779 research outputs found
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 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
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
A new estimation of the recent tropospheric molecular hydrogen budget using atmospheric observations and variational inversion
This paper presents an analysis of the recent tropospheric molecular hydrogen (H2) budget with a particular focus on soil uptake and European surface emissions. A variational inversion scheme is combined with observations from the RAMCES and EUROHYDROS atmospheric networks, which include continuous measurements performed between mid-2006 and mid-2009. Net H2 surface flux, then deposition velocity and surface emissions and finally, deposition velocity, biomass burning, anthropogenic and N2 fixation-related emissions were simultaneously inverted in several scenarios. These scenarios have focused on the sensibility of the soil uptake value to different spatio-temporal distributions. The range of variations of these diverse inversion sets generate an estimate of the uncertainty for each term of the H2 budget. The net H2 flux per region (High Northern Hemisphere, Tropics and High Southern Hemisphere) varies between −8 and +8 Tg yr−1. The best inversion in terms of fit to the observations combines updated prior surface emissions and a soil deposition velocity map that is based on bottom-up and top-down estimations. Our estimate of global H2 soil uptake is −59±9 Tg yr−1. Forty per cent of this uptake is located in the High Northern Hemisphere and 55% is located in the Tropics. In terms of surface emissions, seasonality is mainly driven by biomass burning emissions. The inferred European anthropogenic emissions are consistent with independent H2 emissions estimated using a H2/CO mass ratio of 0.034 and CO emissions within the range of their respective uncertainties. Additional constraints, such as isotopic measurements would be needed to infer a more robust partition of H2 sources and sinks
Phase transitions in biological membranes
Native membranes of biological cells display melting transitions of their
lipids at a temperature of 10-20 degrees below body temperature. Such
transitions can be observed in various bacterial cells, in nerves, in cancer
cells, but also in lung surfactant. It seems as if the presence of transitions
slightly below physiological temperature is a generic property of most cells.
They are important because they influence many physical properties of the
membranes. At the transition temperature, membranes display a larger
permeability that is accompanied by ion-channel-like phenomena even in the
complete absence of proteins. Membranes are softer, which implies that
phenomena such as endocytosis and exocytosis are facilitated. Mechanical signal
propagation phenomena related to nerve pulses are strongly enhanced. The
position of transitions can be affected by changes in temperature, pressure, pH
and salt concentration or by the presence of anesthetics. Thus, even at
physiological temperature, these transitions are of relevance. There position
and thereby the physical properties of the membrane can be controlled by
changes in the intensive thermodynamic variables. Here, we review some of the
experimental findings and the thermodynamics that describes the control of the
membrane function.Comment: 23 pages, 15 figure
Ziyapaş kadın
Amédé Victor Guillemine'in Hizmet'te yayımlanan Ziyapaş Kadın adlı romanının ilk ve son tefrikalarıTefrikanın devamına rastlanmamış, tefrika yarım kalmıştır
Energetic Components of Cooperative Protein Folding
A new lattice protein model with a four-helix bundle ground state is analyzed
by a parameter-space Monte Carlo histogram technique to evaluate the effects of
an extensive variety of model potentials on folding thermodynamics. Cooperative
helical formation and contact energies based on a 5-letter alphabet are found
to be insufficient to satisfy calorimetric and other experimental criteria for
two-state folding. Such proteinlike behaviors are predicted, however, by models
with polypeptide-like local conformational restrictions and
environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press
Engineering a two-helix bundle protein for folding studies
The SAP domain from the Saccharomyces cerevisiae THO1 protein contains a hydrophobic core and just two α-helices. It could provide a system for studying protein folding that bridges the gap between studies on isolated helices and those on larger protein domains. We have engineered the SAP domain for protein folding studies by inserting a tryptophan residue into the hydrophobic core (L31W) and solved its structure. The helical regions had a backbone root mean-squared deviation of 0.9 Å from those of wild type. The mutation L31W destabilised wild type by 0.8 ± 0.1 kcal mol−1. The mutant folded in a reversible, apparent two-state manner with a microscopic folding rate constant of around 3700 s−1 and is suitable for extended studies of folding
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