832 research outputs found
Chirality and Protein Folding
There are several simple criteria of folding to a native state in model
proteins. One of them involves crossing of a threshold value of the RMSD
distance away from the native state. Another checks whether all native contacts
are established, i.e. whether the interacting amino acids come closer than some
characteristic distance. We use Go-like models of proteins and show that such
simple criteria may prompt one to declare folding even though fragments of the
resulting conformations have a wrong sense of chirality. We propose that a
better condition of folding should augment the simple criteria with the
requirement that most of the local values of the chirality should be nearly
native. The kinetic discrepancy between the simple and compound criteria can be
substantially reduced in the Go-like models by providing the Hamiltonian with a
term which favors native values of the local chirality. We study the effects of
this term as a function of its amplitude and compare it to other models such as
with the side groups and with the angle-dependent potentials.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo
Workshop
Effects of confinement and crowding on folding of model proteins
We perform molecular dynamics simulations for a simple coarse-grained model
of crambin placed inside of a softly repulsive sphere of radius R. The
confinement makes folding at the optimal temperature slower and affects the
folding scenarios, but both effects are not dramatic. The influence of crowding
on folding are studied by placing several identical proteins within the sphere,
denaturing them, and then by monitoring refolding. If the interactions between
the proteins are dominated by the excluded volume effects, the net folding
times are essentially like for a single protein. An introduction of
inter-proteinic attractive contacts hinders folding when the strength of the
attraction exceeds about a half of the value of the strength of the single
protein contacts. The bigger the strength of the attraction, the more likely is
the occurrence of aggregation and misfolding
Coarse grained description of the protein folding
We consider two- and three-dimensional lattice models of proteins which were
characterized previously. We coarse grain their folding dynamics by reducing it
to transitions between effective states. We consider two methods of selection
of the effective states. The first method is based on the steepest descent
mapping of states to underlying local energy minima and the other involves an
additional projection to maximally compact conformations. Both methods generate
connectivity patterns that allow to distinguish between the good and bad
folders. Connectivity graphs corresponding to the folding funnel have few loops
and are thus tree-like. The Arrhenius law for the median folding time of a
16-monomer sequence is established and the corresponding barrier is related to
easily identifiable kinetic trap states.Comment: REVTeX, 9 pages, 15 EPS figures, to appear in Phys. Rev.
Energy landscapes, supergraphs, and "folding funnels" in spin systems
Dynamical connectivity graphs, which describe dynamical transition rates
between local energy minima of a system, can be displayed against the
background of a disconnectivity graph which represents the energy landscape of
the system. The resulting supergraph describes both dynamics and statics of the
system in a unified coarse-grained sense. We give examples of the supergraphs
for several two dimensional spin and protein-related systems. We demonstrate
that disordered ferromagnets have supergraphs akin to those of model proteins
whereas spin glasses behave like random sequences of aminoacids which fold
badly.Comment: REVTeX, 9 pages, two-column, 13 EPS figures include
Nanoindentation of virus capsids in a molecular model
A molecular-level model is used to study the mechanical response of empty
cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids.
