1,977 research outputs found
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
Viscosity Dependence of the Folding Rates of Proteins
The viscosity dependence of the folding rates for four sequences (the native
state of three sequences is a beta-sheet, while the fourth forms an
alpha-helix) is calculated for off-lattice models of proteins. Assuming that
the dynamics is given by the Langevin equation we show that the folding rates
increase linearly at low viscosities \eta, decrease as 1/\eta at large \eta and
have a maximum at intermediate values. The Kramers theory of barrier crossing
provides a quantitative fit of the numerical results. By mapping the simulation
results to real proteins we estimate that for optimized sequences the time
scale for forming a four turn \alpha-helix topology is about 500 nanoseconds,
whereas the time scale for forming a beta-sheet topology is about 10
microseconds.Comment: 14 pages, Latex, 3 figures. One figure is also available at
http://www.glue.umd.edu/~klimov/seq_I_H.html, to be published in Physical
Review Letter
Glassy Dynamics of Protein Folding
A coarse grained model of a random polypeptide chain, with only discrete
torsional degrees of freedom and Hookean springs connecting pairs of
hydrophobic residues is shown to display stretched exponential relaxation under
Metropolis dynamics at low temperatures with the exponent , in
agreement with the best experimental results. The time dependent correlation
functions for fluctuations about the native state, computed in the Gaussian
approximation for real proteins, have also been found to have the same
functional form. Our results indicate that the energy landscape exhibits
universal features over a very large range of energies and is relatively
independent of the specific dynamics.Comment: RevTeX, 4 pages, multicolumn, including 5 figures; larger
computations performed, error bars improve
Theta-point universality of polyampholytes with screened interactions
By an efficient algorithm we evaluate exactly the disorder-averaged
statistics of globally neutral self-avoiding chains with quenched random charge
in monomer i and nearest neighbor interactions on
square (22 monomers) and cubic (16 monomers) lattices. At the theta transition
in 2D, radius of gyration, entropic and crossover exponents are well compatible
with the universality class of the corresponding transition of homopolymers.
Further strong indication of such class comes from direct comparison with the
corresponding annealed problem. In 3D classical exponents are recovered. The
percentage of charge sequences leading to folding in a unique ground state
approaches zero exponentially with the chain length.Comment: 15 REVTEX pages. 4 eps-figures . 1 tabl
Conformational Entropy of Compact Polymers
Exact results for the scaling properties of compact polymers on the square
lattice are obtained from an effective field theory. The entropic exponent
\gamma=117/112 is calculated, and a line of fixed points associated with
interacting chains is identified; along this line \gamma varies continuously.
Theoretical results are checked against detailed numerical transfer matrix
calculations, which also yield a precise estimate for the connective constant
\kappa=1.47280(1).Comment: 4 pages, 1 figur
A Solvable Model of Secondary Structure Formation in Random Hetero-Polymers
We propose and solve a simple model describing secondary structure formation
in random hetero-polymers. It describes monomers with a combination of
one-dimensional short-range interactions (representing steric forces and
hydrogen bonds) and infinite range interactions (representing polarity forces).
We solve our model using a combination of mean field and random field
techniques, leading to phase diagrams exhibiting second-order transitions
between folded, partially folded and unfolded states, including regions where
folding depends on initial conditions. Our theoretical results, which are in
excellent agreement with numerical simulations, lead to an appealing physical
picture of the folding process: the polarity forces drive the transition to a
collapsed state, the steric forces introduce monomer specificity, and the
hydrogen bonds stabilise the conformation by damping the frustration-induced
multiplicity of states.Comment: 24 pages, 14 figure
Freezing Transition of Random Heteropolymers Consisting of an Arbitrary Set of Monomers
Mean field replica theory is employed to analyze the freezing transition of
random heteropolymers comprised of an arbitrary number () of types of
monomers. Our formalism assumes that interactions are short range and
heterogeneity comes only from pairwise interactions, which are defined by an
arbitrary matrix. We show that, in general, there exists a
freezing transition from a random globule, in which the thermodynamic
equilibrium is comprised of an essentially infinite number polymer
conformations, to a frozen globule, in which equilibrium ensemble is dominated
by one or very few conformations. We also examine some special cases of
interaction matrices to analyze the relationship between the freezing
transition and the nature of interactions involved.Comment: 30 pages, 1 postscript figur
Exploring the Levinthal limit in protein folding
According to the thermodynamic hypothesis, the native state of proteins is uniquely defined by their amino acid sequence. On the other hand, according to Levinthal, the native state is just a local minimum of the free energy and a given amino acid sequence, in the same thermodynamic conditions, can assume many, very different structures that are as thermodynamically stable as the native state. This is the Levinthal limit explored in this work. Using computer simulations, we compare the interactions that stabilize the native state of four different proteins with those that stabilize three non-native states of each protein and find that the nature of the interactions is very similar for all such 16 conformers. Furthermore, an enhancement of the degree of fluctuation of the non-native conformers can be explained by an insufficient relaxation to their local free energy minimum. These results favor Levinthal's hypothesis that protein folding is a kinetic non-equilibrium process.FCT - Foundation for Science and Technology, Portugal [UID/Multi/04326/2013]; Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP); Conselho Nacional de Desenvolvimento Cientia co e Tecnologico (CNPq
A New Monte Carlo Algorithm for Protein Folding
We demonstrate that the recently proposed pruned-enriched Rosenbluth method
(P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient
algorithms for the folding of simple model proteins. We test them on several
models for lattice heteropolymers, and compare to published Monte Carlo
studies. In all cases our algorithms are faster than all previous ones, and in
several cases we find new minimal energy states. In addition to ground states,
our algorithms give estimates for the partition sum at finite temperatures.Comment: 4 pages, Latex incl. 3 eps-figs., submitted to Phys. Rev. Lett.,
revised version with changes in the tex
DON content in oat grains in Norway related to weather conditions at different growth stages
High concentrations of the mycotoxin deoxynivalenol (DON), produced by Fusarium graminearum have occurred frequently in Norwegian oats recently. Early prediction of DON levels is important for farmers, authorities and the Cereal Industry. In this study, the main weather factors influencing myco-toxin accumulation were identified and two models to predict the risk of DON in oat grains in Norway were developed: (1) as a warning system for farmers to decide if and when to treat with fungicide, and (2) for authorities and industry to use at harvest to identify potential food safety problems. Oat grain samples from farmers’ fields were collected together with weather data (2004–2013)
A mathematical model was developed and used to esti-
mate phenology windows of growth stages in oats (til-
lering, flowering etc.). Weather summarisations were
then calculated within these windows, and the Spearman
rank correlation factor calculated between DON-
contamination in oats at harvest and the weather
summarisations for each phenological window. DON
contamination was most clearly associated with the
weather conditions around flowering and close to har-
vest. Warm, rainy and humid weather during and around
flowering increased the risk of DON accumulation in
oats, as did dry periods during germination/seedling
growth and tillering. Prior to harvest, warm and humid
weather conditions followed by cool and dry conditions
were associated with a decreased risk of DON accumu-
lation. A prediction model, including only pre-flowering
weather conditions, adequately forecasted risk of DON
contamination in oat, and can aid in decisions about
fungicide treatments
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