1,040 research outputs found
Assessing the effect of dynamics on the closed-loop protein-folding hypothesis
The closed-loop (loop-n-lock) hypothesis of protein folding suggests that loops of about 25 residues, closed through interactions between the loop ends (locks), play an important role in protein structure. Coarse-grain elastic network simulations, and examination of loop lengths in a diverse set of proteins, each supports a bias towards loops of close to 25 residues in length between residues of high stability. Previous studies have established a correlation between total contact distance (TCD), a metric of sequence distances between contacting residues (cf. contact order), and the log-folding rate of a protein. In a set of 43 proteins, we identify an improved correlation (
r
2
= 0.76), when the metric is restricted to residues contacting the locks, compared to the equivalent result when all residues are considered (
r
2
= 0.65). This provides qualified support for the hypothesis, albeit with an increased emphasis upon the importance of a much larger set of residues surrounding the locks. Evidence of a similar-sized protein core/extended nucleus (with significant overlap) was obtained from TCD calculations in which residues were successively eliminated according to their hydrophobicity and connectivity, and from molecular dynamics simulations. Our results suggest that while folding is determined by a subset of residues that can be predicted by application of the closed-loop hypothesis, the original hypothesis is too simplistic; efficient protein folding is dependent on a considerably larger subset of residues than those involved in lock formation.
</jats:p
Development of a PbWO4 Detector for Single-Shot Positron Annihilation Lifetime Spectroscopy at the GBAR Experiment
We have developed a PbWO4 (PWO) detector with a large dynamic range to measure the intensity of a positron beam and the absolute density of the ortho-positronium (o-Ps) cloud it creates. A simulation study shows that a setup based on such detectors may be used to determine the angular distribution of the emission and reflection of o-Ps to reduce part of the uncertainties of the measurement. These will allow to improve the precision in the measurement of the cross-section for the (anti)hydrogen formation by (anti)proton-positronium charge exchange and to optimize the yield of antihydrogen ion which is an essential parameter in the GBAR experiment
Background Light in Potential Sites for the ANTARES Undersea Neutrino Telescope
The ANTARES collaboration has performed a series of {\em in situ}
measurements to study the background light for a planned undersea neutrino
telescope. Such background can be caused by K decays or by biological
activity. We report on measurements at two sites in the Mediterranean Sea at
depths of 2400~m and 2700~m, respectively. Three photomultiplier tubes were
used to measure single counting rates and coincidence rates for pairs of tubes
at various distances. The background rate is seen to consist of three
components: a constant rate due to K decays, a continuum rate that
varies on a time scale of several hours simultaneously over distances up to at
least 40~m, and random bursts a few seconds long that are only correlated in
time over distances of the order of a meter. A trigger requiring coincidences
between nearby photomultiplier tubes should reduce the trigger rate for a
neutrino telescope to a manageable level with only a small loss in efficiency.Comment: 18 pages, 8 figures, accepted for publication in Astroparticle
Physic
Search for composite and exotic fermions at LEP 2
A search for unstable heavy fermions with the DELPHI detector at LEP is
reported. Sequential and non-canonical leptons, as well as excited leptons and
quarks, are considered. The data analysed correspond to an integrated
luminosity of about 48 pb^{-1} at an e^+e^- centre-of-mass energy of 183 GeV
and about 20 pb^{-1} equally shared between the centre-of-mass energies of 172
GeV and 161 GeV. The search for pair-produced new leptons establishes 95%
confidence level mass limits in the region between 70 GeV/c^2 and 90 GeV/c^2,
depending on the channel. The search for singly produced excited leptons and
quarks establishes upper limits on the ratio of the coupling of the excited
fermio
Search for charginos in e+e- interactions at sqrt(s) = 189 GeV
An update of the searches for charginos and gravitinos is presented, based on
a data sample corresponding to the 158 pb^{-1} recorded by the DELPHI detector
in 1998, at a centre-of-mass energy of 189 GeV. No evidence for a signal was
found. The lower mass limits are 4-5 GeV/c^2 higher than those obtained at a
centre-of-mass energy of 183 GeV. The (\mu,M_2) MSSM domain excluded by
combining the chargino searches with neutralino searches at the Z resonance
implies a limit on the mass of the lightest neutralino which, for a heavy
sneutrino, is constrained to be above 31.0 GeV/c^2 for tan(beta) \geq 1.Comment: 22 pages, 8 figure
Hadronization properties of b quarks compared to light quarks in e+e- -> q qbar from 183 to 200 GeV
