9,986 research outputs found
Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites
Evolutionary-rate variation among sites within proteins depends on functional and biophysical properties that constrain protein evolution. It is generally accepted that proteins must be able to fold stably in order to function. However, the relationship between stability constraints and among-sites rate variation is not well understood. Here, we present a biophysical model that links the thermodynamic stability changes due to mutations at sites in proteins (ΔΔG) to the rate at which mutations accumulate at those sites over evolutionary time. We find that such a 'stability model' generally performs well, displaying correlations between predicted and empirically observed rates of up to 0.75 for some proteins. We further find that our model has comparable predictive power as does an alternative, recently proposed 'stress model' that explains evolutionary-rate variation among sites in terms of the excess energy needed for mutants to adopt the correct active structure (ΔΔG∗). The two models make distinct predictions, though, and for some proteins the stability model outperforms the stress model and vice versa. We conclude that both stability and stress constrain site-specific sequence evolution in proteins.Fil: Echave, Julián. Universidad Nacional de San MartÃn. Escuela de Ciencia y TecnologÃa; Argentina. Consejo Nacional de Investigaciones CientÃficas y Técnicas; ArgentinaFil: Jackson, Eleisha L.. University of Texas at Austin; Estados UnidosFil: Wilke, Claus O.. University of Texas at Austin; Estados Unido
Dynamic charge inhomogenity in cuprate superconductors
The inelastic x-ray scattering spectrum for phonons of -symmetry
including the CuO bond-stretching phonon dispersion is analyzed by a Lorentz
fit in HgBaCuO and BiSrCuO, respectively, using
recently calculated phonon frequencies as input parameters. The resulting mode
frequencies of the fit are almost all in good agreement with the calculated
data. An exception is the second highest -branch compromising the
bond-stretching modes which disagrees in both compounds with the calculations.
This branch unlike the calculations shows an anomalous softening with a minimum
around the wavevector \vc{q}=\frac{2\pi}{a}(0.25, 0, 0). Such a disparity
with the calculated results, that are based on the assumption of an undisturbed
translation- and point group invariant electronic structure of the CuO plane,
indicates some {\it static} charge inhomogenities in the measured probes. Most
likely these will be charge stripes along the CuO bonds which have the
strongest coupling to certain longitudinal bond-stretching modes that in turn
selfconsistently induce corresponding {\it dynamic} charge inhomogenities. The
symmetry breaking by the mix of dynamic and static charge inhomogenities can
lead to a reconstruction of the Fermi surface into small pockets.Comment: 7 pages, 4 figure
Enhancement of the Critical Current Density of YBa2Cu3Ox Superconductors under Hydrostatic Pressure
The dependence of the critical current density Jc on hydrostatic pressure to
0.6 GPa is determined for a single 25-degree [001]-tilt grain boundary in a
bicrystalline ring of nearly optimally doped melt-textured YBa2Cu3Ox. Jc is
found to increase rapidly under pressure at +20 %/GPa. A new diagnostic method
is introduced (pressure-induced Jc relaxation) which reveals a sizeable
concentration of vacant oxygen sites in the grain boundary region. Completely
filling such sites with oxygen anions should lead to significant enhancements
in Jc.Comment: revised manuscript, graphic errors in figures correcte
Analyzing Machupo virus-receptor binding by molecular dynamics simulations
In many biological applications, we would like to be able to computationally
predict mutational effects on affinity in protein-protein interactions.
However, many commonly used methods to predict these effects perform poorly in
important test cases. In particular, the effects of multiple mutations,
non-alanine substitutions, and flexible loops are difficult to predict with
available tools and protocols. We present here an existing method applied in a
novel way to a new test case; we interrogate affinity differences resulting
from mutations in a host-virus protein-protein interface. We use steered
molecular dynamics (SMD) to computationally pull the machupo virus (MACV) spike
glycoprotein (GP1) away from the human transferrin receptor (hTfR1). We then
approximate affinity using the maximum applied force of separation and the area
under the force-versus-distance curve. We find, even without the rigor and
planning required for free energy calculations, that these quantities can
provide novel biophysical insight into the GP1/hTfR1 interaction. First, with
no prior knowledge of the system we can differentiate among wild type and
mutant complexes. Moreover, we show that this simple SMD scheme correlates well
with relative free energy differences computed via free energy perturbation.
Second, although the static co-crystal structure shows two large
hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate
that one of them may not be important for tight binding. Third, one viral site
known to be critical for infection may mark an important evolutionary
suppressor site for infection-resistant hTfR1 mutants. Finally, our approach
provides a framework to compare the effects of multiple mutations, individually
and jointly, on protein-protein interactions.Comment: 33 pages, 8 figures, 5 table
Quantum Stress Tensor Fluctuations and their Physical Effects
We summarize several aspects of recent work on quantum stress tensor
fluctuations and their role in driving fluctuations of the gravitational field.
The role of correlations and anticorrelations is emphasized. We begin with a
review of the properties of the stress tensor correlation function. We next
consider some illuminating examples of non-gravitational effects of stress
tensors fluctuations, specifically fluctuations of the Casimir force and
radiation pressure fluctuations. We next discuss passive fluctuations of
spacetime geometry and some of their operational signatures. These include
luminosity fluctuations, line broadening, and angular blurring of a source
viewed through a fluctuating gravitational field. Finally, we discuss the
possible role of quantum stress tensor fluctuations in the early universe,
especially in inflation. The fluctuations of the expansion of a congruence of
comoving geodesics grows during the inflationary era, due to non-cancellation
of anticorrelations that would have occurred in flat spacetime. This results in
subsequent non-Gaussian density perturbations and allows one to infer an upper
bound on the duration of inflation. This bound is consistent with adequate
inflation to solve the horizon and flatness problems.Comment: 15 pages, 1 figure; invited talk presented at the 3rd Mexican Meeting
on Experimental and Theoretical Physics, Mexico City, September 10-14, 200
Kondo physics in tunable semiconductor nanowire quantum dots
We have observed the Kondo effect in strongly coupled semiconducting nanowire
quantum dots. The devices are made from indium arsenide nanowires, grown by
molecular beam epitaxy, and contacted by titanium leads. The device
transparency can be tuned by changing the potential on a gate electrode, and
for increasing transparencies the effects dominating the transport changes from
Coulomb Blockade to Universal Conductance Fluctuations with Kondo physics
appearing in the intermediate region.Comment: 4 pages, 4 figure
The scalar sector in the Myers-Pospelov model
We construct a perturbative expansion of the scalar sector in the
Myers-Pospelov model, up to second order in the Lorentz violating parameter and
taking into account its higher-order time derivative character. This expansion
allows us to construct an hermitian positive-definite Hamiltonian which
provides a correct basis for quantization. Demanding that the modified normal
frequencies remain real requires the introduction of an upper bound in the
magnitude |k| of the momentum, which is a manifestation of the effective
character of the model. The free scalar propagator, including the corresponding
modified dispersion relations, is also calculated to the given order, thus
providing the starting point to consider radiative corrections when
interactions are introduced.Comment: Published in AIP Conf.Proc.977:214-223,200
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