6,651 research outputs found
Microscopic Theory of Protein Folding Rates.I: Fine Structure of the Free Energy Profile and Folding Routes from a Variational Approach
A microscopic theory of the free energy barriers and folding routes for
minimally frustrated proteins is presented, greatly expanding on the
presentation of the variational approach outlined previously [J. J. Portman, S.
Takada, P. G. Wolynes, Phys. Rev. Lett. {\bf 81}, 5237 (1998)]. We choose the
-repressor protein as an illustrative example and focus on how the
polymer chain statistics influence free energy profiles and partially ordered
ensembles of structures. In particular, we investigate the role of chain
stiffness on the free energy profile and folding routes. We evaluate the
applicability of simpler approximations in which the conformations of the
protein molecule along the folding route are restricted to have residues that
are either entirely folded or unfolded in contiguous stretches. We find that
the folding routes obtained from only one contiguous folded region corresponds
to a chain with a much greater persistence length than appropriate for natural
protein chains, while the folding route obtained from two contiguous folded
regions is able to capture the relatively folded regions calculated within the
variational approach. The free energy profiles obtained from the contiguous
sequence approximations have larger barriers than the more microscopic
variational theory which is understood as a consequence of partial ordering.Comment: 16 pages, 11 figure
Sulphur abundances in metal-poor stars
We investigate the debated "sulphur discrepancy" found among metal-poor stars
of the Galactic halo with [Fe/H] < -2. This discrepancy stems in part from the
use of two different sets of sulphur lines, the very weak triplet at 8694-95 A
and the stronger triplet lines at 9212 - 9237 A. For three representative cases
of metal-poor dwarf, turnoff and subgiant stars, we argue that the abundances
from the 8694-95 lines have been overestimated which has led to a continually
rising trend of [S/Fe] as metallicity decreases. Given that the near-IR region
is subject to CCD fringing, these weak lines become excessively difficult to
measure accurately in the metallicity regime of [Fe/H] < -2. Based on
homogeneously determined spectroscopic stellar parameters, we also present
updated [S/Fe] ratios from the 9212-9237 lines which suggest a plateau-like
behaviour similar to that seen for other alpha elements.Comment: accepted by A&A, 4 pages, 3 tables, 1 figure; v2: Table2 updated with
metallicities from other work
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A point mutation of integrin beta 1 subunit blocks binding of alpha 5 beta 1 to fibronectin and invasin but not recruitment to adhesion plaques.
A point mutation in a highly conserved region of the beta 1 subunit, Asp130 to Ala (D130A) substitution, abrogates the Arg-Gly-Asp (RGD)-dependent binding of alpha 5 beta 1 to fibronectin (FN) without disrupting gross structure or heterodimer assembly. The D130A mutation also interferes with binding to invasin, a ligand that lacks RGD sequence. In spite of the lack of detectable FN binding by alpha 5 beta 1(D130A), it was recruited to adhesion plaques formed on FN by endogenous hamster receptors. Thus, intact ligand binding function is not required for recruitment of alpha 5 beta 1 to adhesion plaques. Overexpression of beta 1(D130A) partially interfered with endogenous alpha 5 beta 1 function, thus defining a dominant negative beta 1 integrin mutation
Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics
The motion involved in barrier crossing for protein folding are investigated
in terms of the chain dynamics of the polymer backbone, completing the
microscopic description of protein folding presented in the previous paper.
Local reaction coordinates are identified as collective growth modes of the
unstable fluctuations about the saddle-points in the free energy surface. The
description of the chain dynamics incorporates internal friction (independent
of the solvent viscosity) arising from the elementary isomerizations of the
backbone dihedral angles. We find that the folding rate depends linearly on the
solvent friction for high viscosity, but saturates at low viscosity because of
internal friction. For -repressor, the calculated folding rate
prefactor, along with the free energy barrier from the variational theory,
gives a folding rate that agrees well with the experimentally determined rate
under highly stabilizing conditions, but the theory predicts too large a
folding rate at the transition midpoint. This discrepancy obtained using a
fairly complete quantitative theory inspires a new set of questions about chain
dynamics, specifically detailed motions in individual contact formation.Comment: 18 pages, 8 figure
The infrared conductivity of NaCoO: evidence of gapped states
We present infrared ab-plane conductivity data for the layered cobaltate
NaCoO at three different doping levels (, and 0.75). The
Drude weight increases monotonically with hole doping, . At the lowest
hole doping level =0.75 the system resembles the normal state of underdoped
cuprate superconductors with a scattering rate that varies linearly with
frequency and temperature and there is an onset of scattering by a bosonic mode
at 600 \cm. Two higher hole doped samples ( and 0.25) show two
different-size gaps (110 \cm and 200 \cm, respectively) in the optical
conductivities at low temperatures and become insulators. The spectral weights
lost in the gap region of 0.50 and 0.25 samples are shifted to prominent peaks
at 200 \cm and 800 \cm, respectively. We propose that the two gapped states of
the two higher hole doped samples (=0.50 and 0.25) are pinned charge ordered
states.Comment: 4 pages, 3 figure
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Distinct functions of integrin alpha and beta subunit cytoplasmic domains in cell spreading and formation of focal adhesions.