The DELPHI detector at LEP has collected 54 pb^{-1} of data at a
centre-of-mass energy around 183 GeV during 1997, 158 pb^{-1} around 189 GeV
during 1998, and 187 pb^{-1} between 192 and 200 GeV during 1999. These data
were used to measure the average charged particle multiplicity in e+e- -> b
bbar events, _{bb}, and the difference delta_{bl} between _{bb} and the
multiplicity, _{ll}, in generic light quark (u,d,s) events: delta_{bl}(183
GeV) = 4.55 +/- 1.31 (stat) +/- 0.73 (syst) delta_{bl}(189 GeV) = 4.43 +/- 0.85
(stat) +/- 0.61 (syst) delta_{bl}(200 GeV) = 3.39 +/- 0.89 (stat) +/- 1.01
(syst). This result is consistent with QCD predictions, while it is
inconsistent with calculations assuming that the multiplicity accompanying the
decay of a heavy quark is independent of the mass of the quark itself.Comment: 13 pages, 2 figure
Search for lightest neutralino and stau pair production in light gravitino scenarios with stau NLSP
Promptly decaying lightest neutralinos and long-lived staus are searched for
in the context of light gravitino scenarios. It is assumed that the stau is the
next to lightest supersymmetric particle (NLSP) and that the lightest
neutralino is the next to NLSP (NNLSP). Data collected with the Delphi detector
at centre-of-mass energies from 161 to 183 \GeV are analysed. No evidence of
the production of these particles is found. Hence, lower mass limits for both
kinds of particles are set at 95% C.L.. The mass of gaugino-like neutralinos is
found to be greater than 71.5 GeV/c^2. In the search for long-lived stau,
masses less than 70.0 to 77.5 \GeVcc are excluded for gravitino masses from 10
to 150 \eVcc . Combining this search with the searches for stable heavy leptons
and Minimal Supersymmetric Standard Model staus a lower limit of 68.5 \GeVcc
may be set for the stau mas
Search for supersymmetric particles in scenarios with a gravitino LSP and stau NLSP
Sleptons, neutralinos and charginos were searched for in the context of
scenarios where the lightest supersymmetric particle is the gravitino. It was
assumed that the stau is the next-to-lightest supersymmetric particle. Data
collected with the DELPHI detector at a centre-of-mass energy near 189 GeV were
analysed combining the methods developed in previous searches at lower
energies. No evidence for the production of these supersymmetric particles was
found. Hence, limits were derived at 95% confidence level.Comment: 31 pages, 14 figure
Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling
The Joint Evolutionary Trees (JET) method detects protein interfaces, the core
residues involved in the folding process, and residues susceptible to
site-directed mutagenesis and relevant to molecular recognition. The approach,
based on the Evolutionary Trace (ET) method, introduces a novel way to treat
evolutionary information. Families of homologous sequences are analyzed through
a Gibbs-like sampling of distance trees to reduce effects of erroneous multiple
alignment and impacts of weakly homologous sequences on distance tree
construction. The sampling method makes sequence analysis more sensitive to
functional and structural importance of individual residues by avoiding effects
of the overrepresentation of highly homologous sequences and improves
computational efficiency. A carefully designed clustering method is parametrized
on the target structure to detect and extend patches on protein surfaces into
predicted interaction sites. Clustering takes into account residues'
physical-chemical properties as well as conservation. Large-scale application of
JET requires the system to be adjustable for different datasets and to guarantee
predictions even if the signal is low. Flexibility was achieved by a careful
treatment of the number of retrieved sequences, the amino acid distance between
sequences, and the selective thresholds for cluster identification. An iterative
version of JET (iJET) that guarantees finding the most likely interface residues
is proposed as the appropriate tool for large-scale predictions. Tests are
carried out on the Huang database of 62 heterodimer, homodimer, and transient
complexes and on 265 interfaces belonging to signal transduction proteins,
enzymes, inhibitors, antibodies, antigens, and others. A specific set of
proteins chosen for their special functional and structural properties
illustrate JET behavior on a large variety of interactions covering proteins,
ligands, DNA, and RNA. JET is compared at a large scale to ET and to Consurf,
Rate4Site, siteFiNDER|3D, and SCORECONS on specific structures. A significant
improvement in performance and computational efficiency is shown
Towards a test of the weak equivalence principle of gravity using anti-hydrogen at CERN
International audienceThe aim of the GBAR (Gravitational Behavior of Antimatter at Rest) experiment is to measure the free fall acceleration of an antihydrogen atom, in the terrestrial gravitational field at CERN and therefore test the Weak Equivalence Principle with antimatter. The aim is to measure the local gravity with a 1% uncertainty which can be reduced to few parts of 10-3
- âŠ