1,693 research outputs found
A Conditional Yeast E1 Mutant Blocks the Ubiquitin–Proteasome Pathway and Reveals a Role for Ubiquitin Conjugates in Targeting Rad23 to the Proteasome
E1 ubiquitin activating enzyme catalyzes the initial step in all ubiquitin-dependent processes. We report the isolation of uba1-204, a temperature-sensitive allele of the essential Saccharomyces cerevisiae E1 gene, UBA1. Uba1-204 cells exhibit dramatic inhibition of the ubiquitin–proteasome system, resulting in rapid depletion of cellular ubiquitin conjugates and stabilization of multiple substrates. We have employed the tight phenotype of this mutant to investigate the role ubiquitin conjugates play in the dynamic interaction of the UbL/UBA adaptor proteins Rad23 and Dsk2 with the proteasome. Although proteasomes purified from mutant cells are intact and proteolytically active, they are depleted of ubiquitin conjugates, Rad23, and Dsk2. Binding of Rad23 to these proteasomes in vitro is enhanced by addition of either free or substrate-linked ubiquitin chains. Moreover, association of Rad23 with proteasomes in mutant and wild-type cells is improved upon stabilizing ubiquitin conjugates with proteasome inhibitor. We propose that recognition of polyubiquitin chains by Rad23 promotes its shuttling to the proteasome in vivo
Allosteric control of Ubp6 and the proteasome via a bidirectional switch
The interplay of the proteasome and deubiquitinase Ubp6 is crucial for the degradation of ubiquitylated substrates. Here, the authors provide structural insights into the allosteric mechanism by which the activities of both Ubp6 and the proteasome are regulated. The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by deubiquitinating enzyme Ubp6. The proteasome activates Ubp6, whereas Ubp6 inhibits the proteasome through deubiquitination and a noncatalytic effect. Here, we report cryo-EM structures of the proteasome bound to Ubp6, based on which we identify mutants in Ubp6 and proteasome subunit Rpt1 that abrogate Ubp6 activation. The Ubp6 mutations define a conserved region that we term the ILR element. The ILR is found within the BL1 loop, which obstructs the catalytic groove in free Ubp6. Rpt1-ILR interaction opens the groove by rearranging not only BL1 but also a previously undescribed network of three interconnected active-site-blocking loops. Ubp6 activation and noncatalytic proteasome inhibition are linked in that they are eliminated by the same mutations. Ubp6 and ubiquitin together drive proteasomes into a unique conformation associated with proteasome inhibition. Thus, a multicomponent allosteric switch exerts simultaneous control over both Ubp6 and the proteasome
Organic molecular markers and signature from wood combustion particles in winter ambient aerosols: aerosol mass spectrometer (AMS) and high time-resolved GC-MS measurements in Augsburg, Germany
The impact of wood combustion on ambient aerosols was investigated in
Augsburg, Germany during a winter measurement campaign of a six-week period.
Special attention was paid to the high time resolution observations of wood
combustion with different mass spectrometric methods. Here we present and
compare the results from an Aerodyne aerosol mass spectrometer (AMS) and gas
chromatographic – mass spectrometric (GC-MS) analysed PM<sub>1</sub> filters on an
hourly basis. This includes source apportionment of the AMS derived organic
matter (OM) using positive matrix factorisation (PMF) and analysis of
levoglucosan as wood combustion marker, respectively.
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During the measurement period nitrate and OM mass are the main contributors
to the defined submicron particle mass of AMS and Aethalometer with 28%
and 35%, respectively. Wood combustion organic aerosol (WCOA) contributes
to OM with 23% on average and 27% in the evening and night time.
Conclusively, wood combustion has a strong influence on the organic matter
and overall aerosol composition. Levoglucosan accounts for 14% of WCOA
mass with a higher percentage in comparison to other studies. The ratio
between the mass of levoglucosan and organic carbon amounts to 0.06.
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This study is unique in that it provides a one-hour time resolution
comparison between the wood combustion results of the AMS and the GC-MS
analysed filter method at a PM<sub>1</sub> particle size range. The comparison of
the concentration variation with time of the PMF WCOA factor, levoglucosan
estimated by the AMS data and the levoglucosan measured by GC-MS is highly
correlated (<i>R</i><sup>2</sup> = 0.84), and a detailed discussion on the contributors
to the wood combustion marker ion at mass-to-charge ratio 60 is given. At
the end, both estimations, the WCOA factor and the levoglucosan
concentration estimated by AMS data, allow to observe the variation with
time of wood combustion emissions (gradient correlation with GC-MS
levoglucosan of <i>R</i><sup>2</sup> = 0.84). In the case of WCOA, it provides the
estimated magnitude of wood combustion emission. Quantitative estimation of
the levoglucosan concentration from the AMS data is problematic due to its
overestimation in comparison to the levoglucosan measured by the GC-MS
Internally Electrodynamic Particle Model: Its Experimental Basis and Its Predictions
The internally electrodynamic (IED) particle model was derived based on
overall experimental observations, with the IED process itself being built
directly on three experimental facts, a) electric charges present with all
material particles, b) an accelerated charge generates electromagnetic waves
according to Maxwell's equations and Planck energy equation and c) source
motion produces Doppler effect. A set of well-known basic particle equations
and properties become predictable based on first principles solutions for the
IED process; several key solutions achieved are outlined, including the de
Broglie phase wave, de Broglie relations, Schr\"odinger equation, mass,
Einstein mass-energy relation, Newton's law of gravity, single particle self
interference, and electromagnetic radiation and absorption; these equations and
properties have long been broadly experimentally validated or demonstrated. A
specific solution also predicts the Doebner-Goldin equation which emerges to
represent a form of long-sought quantum wave equation including gravity. A
critical review of the key experiments is given which suggests that the IED
process underlies the basic particle equations and properties not just
sufficiently but also necessarily.Comment: Presentation at the 27th Int Colloq on Group Theo Meth in Phys, 200
The degradation of p53 and its major E3 ligase Mdm2 is differentially dependent on the proteasomal ubiquitin receptor S5a.