Integrin-mediated cell adhesion often results in cell spreading and the formation of focal adhesions. We exploited the capacity of recombinant human alpha IIb beta 3 integrin to endow heterologous cells with the ability to adhere and spread on fibrinogen to study the role of integrin cytoplasmic domains in initiation of cell spreading and focal adhesions. The same constructs were also used to analyze the role of the cytoplasmic domains in maintenance of the fidelity of the integrin repertoire at focal adhesions. Truncation mutants of the cytoplasmic domain of alpha IIb did not interfere with the ability of alpha IIb beta 3 to initiate cell spreading and form focal adhesions. Nevertheless, deletion of the alpha IIb cytoplasmic domain allowed indiscriminate recruitment of alpha IIb beta 3 to focal adhesions formed by other integrins. Truncation of the beta 3 subunit cytoplasmic domain abolished cell spreading mediated by alpha IIb beta 3 and also abrogated recruitment of alpha IIb beta 3 to focal adhesions. This truncation also dramatically impaired the ability of alpha IIb beta 3 to mediate the contraction of fibrin gels. In contrast, the beta 3 subunit cytoplasmic truncation did not reduce the fibrinogen binding affinity of alpha IIb beta 3. Thus, the integrin beta 3 subunit cytoplasmic domain is necessary and sufficient for initiation of cell spreading and focal adhesion formation. Further, the beta 3 cytoplasmic domain is required for the transmission of intracellular contractile forces to fibrin gels. The alpha subunit cytoplasmic domain maintains the fidelity of recruitment of the integrins to focal adhesions and thus regulates their repertoire of integrins
Halo-Galaxy Lensing: A Full Sky Approach
The halo-galaxy lensing correlation function or the average tangential shear
profile over sampled halos is a very powerful means of measuring the halo
masses, the mass profile, and the halo-mass correlation function of very large
separations in the linear regime. We reformulate the halo-galaxy lensing
correlation in harmonic space. We find that, counter-intuitively, errors in the
conventionally used flat-sky approximation remain at a % level even at very
small angles. The errors increase at larger angles and for lensing halos at
lower redshifts: the effect is at a few % level at the baryonic acoustic
oscillation scales for lensing halos of , and comparable with the
effect of primordial non-Gaussianity with at large
separations. Our results allow to readily estimate/correct for the full-sky
effect on a high-precision measurement of the average shear profile available
from upcoming wide-area lensing surveys.Comment: 12 pages, 4 figure
Electronic Collective Modes and Superconductivity in Layered Conductors
A distinctive feature of layered conductors is the presence of low-energy
electronic collective modes of the conduction electrons. This affects the
dynamic screening properties of the Coulomb interaction in a layered material.
We study the consequences of the existence of these collective modes for
superconductivity. General equations for the superconducting order parameter
are derived within the strong-coupling phonon-plasmon scheme that account for
the screened Coulomb interaction. Specifically, we calculate the
superconducting critical temperature Tc taking into account the full
temperature, frequency and wave-vector dependence of the dielectric function.
We show that low-energy plasmons may contribute constructively to
superconductivity. Three classes of layered superconductors are discussed
within our model: metal-intercalated halide nitrides, layered organic materials
and high-Tc oxides. In particular, we demonstrate that the plasmon contribution
(electronic mechanism) is dominant in the first class of layered materials. The
theory shows that the description of so-called ``quasi-two-dimensional
superconductors'' cannot be reduced to a purely 2D model, as commonly assumed.
While the transport properties are strongly anisotropic, it remains essential
to take into account the screened interlayer Coulomb interaction to describe
the superconducting state of layered materials.Comment: Final version (minor changes) 14 pages, 6 figure
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