattice models for protein-DNA binding are well
established as a method to describe complex ligand binding equilibriums
measured in vitro with purified DNA and protein components. Recently, a new
field of applications has opened up for this approach since it has become
possible to experimentally quantify genome-wide protein occupancies in relation
to the DNA sequence. In particular, the organization of the eukaryotic genome
by histone proteins into a nucleoprotein complex termed chromatin has been
recognized as a key parameter that controls the access of transcription factors
to the DNA sequence. New approaches have to be developed to derive statistical
mechanical lattice descriptions of chromatin-associated protein-DNA
interactions. Here, we present the theoretical framework for lattice models of
histone-DNA interactions in chromatin and investigate the (competitive) DNA
binding of other chromosomal proteins and transcription factors. The results
have a number of applications for quantitative models for the regulation of
gene expression.Comment: 19 pages, 7 figures, accepted author manuscript, to appear in J.
Phys.: Cond. Mat
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