Mining the TRAF6/p62 interactome for a selective ubiquitination motif

A new approach is described here to predict ubiquitinated substrates of the E3 ubiquitin ligase, TRAF6, which takes into account its interaction with the scaffold protein SQSTM1/p62. A novel TRAF6 ubiquitination motif defined as [–(hydrophobic)–k–(hydrophobic)–x–x–(hydrophobic)– (polar)–(hydrophobic)–(polar)–(hydrophobic)] was identified and used to screen the TRAF6/p62 interactome composed of 155 proteins, that were either TRAF6 or p62 interactors, or a negative dataset, composed of 54 proteins with no known association to either TRAF6 or p62. NRIF (K19), TrkA (K485), TrkB (K811), TrkC (K602 and K815), NTRK2 (K828), NTRK3 (K829) and MBP (K169) were found to possess a perfect match for the amino acid consensus motif for TRAF6/p62 ubiquitination. Subsequent analyses revealed that this motif was biased to the C-terminal regions of the protein (nearly 50% the sites), and had preference for loops (~50%) and helices (~37%) over beta-strands (15% or less). In addition, the motif was observed to be in regions that were highly solvent accessible (nearly 90%). Our findings suggest that specific Lysines may be selected for ubiquitination based upon an embedded code defined by a specific amino acid motif with structural determinants. Collectively, our results reveal an unappreciated role for the scaffold protein in targeting ubiquitination. The findings described herein could be used to aid in identification of other E3/scaffold ubiquitination sites

Signaling, Polyubiquitination, Trafficking, and Inclusions: Sequestosome 1/p62's Role in Neurodegenerative Disease

Aggregated misfolded proteins are hallmarks of most neurodegenerative diseases. In a chronic disease state, including pathologic situations of oxidative stress, these proteins are sequestered into inclusions. Accumulation of aggregated proteins can be prevented by chaperones, or by targeting their degradation to the UPS. If the accumulation of these proteins exceeds their degradation, they may impair the function of the proteasome. Alternatively, the function of the proteasome may be preserved by directing aggregated proteins to the autophagy-lysosome pathway for degradation. Sequestosome 1/p62 has recently been shown to interact with polyubiquitinated proteins through its UBA domain and may direct proteins to either the UPS or autophagosome. P62 is present in neuronal inclusions of individuals with Alzheimer's disease and other neurodegenerative diseases. Herein, we review p62's role in signaling, aggregation, and inclusion formation, and specifically as a possible contributor to Alzheimer's disease. The use of p62 as a potential target for the development of therapeutics and as a disease biomarker is also discussed

Evaluation of Born and local effective charges in unoriented materials from vibrational spectra

We present an application of the Lorentz model in which fits to vibrational spectra or a Kramers Kronig analysis are employed along with several useful formalisms to quantify microscopic charge in unoriented (powdered) materials. The conditions under which these techniques can be employed are discussed, and we analyze the vibrational response of a layered transition metal dichalcogenide and its nanoscale analog to illustrate the utility of this approach.Comment: 9 pages, 1 figur

The a-axis optical conductivity of detwinned ortho-II YBa_2Cu_3O_6.50

The a-axis optical properties of a detwinned single crystal of YBa_2Cu_3O_6.50 in the ortho II phase (Ortho II Y123, T_c= 59 K) were determined from reflectance data over a wide frequency range (70 - 42 000 cm^-1) for nine temperature values between 28 and 295 K. Above 200 K the spectra are dominated by a broad background of scattering that extends to 1 eV. Below 200 K a shoulder in the reflectance appears and signals the onset of scattering at 400 cm^-1. In this temperature range we also observe a peak in the optical conductivity at 177 cm^-1. Below 59 K, the superconducting transition temperature, the spectra change dramatically with the appearance of the superconducting condensate. Its spectral weight is consistent, to within experimental error, with the Ferrell-Glover-Tinkham (FGT) sum rule. We also compare our data with magnetic neutron scattering on samples from the same source that show a strong resonance at 31 meV. We find that the scattering rates can be modeled as the combined effect of the neutron resonance and a bosonic background in the presence of a density of states with a pseudogap. The model shows that the decreasing amplitude of the neutron resonance with temperature is compensated for by an increasing of the bosonic background yielding a net temperature independent scattering rate at high frequencies. This is in agreement with the experiments.Comment: 13 pages 16 figure

UNIQUE RADIOANALYTICAL PROTOCOLS FOR CHARACTERIZATION AND VERIFICATION DURING DECONTAMINATION AND DECOMMISSIONING

In order to successfully decontaminate, deactivate and decommission surplus Department of Energy (DOE) facilities throughout the Savannah River Site (SRS), a variety of characterizations must be completed to sufficiently identify and quantify potential contaminants of concern. The ultimate goal is to rapidly and efficiently characterize, decontaminate (if necessary), and verify that the remnants meet specified limits established by either an industrial worker model or a groundwater model. To meet this end, the Savannah River National Laboratory (SRNL) developed a series of radioanalytical strategies and methodologies which can be used to characterize targeted facilities and prove that decontamination has been sufficient. To our knowledge, this is the first application of this novel methodology within the DOE complex. This methodology has been successfully utilized with nearly 1000 samples from over a dozen facilities. The application of this approach to just a single facility shortened the schedule by 30 days and resulted in non-labor dollar savings of over $60K. Cost savings for a second facility was determined to be$375K. Based on the success of this methodology at SRS, this approach will be valuable to other nuclear facilities in the USA and abroad involved with the decontamination and decommissioning process

