746 research outputs found
Origin of entropy convergence in hydrophobic hydration and protein folding
An information theory model is used to construct a molecular explanation why
hydrophobic solvation entropies measured in calorimetry of protein unfolding
converge at a common temperature. The entropy convergence follows from the weak
temperature dependence of occupancy fluctuations for molecular-scale volumes in
water. The macroscopic expression of the contrasting entropic behavior between
water and common organic solvents is the relative temperature insensitivity of
the water isothermal compressibility. The information theory model provides a
quantitative description of small molecule hydration and predicts a negative
entropy at convergence. Interpretations of entropic contributions to protein
folding should account for this result.Comment: Phys. Rev. Letts. (in press 1996), 3 pages, 3 figure
Solvent-induced micelle formation in a hydrophobic interaction model
We investigate the aggregation of amphiphilic molecules by adapting the
two-state Muller-Lee-Graziano model for water, in which a solvent-induced
hydrophobic interaction is included implicitly. We study the formation of
various types of micelle as a function of the distribution of hydrophobic
regions at the molecular surface. Successive substitution of non-polar surfaces
by polar ones demonstrates the influence of hydrophobicity on the upper and
lower critical solution temperatures. Aggregates of lipid molecules, described
by a refinement of the model in which a hydrophobic tail of variable length
interacts with different numbers of water molecules, are stabilized as the
length of the tail increases. We demonstrate that the essential features of
micelle formation are primarily solvent-induced, and are explained within a
model which focuses only on the alteration of water structure in the vicinity
of the hydrophobic surface regions of amphiphiles in solution.Comment: 11 pages, 10 figures; some rearrangement of introduction and
discussion sections, streamlining of formalism and general compression; to
appear in Phys. Rev.
A possible mechanism for cold denaturation of proteins at high pressure
We study cold denaturation of proteins at high pressures. Using
multicanonical Monte Carlo simulations of a model protein in a water bath, we
investigate the effect of water density fluctuations on protein stability. We
find that above the pressure where water freezes to the dense ice phase
( kbar), the mechanism for cold denaturation with decreasing
temperature is the loss of local low-density water structure. We find our
results in agreement with data of bovine pancreatic ribonuclease A.Comment: 4 pages for double column and single space. 3 figures Added
references Changed conten
The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics
Protein folding is a universal process, very fast and accurate, which works
consistently (as it should be) in a wide range of physiological conditions. The
present work is based on three premises, namely: () folding reaction is a
process with two consecutive and independent stages, namely the search
mechanism and the overall productive stabilization; () the folding kinetics
results from a mechanism as fast as can be; and () at nanoscale
dimensions, local thermal fluctuations may have important role on the folding
kinetics. Here the first stage of folding process (search mechanism) is focused
exclusively. The effects and consequences of local thermal fluctuations on the
configurational kinetics, treated here in the context of non extensive
statistical mechanics, is analyzed in detail through the dependence of the
characteristic time of folding () on the temperature and on the
nonextensive parameter .The model used consists of effective residues
forming a chain of 27 beads, which occupy different sites of a D infinite
lattice, representing a single protein chain in solution. The configurational
evolution, treated by Monte Carlo simulation, is driven mainly by the change in
free energy of transfer between consecutive configurations. ...Comment: 19 pages, 3 figures, 1 tabl
Quantifying Self-Organization with Optimal Predictors
Despite broad interest in self-organizing systems, there are few
quantitative, experimentally-applicable criteria for self-organization. The
existing criteria all give counter-intuitive results for important cases. In
this Letter, we propose a new criterion, namely an internally-generated
increase in the statistical complexity, the amount of information required for
optimal prediction of the system's dynamics. We precisely define this
complexity for spatially-extended dynamical systems, using the probabilistic
ideas of mutual information and minimal sufficient statistics. This leads to a
general method for predicting such systems, and a simple algorithm for
estimating statistical complexity. The results of applying this algorithm to a
class of models of excitable media (cyclic cellular automata) strongly support
our proposal.Comment: Four pages, two color figure
Lattice model for cold and warm swelling of polymers in water
We define a lattice model for the interaction of a polymer with water. We
solve the model in a suitable approximation. In the case of a non-polar
homopolymer, for reasonable values of the parameters, the polymer is found in a
non-compact conformation at low temperature; as the temperature grows, there is
a sharp transition towards a compact state, then, at higher temperatures, the
polymer swells again. This behaviour closely reminds that of proteins, that are
unfolded at both low and high temperatures.Comment: REVTeX, 5 pages, 2 EPS figure
Finite size effects on thermal denaturation of globular proteins
Finite size effects on the cooperative thermal denaturation of proteins are
considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta,
where N is the number of amino acids. Surprisingly, we find that zeta is
universal with zeta = 1 + gamma, where the exponent gamma characterizes the
divergence of the susceptibility for a self-avoiding walk. Our lattice model
simulations and experimental data are consistent with the theory. Our finding
rationalizes the marginal stability of proteins and substantiates the earlier
predictions that the efficient folding of two-state proteins requires the
folding transition temperature to be close to the collapse temperature.Comment: 3 figures. Physical Review Letters (in press
A study of high-energy proton induced damage in Cerium Fluoride in comparison with measurements in Lead Tungstate calorimeter crystals
A Cerium Fluoride crystal produced during early R&D studies for calorimetry
at the CERN Large Hadron Collider was exposed to a 24 GeV/c proton fluence
Phi_p=(2.78 +- 0.20) x 10EE13 cm-2 and, after one year of measurements tracking
its recovery, to a fluence Phi_p=(2.12 +- 0.15) x 10EE14 cm-2. Results on
proton-induced damage to the crystal and its spontaneous recovery after both
irradiations are presented here, along with some new, complementary data on
proton-damage in Lead Tungstate. A comparison with FLUKA Monte Carlo simulation
results is performed and a qualitative understanding of high-energy damage
mechanism is attempted.Comment: Submitted to Elsevier Science on May 6th, 2010; 11 pages, 8 figure
Thermodynamics of Heat Shock Response
Production of heat shock proteins are induced when a living cell is exposed
to a rise in temperature. The heat shock response of protein DnaK synthesis in
E.coli for temperature shifts from temperature T to T plus 7 degrees,
respectively to T minus 7 degrees is measured as function of the initial
temperature T. We observe a reversed heat shock at low T. The magnitude of the
shock increases when one increase the distance to the temperature , thereby mimicking the non monotous stability of proteins at low
temperature. Further we found that the variation of the heat shock with T
quantitatively follows the thermodynamic stability of proteins with
temperature. This suggest that stability related to hot as well as cold
unfolding of proteins is directly implemented in the biological control of
protein folding. We demonstrate that such an implementation is possible in a
minimalistic chemical network.Comment: To be published in Physical Review Letter
Entropic Barriers, Frustration and Order: Basic Ingredients in Protein Folding
We solve a model that takes into account entropic barriers, frustration, and
the organization of a protein-like molecule. For a chain of size , there is
an effective folding transition to an ordered structure. Without frustration,
this state is reached in a time that scales as , with
. This scaling is limited by the amount of frustration which
leads to the dynamical selectivity of proteins: foldable proteins are limited
to monomers; and they are stable in {\it one} range of temperatures,
independent of size and structure. These predictions explain generic properties
of {\it in vivo} proteins.Comment: 4 pages, 4 Figures appended as postscript fil
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