664 research outputs found
Cooperative Chiral Order in Copolymers of Chiral and Achiral Units
Polyisocyanates can be synthesized with chiral and achiral pendant groups
distributed randomly along the chains. The overall chiral order, measured by
optical activity, is strongly cooperative and depends sensitively on the
concentration of chiral pendant groups. To explain this cooperative chiral
order theoretically, we map the random copolymer onto the one-dimensional
random-field Ising model. We show that the optical activity as a function of
composition is well-described by the predictions of this theory.Comment: 13 pages, including 3 postscript figures, uses REVTeX 3.0 and
epsf.st
Reconstruction of protein structures from a vectorial representation
We show that the contact map of the native structure of globular proteins can
be reconstructed starting from the sole knowledge of the contact map's
principal eigenvector, and present an exact algorithm for this purpose. Our
algorithm yields a unique contact map for all 221 globular structures of
PDBselect25 of length . We also show that the reconstructed contact
maps allow in turn for the accurate reconstruction of the three-dimensional
structure. These results indicate that the reduced vectorial representation
provided by the principal eigenvector of the contact map is equivalent to the
protein structure itself. This representation is expected to provide a useful
tool in bioinformatics algorithms for protein structure comparison and
alignment, as well as a promising intermediate step towards protein structure
prediction.Comment: 4 pages, 1 figur
P16-52. HIV-activated human plasmacytoid DCs induce Tregs through an indoleamine 2,3-dioxygenase-dependent mechanism
International audiencen.
Lifelongα-tocopherol supplementation increases the median life span of C57BL/6 mice in the cold but has only minor effects on oxidative damage
The effects of dietary antioxidant supplementation on oxidative stress and life span are confused. We maintained C57BL/6 mice at 7 ± 2°C and supplemented their diet with α-tocopherol from 4 months of age. Supplementation significantly increased (p = 0.042) median life span by 15% (785 days, n = 44) relative to unsupplemented controls (682 days, n = 43) and also increased maximum life span (oldest 10%, p = 0.028). No sex or sex by treatment interaction effects were observed on life span, with treatment having no effect on resting or daily metabolic rate. Lymphocyte and hepatocyte oxidative DNA damage and hepatic lipid peroxidation were unaffected by supplementation, but hepatic oxidative DNA damage increased with age. Using a cDNA macroarray, genes associated with xenobiotic metabolism were significantly upregulated in the livers of female mice at 6 months of age (2 months supplementation). At 22 months of age (18 months supplementation) this response had largely abated, but various genes linked to the p21 signaling pathway were upregulated at this time. We suggest that α-tocopherol may initially be metabolized as a xenobiotic, potentially explaining why previous studies observe a life span extension generally when lifelong supplementation is initiated early in life. The absence of any significant effect on oxidative damage suggests that the life span extension observed was not mediated via any antioxidant properties of α-tocopherol. We propose that the life span extension observed following α-tocopherol supplementation may be mediated via upregulation of cytochrome p450 genes after 2 months of supplementation and/or upregulation of p21 signaling genes after 18 months of supplementation. However, these signaling pathways now require further investigation to establish their exact role in life span extension following α-tocopherol supplementation
Statistical Properties of Contact Maps
A contact map is a simple representation of the structure of proteins and
other chain-like macromolecules. This representation is quite amenable to
numerical studies of folding. We show that the number of contact maps
corresponding to the possible configurations of a polypeptide chain of N amino
acids, represented by (N-1)-step self avoiding walks on a lattice, grows
exponentially with N for all dimensions D>1. We carry out exact enumerations in
D=2 on the square and triangular lattices for walks of up to 20 steps and
investigate various statistical properties of contact maps corresponding to
such walks. We also study the exact statistics of contact maps generated by
walks on a ladder.Comment: Latex file, 15 pages, 12 eps figures. To appear on Phys. Rev.
Information Loss in Coarse Graining of Polymer Configurations via Contact Matrices
Contact matrices provide a coarse grained description of the configuration
omega of a linear chain (polymer or random walk) on Z^n: C_{ij}(omega)=1 when
the distance between the position of the i-th and j-th step are less than or
equal to some distance "a" and C_{ij}(omega)=0 otherwise. We consider models in
which polymers of length N have weights corresponding to simple and
self-avoiding random walks, SRW and SAW, with "a" the minimal permissible
distance. We prove that to leading order in N, the number of matrices equals
the number of walks for SRW, but not for SAW. The coarse grained Shannon
entropies for SRW agree with the fine grained ones for n <= 2, but differs for
n >= 3.Comment: 18 pages, 2 figures, latex2e Main change: the introduction is
rewritten in a less formal way with the main results explained in simple
term
Formation of helical states in wormlike polymer chains
We propose a potential for wormlike polymer chains which can be used to model
the low-temperature conformational structures. We successfully reproduced helix
ground states up to 6.5 helical loops, using the multicanonical Monte Carlo
simulation method. We demonstrate that the coil-helix transition involves four
distinct phases: coil(gaslike), collapsed globular(liquidlike), and two helical
phases I and II (both solidlike). The helix I phase is characterized by a
helical structure with dangling loose ends, and the helix II phase corresponds
to a near perfect helix ordering in the entire crystallized chain.Comment: 5 pages, 2 figures, Submitted to PR
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone
Motivation: One of the most successful methods to date for recognizing protein sequences that are evolutionarily related has been profile hidden Markov models (HMMs). However, these models do not capture pairwise statistical preferences of residues that are hydrogen bonded in beta sheets. These dependencies have been partially captured in the HMM setting by simulated evolution in the training phase and can be fully captured by Markov random fields (MRFs). However, the MRFs can be computationally prohibitive when beta strands are interleaved in complex topologies. We introduce SMURFLite, a method that combines both simplified MRFs and simulated evolution to substantially improve remote homology detection for beta structures. Unlike previous MRF-based methods, SMURFLite is computationally feasible on any beta-structural motif
Ability of herpes simplex virus vectors to boost immune responses to DNA vectors and to protect against challenge by simian immunodeficiency virus
AbstractThe immunogenicity and protective capacity of replication-defective herpes simplex virus (HSV) vector-based vaccines were examined in rhesus macaques. Three macaques were inoculated with recombinant HSV vectors expressing Gag, Env, and a Tat-Rev-Nef fusion protein of simian immunodeficiency virus (SIV). Three other macaques were primed with recombinant DNA vectors expressing Gag, Env, and a Pol-Tat-Nef-Vif fusion protein prior to boosting with the HSV vectors. Robust anti-Gag and anti-Env cellular responses were detected in all six macaques. Following intravenous challenge with wild-type, cloned SIV239, peak and 12-week plasma viremia levels were significantly lower in vaccinated compared to control macaques. Plasma SIV RNA in vaccinated macaques was inversely correlated with anti-Rev ELISPOT responses on the day of challenge (P value<0.05), anti-Tat ELISPOT responses at 2 weeks post challenge (P value <0.05) and peak neutralizing antibody titers pre-challenge (P value 0.06). These findings support continued study of recombinant herpesviruses as a vaccine approach for AIDS
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