Novel translocation responses of cytosolic phospholipase A2α fluorescent proteins

AbstractCytosolic phospholipase A2 (cPLA2)α responds to the rise in cytosolic Ca2+ ([Ca2+]i) attending cell stimulation by moving to intracellular membranes, releasing arachidonic acid (AA) from these membranes, and thereby initiating the synthesis of various lipid mediators. Under some conditions, however, cPLA2α translocation occurs without any corresponding changes in [Ca2+]i. The signal for such responses has not been identified. Using confocal microscopy to track fluorescent proteins fused to cPLA2α or cPLA2α's C2 domain, we find that AA mimics Ca2+ ionophores in stimulating cPLA2α translocations to the perinuclear ER and to a novel site, the lipid body. Unlike the ionophores, AA acted independently of [Ca2+]i rises and did not translocate the proteins to the Golgi. AA's action did not involve its metabolism to eicosanoids or acylation into cellular lipids. Receptor agonists also stimulated translocations targeting lipid bodies. We propose that AA is a signal for Ca2+-independent cPLA2α translocation and that lipid bodies are common targets of cPLA2α and contributors to stimulus-induced lipid mediator synthesis

Structural, electronic, and dynamical properties of amorphous gallium arsenide: a comparison between two topological models

We present a detailed study of the effect of local chemical ordering on the structural, electronic, and dynamical properties of amorphous gallium arsenide. Using the recently-proposed ``activation-relaxation technique'' and empirical potentials, we have constructed two 216-atom tetrahedral continuous random networks with different topological properties, which were further relaxed using tight-binding molecular dynamics. The first network corresponds to the traditional, amorphous, Polk-type, network, randomly decorated with Ga and As atoms. The second is an amorphous structure with a minimum of wrong (homopolar) bonds, and therefore a minimum of odd-membered atomic rings, and thus corresponds to the Connell-Temkin model. By comparing the structural, electronic, and dynamical properties of these two models, we show that the Connell-Temkin network is energetically favored over Polk, but that most properties are little affected by the differences in topology. We conclude that most indirect experimental evidence for the presence (or absence) of wrong bonds is much weaker than previously believed and that only direct structural measurements, i.e., of such quantities as partial radial distribution functions, can provide quantitative information on these defects in a-GaAs.Comment: 10 pages, 7 ps figures with eps

Magneto-optical investigation of the field-induced spin-glass insulator to ferromagnetic metallic transition of the bilayer manganite (La0.4_{0.4}Pr0.6_{0.6})1.2_{1.2}Sr1.8_{1.8}Mn2_2O7_7

We measured the magneto-optical response of (La$_{0.4}$Pr$_{0.6}$)$_{1.2}$Sr$_{1.8}$Mn$_2$O$_7$ in order to investigate the microscopic aspects of the magnetic field driven spin-glass insulator to ferromagnetic metal transition. Application of a magnetic field recovers the ferromagnetic state with an overall redshift of the electronic structure, growth of the bound carrier localization associated with ferromagnetic domains, development of a pseudogap, and softening of the Mn-O stretching and bending modes that indicate a structural change. We discuss field- and temperature-induced trends within the framework of the Tomioka-Tokura global electronic phase diagram picture and suggest that controlled disorder near a phase boundary can be used to tune the magnetodielectric response. Remnants of the spin-glass insulator to ferromagnetic metallic transition can also drive 300 K color changes in (La$_{0.4}$Pr$_{0.6}$)$_{1.2}$Sr$_{1.8}$Mn$_2$O$_7$.Comment: 9 pages, 8 figure

Topology of amorphous tetrahedral semiconductors on intermediate lengthscales

Using the recently-proposed ``activation-relaxation technique'' for optimizing complex structures, we develop a structural model appropriate to a-GaAs which is almost free of odd-membered rings, i.e., wrong bonds, and possesses an almost perfect coordination of four. The model is found to be superior to structures obtained from much more computer-intensive tight-binding or quantum molecular-dynamics simulations. For the elemental system a-Si, where wrong bonds do not exist, the cost in elastic energy for removing odd-membered rings is such that the traditional continuous-random network is appropriate. Our study thus provides, for the first time, direct information on the nature of intermediate-range topology in amorphous tetrahedral semiconductors.Comment: 4 pages, Latex and 2 postscript figure

Optical and thermodynamic properties of the high-temperature superconductor HgBa_2CuO_4+delta

In- and out-of-plane optical spectra and specific heat measurements for the single layer cuprate superconductor Hg-1201 at optimal doping (Tc = 97 K) are presented. Both the in-plane and out-of-plane superfluid density agree well with a recently proposed scaling relation rho_{s}=sigma_{dc}T_{c}. It is shown that there is a superconductivity induced increase of the in-plane low frequency spectral weight which follows the trend found in underdoped and optimally doped Bi-2212 and optimally doped Bi-2223. We observe an increase of optical spectral weight which corresponds to a change in kinetic energy of approximately 0.5 meV/Cu which is more than enough to explain the condensation energy. The specific heat anomaly is 10 times smaller than in YBCO and 3 times smaller than in Bi-2212. The shape of the anomaly is similar to the one observed in YBCO showing that the superconducting transition is governed by thermal fluctuations.Comment: 11 pages, 13 figure