Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance

Chromatin is a highly regulated environment, and protein association with chromatin is often controlled by post-translational modifications and the corresponding enzymatic machinery. Specifically, SUMO-targeted ubiquitin ligases (STUbLs) have emerged as key players in nuclear quality control, genome maintenance, and transcription. However, how STUbLs select specific substrates among myriads of SUMOylated proteins on chromatin remains unclear. Here, we reveal a remarkable co-localization of the budding yeast STUbL Slx5/Slx8 and ubiquitin at seven genomic loci that we term "ubiquitin hotspots". Ubiquitylation at these sites depends on Slx5/Slx8 and protein turnover on the Cdc48 segregase. We identify the transcription factor-like Ymr111c/Euc1 to associate with these sites and to be a critical determinant of ubiquitylation. Euc1 specifically targets Slx5/Slx8 to ubiquitin hotspots via bipartite binding of Slx5 that involves the Slx5 SUMO-interacting motifs and an additional, novel substrate recognition domain. Interestingly, the Euc1-ubiquitin hotspot pathway acts redundantly with chromatin modifiers of the H2A.Z and Rpd3L pathways in specific stress responses. Thus, our data suggest that STUbL-dependent ubiquitin hotspots shape chromatin during stress adaptation

Fractal Analysis of Protein Potential Energy Landscapes

The fractal properties of the total potential energy V as a function of time t are studied for a number of systems, including realistic models of proteins (PPT, BPTI and myoglobin). The fractal dimension of V(t), characterized by the exponent \gamma, is almost independent of temperature and increases with time, more slowly the larger the protein. Perhaps the most striking observation of this study is the apparent universality of the fractal dimension, which depends only weakly on the type of molecular system. We explain this behavior by assuming that fractality is caused by a self-generated dynamical noise, a consequence of intermode coupling due to anharmonicity. Global topological features of the potential energy landscape are found to have little effect on the observed fractal behavior.Comment: 17 pages, single spaced, including 12 figure

Possible Dibaryons with Strangeness s=-5

In the framework of $RGM$, the binding energy of the six quark system with strangeness s=-5 is systematically investigated under the SU(3) chiral constituent quark model. The single $\Xi^*\Omega$ channel calculation with spins S=0 and 3 and the coupled $\Xi\Omega$ and $\Xi^*\Omega$ channel calculation with spins S=1 and 2 are considered, respectively. The results show following observations: In the spin=0 case, $\Xi^* \Omega$ is a bound dibaryon with the binding energy being $80.0 \sim 92.4 MeV$. In the S=1 case, $\Xi\Omega$ is also a bound dibaryon. Its binding energy is ranged from $26.2 MeV$ to $32.9 MeV$. In the S=2 and S=3 cases, no evidence of bound dibaryons are found. The phase shifts and scattering lengths in the S=0 and S=1 cases are also given.Comment: 10 pages, late

Cronin Effect in Hadron Production off Nuclei

Recent data from RHIC for high-$p_T$ hadrons in gold-gold collisions raised again the long standing problem of quantitatively understanding the Cronin effect, i.e. nuclear enhancement of high-$p_T$ hadrons due to multiple interactions in nuclear matter. In nucleus-nucleus collisions this effect has to be reliably calculated as baseline for a signal of new physics in high-$p_T$ hadron production. The only possibility to test models is to compare with available data for $pA$ collisions, however, all existing models for the Cronin effect rely on a fit to the data to be explained. We develop a phenomenological description based on the light-cone QCD-dipole approach which allows to explain available data without fitting to them and to provide predictions for $pA$ collisions at RHIC and LHC. We point out that the mechanism causing Cronin effect drastically changes between the energies of fixed target experiments and RHIC-LHC. High-$p_T$ hadrons are produced incoherently on different nucleons at low energies, whereas the production amplitudes interfere if the energy is sufficiently high.Comment: the final version to appear in Phys. Rev. Let

Image resonance in the many-body density of states at a metal surface

The electronic properties of a semi-infinite metal surface without a bulk gap are studied by a formalism that is able to account for the continuous spectrum of the system. The density of states at the surface is calculated within the GW approximation of many-body perturbation theory. We demonstrate the presence of an unoccupied surface resonance peaked at the position of the first image state. The resonance encompasses the whole Rydberg series of image states and cannot be resolved into individual peaks. Its origin is the shift in spectral weight when many-body correlation effects are taken into account

Anti-phospholipid-antibodies in patients with relapsing polychondritis

Relapsing polychondritis (RP) is an extremly rare multisystemic disease thought to be of autoimmune origin. In order to assess if RP is associated with anti-phospholipid antibodies (aPL), clinical data and sera of 21 patients with RP were collected in a multicentre study. Concentration of anti-cardiolipin antibodies (aCL) (IgG-, IgM-and IgA-isotypes), anti-phosphatidylserine-antibodies (aPS) (IgG-and IgM-isotypes) and anti-β-2-glycoprotein I-antibodies (aβ2 GPI) were measured by ELISA. In eight patients aCL were found to be elevated. One patient had elevated aPS. No patient had elevated aβ2 GPI. No patient had clinical signs and symptoms of a aPL syndrome. Interestingly, the two RP patients with the highest aPL had concomitant systemic lupus erythematosus (SLE). Therefore the presence of elevated aPL in RP is probably more closely related to an associated SLE than to RP itself. There is no convincing evidence that aPL are associated with RP

Quantitative Imaging of Protein-Protein Interactions by Multiphoton Fluorescence Lifetime Imaging Microscopy using a Streak camera

Fluorescence Lifetime Imaging Microscopy (FLIM) using multiphoton excitation techniques is now finding an important place in quantitative imaging of protein-protein interactions and intracellular physiology. We review here the recent developments in multiphoton FLIM methods and also present a description of a novel multiphoton FLIM system using a streak camera that was developed in our laboratory. We provide an example of a typical application of the system in which we measure the fluorescence resonance energy transfer between a donor/acceptor pair of fluorescent proteins within a cellular specimen.Comment: Overview of FLIM techniques, StreakFLIM instrument, FRET application

Remnant Fermi surface in the presence of an underlying instability in layered 1T-TaS_2

We report high resolution angle-scanned photoemission and Fermi surface (FS) mapping experiments on the layered transition-metal dichalcogenide 1T-TaS_2 in the quasi commensurate (QC) and the commensurate (C) charge-density-wave (CDW) phase. Instead of a nesting induced partially removed FS in the CDW phase we find a pseudogap over large portions of the FS. This remnant FS exhibits the symmetry of the one-particle normal state FS even when passing from the QC-phase to the C-phase. Possibly, this Mott localization induced transition represents the underlying instability responsible for the pseudogapped FS