The model is based on the native structure of the proteins that consitute the
capsids and is described in terms of the C-alpha atoms. Nanoindentation by a
large tip is modeled as compression between parallel plates. Plots of the
compressive force versus plate separation for CCMV are qualitatively consistent
with continuum models and experiments, showing an elastic region followed by an
irreversible drop in force. The mechanical response of CPMV has not been
studied, but the molecular model predicts an order of magnitude higher
stiffness and a much shorter elastic region than for CCMV. These large changes
result from small structural changes that increase the number of bonds by only
30% and would be difficult to capture in continuum models. Direct comparison of
local deformations in continuum and molecular models of CCMV shows that the
molecular model undergoes a gradual symmetry breaking rotation and accommodates
more strain near the walls than the continuum model. The irreversible drop in
force at small separations is associated with rupturing nearly all of the bonds
between capsid proteins in the molecular model while a buckling transition is
observed in continuum models.Comment: 18 figure
Experimental Limits on Primordial Black Hole Dark Matter from the First Two Years of Kepler Data
We present the analysis on our new limits of the dark matter (DM) halo
consisting of primordial black holes (PBHs) or massive compact halo objects
(MACHOs). We present a search of the first two years of publicly available
Kepler mission data for potential signatures of gravitational microlensing
caused by these objects, as well as an extensive analysis of the astrophysical
sources of background error. These include variable stars, flare events, and
comets or asteroids which are moving through the Kepler field. We discuss the
potential of detecting comets using the Kepler lightcurves, presenting
measurements of two known comets and one unidentified object, most likely an
asteroid or comet. After removing the background events with statistical cuts,
we find no microlensing candidates. We therefore present our Monte Carlo
efficiency calculation in order to constrain the PBH DM with masses in the
range of 2 x 10^-9 solar masses to 10^-7 solar masses. We find that PBHs in
this mass range cannot make up the entirety of the DM, thus closing a full
order of magnitude in the allowed mass range for PBH DM.Comment: 12 pages, 6 figure
Doping effects of Co, Ni, and Cu in FeTe0.65Se0.35 single crystals
The resistivity, magnetoresistance, and magnetic susceptibility are measured
in single crystals of FeTe0.65Se0.35 with Cu, Ni, and Co substitutions for Fe.
The crystals are grown by Bridgman's method. The resistivity measurements show
that superconductivity disappears with the rate which correlates with the
nominal valence of the impurity. From magnetoresistance we evaluate doping
effect on the basic superconducting parameters, such as upper critical field
and coherence length. We find indications that doping leads to two component
superconducting behavior, possibly because of local charge depression around
impurities.Comment: 4 pages, 4 figures, 1 table, Proceedings of the XV-th National School
"Hundred Years of Superconductivity", Kazimierz Dolny, October 9-13, 201
Response approach to the squeezed-limit bispectrum: application to the correlation of quasar and Lyman- forest power spectrum
The squeezed-limit bispectrum, which is generated by nonlinear gravitational
evolution as well as inflationary physics, measures the correlation of three
wavenumbers, in the configuration where one wavenumber is much smaller than the
other two. Since the squeezed-limit bispectrum encodes the impact of a
large-scale fluctuation on the small-scale power spectrum, it can be understood
as how the small-scale power spectrum "responds" to the large-scale
fluctuation. Viewed in this way, the squeezed-limit bispectrum can be
calculated using the response approach even in the cases which do not submit to
perturbative treatment. To illustrate this point, we apply this approach to the
cross-correlation between the large-scale quasar density field and small-scale
Lyman- forest flux power spectrum. In particular, using separate
universe simulations which implement changes in the large-scale density,
velocity gradient, and primordial power spectrum amplitude, we measure how the
Lyman- forest flux power spectrum responds to the local,
long-wavelength quasar overdensity, and equivalently their squeezed-limit
bispectrum. We perform a Fisher forecast for the ability of future experiments
to constrain local non-Gaussianity using the bispectrum of quasars and the
Lyman- forest. Combining with quasar and Lyman- forest power
spectra to constrain the biases, we find that for DESI the expected
constraint is . Ability for DESI to measure
through this channel is limited primarily by the aliasing and
instrumental noise of the Lyman- forest flux power spectrum. The
combination of response approach and separate universe simulations provides a
novel technique to explore the constraints from the squeezed-limit bispectrum
between different observables.Comment: 20 pages, 4 figures; matches JCAP accepted versio
Scaling of folding properties in simple models of proteins
Scaling of folding properties of proteins is studied in a toy system -- the
lattice Go model with various two- and three- dimensional geometries of the
maximally compact native states. Characteristic folding times grow as power
laws with the system size. The corresponding exponents are not universal.
Scaling of the thermodynamic stability also indicates size-related
deterioration of the folding properties.Comment: REVTeX, 4 pages, 4 EPS figures, PRL (in press
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