1,928 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
DNA folding: structural and mechanical properties of the two-angle model for chromatin
We present a theoretical analysis of the structural and mechanical properties
of the 30-nm chromatin fiber. Our study is based on the two-angle model
introduced by Woodcock et al. (Woodcock, C. L., S. A. Grigoryev, R. A.
Horowitz, and N. Whitaker. 1993. PNAS 90:9021-9025) that describes the
chromatin fiber geometry in terms of the entry-exit angle of the nucleosomal
DNA and the rotational setting of the neighboring nucleosomes with respect to
each other. We explore analytically the different structures that arise from
this building principle, and demonstrate that the geometry with the highest
density is close to the one found in native chromatin fibers under
physiological conditions. On the basis of this model we calculate mechanical
properties of the fiber under stretching. We obtain expressions for the
stress-strain characteristics which show good agreement with the results of
recent stretching experiments (Cui, Y., and C. Bustamante. 2000. PNAS
97:127-132) and computer simulations (Katritch, V., C. Bustamante, and W. K.
Olson. 2000. J. Mol. Biol. 295:29-40), and which provide simple physical
insights into correlations between the structural and elastic properties of
chromatin.Comment: 23 pages, 6 figures, to be published in Biophys.
The influence of the cylindrical shape of the nucleosomes and H1 defects on properties of chromatin
We present a model improving the two-angle model for interphase chromatin
(E2A model). This model takes into account the cylindrical shape of the histone
octamers, the H1 histones in front of the nucleosomes and the vertical distance
between the in and outgoing DNA strands. Factoring these chromatin features
in, one gets essential changes in the chromatin phase diagram: Not only the
shape of the excluded-volume borderline changes but also the vertical distance
has a dramatic influence on the forbidden area. Furthermore, we examined
the influence of H1 defects on the properties of the chromatin fiber. Thus we
present two possible strategies for chromatin compaction: The use of very dense
states in the phase diagram in the gaps in the excluded volume borderline or
missing H1 histones which can lead to very compact fibers. The chromatin fiber
might use both of these mechanisms to compact itself at least locally. Line
densities computed within the model coincident with the experimental values
A Circular Dichroic Study of Cu (II) -Ribonuclease Complexes
The visible and ultraviolet circular dichroic (CD) spectra resulting from the interaction of ribonuclease with successive Cu(I1) ions have been recorded under a variety of conditions. At pH 7 in the presence of 0.16 M KC1 a broad, negative band was found in the visible region. This band increased in intensity and changed in shape as successive coppers were added. The circular dichroic spectra could be analyzed in terms of two kinds of binding sites: a single strong site with CD minimum at about 710 nm, and four weaker sites with CD minimum at about 600 nm. The binding constants observed are close to those obtained by more conventional means. Carboxymethylation of one histidine results in loss of one of the weaker sites. In 0.01 M salt, only the 600-nm band is seen. Binding at pH 9.6 differed in that saturation did not occur until about 33 sites had been filled. The presence of tetra coordination at this pH was indicated by the shift of the primary d-d transition down to 530 nm. Additional structure in the visible and near ultraviolet CD was now present in the form of a negative band at 355 nm and, for the first two Cu(II)‘s added, a positive one at 480 nm. Strong positive bands were observed at 251 and 305 nm for all pH values ≥7. These are tentatively ascribed to charge transfer complexes between Cu(I1) and the peptide backbone. The relationship of the Cu(II)-ribonuclease CD spectra to those of natural, copper-containing metalloproteins, both “blue” and “non-blue”, is discussed, with special emphasis on the oxyhemocyanins
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
5,6-dihydroxyindole-2-carboxylic acid (DHICA): a First Principles Density-Functional Study
We report first principles density functional calculations for
5,6-dihydroxyindole-2-carboxylic acid (DHICA) and several reduced forms. DHICA
and 5,6-dihydroxyindole (DHI) are believed to be the basic building blocks of
the eumelanins. Our results show that carboxylation has a significant effect on
the physical properties of the molecules. In particular, the relative
stabilities and the HOMO-LUMO gaps (calculated with the SCF method) of
the various redox forms are strongly affected. We predict that, in contrast to
DHI, the density of unpaired electrons, and hence the ESR signal, in DHICA is
negligibly small.Comment: 5 pages, 2 figure
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