1,718 research outputs found
Structure and function of proteins and nucleic acid Progress report, 1 Jul. - 31 Dec. 1967
Conformation of pyridine nucleotide coenzymes by rotary dispersion and dichrois
A Fluorescent Probe at the Active Site of Alpha Chymotrypsin
Spectrofluorimetric analysis of mobility and polarity of active sites of alpha chymotrypsi
Mean field approaches to the totally asymmetric exclusion process with quenched disorder and large particles
The process of protein synthesis in biological systems resembles a one
dimensional driven lattice gas in which the particles (ribosomes) have spatial
extent, covering more than one lattice site. Realistic, nonuniform gene
sequences lead to quenched disorder in the particle hopping rates. We study the
totally asymmetric exclusion process with large particles and quenched disorder
via several mean field approaches and compare the mean field results with Monte
Carlo simulations. Mean field equations obtained from the literature are found
to be reasonably effective in describing this system. A numerical technique is
developed for computing the particle current rapidly. The mean field approach
is extended to include two-point correlations between adjacent sites. The
two-point results are found to match Monte Carlo simulations more closely
Multi-site H-bridge breathers in a DNA--shaped double strand
We investigate the formation process of nonlinear vibrational modes
representing broad H-bridge multi--site breathers in a DNA--shaped double
strand.
Within a network model of the double helix we take individual motions of the
bases within the base pair plane into account. The resulting H-bridge
deformations may be asymmetric with respect to the helix axis. Furthermore the
covalent bonds may be deformed distinctly in the two backbone strands.
Unlike other authors that add different extra terms we limit the interaction
to the hydrogen bonds within each base pair and the covalent bonds along each
strand. In this way we intend to make apparent the effect of the characteristic
helicoidal structure of DNA. We study the energy exchange processes related
with the relaxation dynamics from a non-equilibrium conformation. It is
demonstrated that the twist-opening relaxation dynamics of a radially distorted
double helix attains an equilibrium regime characterized by a multi-site
H-bridge breather.Comment: 27 pages and 10 figure
Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium
We study the nonlinear dynamics of a protein-DNA molecular system by treating
DNA as a set of two coupled linear chains and protein in the form of a single
linear chain sliding along the DNA at the physiological temperature in a
viscous medium. The nonlinear dynamics of the above molecular system in general
is governed by a perturbed nonlinear Schr\"{o}dinger equation. In the
non-viscous limit, the equation reduces to the completely integrable nonlinear
Schr\"{o}dinger (NLS) equation which admits N-soliton solutions. The soliton
excitations of the DNA bases make localized base pair opening and travel along
the DNA chain in the form of a bubble. This may represent the bubble generated
during the transcription process when an RNA-polymerase binds to a promoter
site in the DNA double helical chain. The perturbed NLS equation is solved
using a perturbation theory by treating the viscous effect due to surrounding
as a weak perturbation and the results show that the viscosity of the solvent
in the surrounding damps out the amplitude of the soliton.Comment: 4. Submitted to Phys. Rev.
Structurally specific thermal fluctuations identify functional sites for DNA transcription
We report results showing that thermally-induced openings of double stranded
DNA coincide with the location of functionally relevant sites for
transcription. Investigating both viral and bacterial DNA gene promoter
segments, we found that the most probable opening occurs at the transcription
start site. Minor openings appear to be related to other regulatory sites. Our
results suggest that coherent thermal fluctuations play an important role in
the initiation of transcription. Essential elements of the dynamics, in
addition to sequence specificity, are nonlinearity and entropy, provided by
local base-pair constraints
Highly Designable Protein Structures and Inter Monomer Interactions
By exact computer enumeration and combinatorial methods, we have calculated
the designability of proteins in a simple lattice H-P model for the protein
folding problem.
We show that if the strength of the non-additive part of the interaction
potential becomes larger than a critical value, the degree of designability of
structures will depend on the parameters of potential. We also show that the
existence of a unique ground state is highly sensitive to mutation in certain
sites.Comment: 14 pages, Latex file, 3 latex and 6 eps figures are include
Imaging density disturbances in water with 41.3 attosecond time resolution
We show that the momentum flexibility of inelastic x-ray scattering may be
exploited to invert its loss function, alowing real time imaging of density
disturbances in a medium. We show the disturbance arising from a point source
in liquid water, with a resolution of 41.3 attoseconds (
sec) and 1.27 ( cm). This result is used to
determine the structure of the electron cloud around a photoexcited molecule in
solution, as well as the wake generated in water by a 9 MeV gold ion. We draw
an analogy with pump-probe techniques and suggest that energy-loss scattering
may be applied more generally to the study of attosecond phenomena.Comment: 4 pages, 4 color figure
Inferring processes underlying B-cell repertoire diversity
We quantify the VDJ recombination and somatic hypermutation processes in
human B-cells using probabilistic inference methods on high-throughput DNA
sequence repertoires of human B-cell receptor heavy chains. Our analysis
captures the statistical properties of the naive repertoire, first after its
initial generation via VDJ recombination and then after selection for
functionality. We also infer statistical properties of the somatic
hypermutation machinery (exclusive of subsequent effects of selection). Our
main results are the following: the B-cell repertoire is substantially more
diverse than T-cell repertoires, due to longer junctional insertions; sequences
that pass initial selection are distinguished by having a higher probability of
being generated in a VDJ recombination event; somatic hypermutations have a
non-uniform distribution along the V gene that is well explained by an
independent site model for the sequence context around the hypermutation site.Comment: acknowledgement adde
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