p53 and its major E3 ligase Mdm2 are both ubiquitinated and targeted to the proteasome for degradation. Despite the importance of this in regulating the p53 pathway, little is known about the mechanisms of proteasomal recognition of ubiquitinated p53 and Mdm2. In this study, we show that knockdown of the proteasomal ubiquitin receptor S5a/PSMD4/Rpn10 inhibits p53 protein degradation and results in the accumulation of ubiquitinated p53. Overexpression of a dominant-negative deletion of S5a lacking its ubiquitin-interacting motifs (UIM)s, but which can be incorporated into the proteasome, also causes the stabilization of p53. Furthermore, small-interferring RNA (siRNA) rescue experiments confirm that the UIMs of S5a are required for the maintenance of low p53 levels. These observations indicate that S5a participates in the recognition of ubiquitinated p53 by the proteasome. In contrast, targeting S5a has no effect on the rate of degradation of Mdm2, indicating that proteasomal recognition of Mdm2 can be mediated by an S5a-independent pathway. S5a knockdown results in an increase in the transcriptional activity of p53. The selective stabilization of p53 and not Mdm2 provides a mechanism for p53 activation. Depletion of S5a causes a p53-dependent decrease in cell proliferation, demonstrating that p53 can have a dominant role in the response to targeting S5a. This study provides evidence for alternative pathways of proteasomal recognition of p53 and Mdm2. Differences in recognition by the proteasome could provide a means to modulate the relative stability of p53 and Mdm2 in response to cellular signals. In addition, they could be exploited for p53-activating therapies. This work shows that the degradation of proteins by the proteasome can be selectively dependent on S5a in human cells, and that this selectivity can extend to an E3 ubiquitin ligase and its substrate
A finite model of two-dimensional ideal hydrodynamics
A finite-dimensional su() Lie algebra equation is discussed that in the
infinite limit (giving the area preserving diffeomorphism group) tends to
the two-dimensional, inviscid vorticity equation on the torus. The equation is
numerically integrated, for various values of , and the time evolution of an
(interpolated) stream function is compared with that obtained from a simple
mode truncation of the continuum equation. The time averaged vorticity moments
and correlation functions are compared with canonical ensemble averages.Comment: (25 p., 7 figures, not included. MUTP/92/1
Study of and decays and determination of the CKM angle
We report a study of the suppressed and favored
decays, where the neutral meson is detected
through its decays to the and CP-even and
final states. The measurement is carried out using a proton-proton
collision data sample collected by the LHCb experiment, corresponding to an
integrated luminosity of 3.0~fb. We observe the first significant
signals in the CP-even final states of the meson for both the suppressed
and favored modes, as well as
in the doubly Cabibbo-suppressed final state of the decay. Evidence for the ADS suppressed decay , with , is also presented. From the observed
yields in the , and their
charge conjugate decay modes, we measure the value of the weak phase to be
. This is one of the most precise
single-measurement determinations of to date.Comment: 22 pages, 9 figures; All figures and tables, along with any
supplementary material and additional information, are available at
https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2015-020.htm
Study of boson production in association with beauty and charm
The associated production of a boson with a jet originating from either a
light parton or heavy-flavor quark is studied in the forward region using
proton-proton collisions. The analysis uses data corresponding to integrated
luminosities of 1.0 and collected with the LHCb detector
at center-of-mass energies of 7 and 8 TeV, respectively. The bosons are
reconstructed using the decay and muons with a transverse
momentum, , larger than 20 GeV in the pseudorapidity range
GeV
and . The sum of the muon and jet momenta must satisfy
GeV. The fraction of jet events that originate from beauty
and charm quarks is measured, along with the charge asymmetries of the
and production cross-sections. The ratio of the jet to
jet production cross-sections is also measured using the
decay. All results are in agreement with Standard Model predictions
Observation of resonances consistent with pentaquark states in decays
Observations of exotic structures in the channel, that we refer to
as pentaquark-charmonium states, in decays are
presented. The data sample corresponds to an integrated luminosity of 3/fb
acquired with the LHCb detector from 7 and 8 TeV pp collisions. An amplitude
analysis is performed on the three-body final-state that reproduces the
two-body mass and angular distributions. To obtain a satisfactory fit of the
structures seen in the mass spectrum, it is necessary to include two
Breit-Wigner amplitudes that each describe a resonant state. The significance
of each of these resonances is more than 9 standard deviations. One has a mass
of MeV and a width of MeV, while the second
is narrower, with a mass of MeV and a width of MeV. The preferred assignments are of opposite parity, with one
state having spin 3/2 and the other 5/2.Comment: 48 pages, 18 figures including the supplementary material, v2 after
referee's comments, now 19 figure
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