571 research outputs found
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
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
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
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
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
Spin-boson models for quantum decoherence of electronic excitations of biomolecules and quantum dots in a solvent
We give a theoretical treatment of the interaction of electronic excitations
(excitons) in biomolecules and quantum dots with the surrounding polar solvent.
Significant quantum decoherence occurs due to the interaction of the electric
dipole moment of the solute with the fluctuating electric dipole moments of the
individual molecules in the solvent. We introduce spin boson models which could
be used to describe the effects of decoherence on the quantum dynamics of
biomolecules which undergo light-induced conformational change and on
biomolecules or quantum dots which are coupled by Forster resonant energy
transfer.Comment: More extended version, to appear in Journal of Physics: Condensed
Matter. 13 pages, 3 figure
Monte Carlo Simulations indicate that Chromati: Nanostructure is accessible by Light Microscopy
A long controversy exists about the structure of chromatin. Theoretically, this structure could be resolved by scattering experiments if one determines the scattering function - or equivalently the pair distribution function - of the nucleosomes. Unfortunately, scattering experiments with live cells are very difficult and limited to only a couple of nucleosomes
Saturation Behavior: a general relationship described by a simple second-order differential equation
<p>Abstract</p> <p>Background</p> <p>The numerous natural phenomena that exhibit saturation behavior, <it>e.g</it>., ligand binding and enzyme kinetics, have been approached, to date, via empirical and particular analyses. This paper presents a mechanism-free, and assumption-free, second-order differential equation, designed only to describe a typical relationship between the variables governing these phenomena. It develops a mathematical model for this relation, based solely on the analysis of the typical experimental data plot and its saturation characteristics. Its utility complements the traditional empirical approaches.</p> <p>Results</p> <p>For the general saturation curve, described in terms of its independent (<it>x</it>) and dependent (<it>y</it>) variables, a second-order differential equation is obtained that applies to any saturation phenomena. It shows that the driving factor for the basic saturation behavior is the probability of the interactive site being free, which is described quantitatively. Solving the equation relates the variables in terms of the two empirical constants common to all these phenomena, the initial slope of the data plot and the limiting value at saturation. A first-order differential equation for the slope emerged that led to the concept of the effective binding rate at the active site and its dependence on the calculable probability the interactive site is free. These results are illustrated using specific cases, including ligand binding and enzyme kinetics. This leads to a revised understanding of how to interpret the empirical constants, in terms of the variables pertinent to the phenomenon under study.</p> <p>Conclusions</p> <p>The second-order differential equation revealed the basic underlying relations that describe these saturation phenomena, and the basic mathematical properties of the standard experimental data plot. It was shown how to integrate this differential equation, and define the common basic properties of these phenomena. The results regarding the importance of the slope and the new perspectives on the empirical constants governing the behavior of these phenomena led to an alternative perspective on saturation behavior kinetics. Their essential commonality was revealed by this analysis, based on the second-order differential equation.</p
Isolation, Characterization and Lipid-Binding Properties of the Recalcitrant FtsA Division Protein from Escherichia coli
We have obtained milligram amounts of highly pure Escherichia coli division protein FtsA from inclusion bodies with an optimized purification method that, by overcoming the reluctance of FtsA to be purified, surmounts a bottleneck for the analysis of the molecular basis of FtsA function. Purified FtsA is folded, mostly monomeric and interacts with lipids. The apparent affinity of FtsA binding to the inner membrane is ten-fold higher than to phospholipids, suggesting that inner membrane proteins could modulate FtsA-membrane interactions. Binding of FtsA to lipids and membranes is insensitive to ionic strength, indicating that a net contribution of hydrophobic interactions is involved in the association of FtsA to lipid/membrane structures
An All-Atom Model of the Chromatin Fiber Containing Linker Histones Reveals a Versatile Structure Tuned by the Nucleosomal Repeat Length
In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties
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