Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway

The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al

The 6^{6}H states studied in the d(8He,α)d(^8\text{He},\alpha) reaction and evidence of extremely correlated character of the 5^{5}H ground state

The extremely neutron-rich system $^{6}$H was studied in the direct $^2\text{H}(^8\text{He},{^4\text{He}})^{6}$H transfer reaction with a 26 $A$ MeV secondary $^{8}$He beam. The measured missing mass spectrum shows a resonant state in $^{6}$H at $6.8(3)$ MeV relative to the $^3$H+$3n$ threshold. The population cross section of the presumably $p$-wave states in the energy range from 4 to 8 MeV is $d\sigma/d\Omega_{\text{c.m.}} \simeq 190(40)$ $\mu$b/sr in the angular range $5^{\circ}<\theta_{\text{c.m.}}<16^{\circ}$. The obtained missing mass spectrum is free of the $^{6}$H events below 3.5 MeV ($d\sigma/d\Omega_{\text{c.m.}} \lesssim 3$ $\mu$b/sr in the same angular range). The steep rise of the $^{6}$H missing mass spectrum at 3 MeV allows to show that $4.5(3)$ MeV is the lower limit for the possible resonant state energy in $^{6}$H tolerated by our data. According to paring energy estimates, such a $4.5(3)$ MeV resonance is a realistic candidate for the $^{6}$H ground state (g.s.). The obtained results confirm that the decay mechanism of the $^{7}$H g.s.\ (located at 2.2 MeV above the $^{3}$H+$4n$ threshold) is the ``true'' (or simultaneous) $4n$ emission. The resonance energy profiles and the momentum distributions of the sequential $^{6}$H \,\rightarrow \, ^5H(g.s.)+n\, \rightarrow \, ^3H+$3n$ decay fragments were analyzed by the theoretically-updated direct four-body-decay and sequential-emission mechanisms. The measured momentum distributions of the $^{3}$H fragments in the $^{6}$H rest frame indicate very strong ``dineutron-type'' correlations in the $^{5}$H ground state decay.Comment: 9 pages, 11 figure

Study of Proton and Deuteron Pickup Reactions 2H(10Be,3He)9Li an 2H(10Be,4He)8Li with 44 A MeV 10Be Radioactive Beam at ACCULINNA-2 Fragment Separator

The proton and deuteron pickup reactions 2H(10Be,3He)9Li and\\ 2H(10Be,4He)8Li radioactive beam produced by the new fragment separator ACCULINNA-2 at FLNR, JINR\@. These measurements were initially motivated as test reactions intended for the elucidation of results obtained in the study of the extremely neutron-rich 7H and 6H systems created in the 2H(10Be,3He)9Li and 2H(10Be,4He)8Li reactions using the same setup. In the 2H(10Be,3He)9Li reaction the 9Li ground-state ($3/2^-$) and its first excited state (2.69~MeV, $1/2^-$) were identified in the low-energy region of its excitation spectrum. The differential cross sections for the 9Li g.~s.) population were extracted at forward center-of-mass angles ($3^\circ-13^\circ$) and compared with the FRESCO calculations. Spectroscopic factor of $\sim 1.7$, derived by a model for the 10Be$= p +$9Li(g.s.) clustering was found in accord with the experimental data. The energy spectrum of 8Li populated in the 2H(10Be,4He)8Li reaction shows the strong peak which corresponds to excitation of the second excited state of 8Li (2.25 MeV, $3^+$). The fact that the ground and the first excited states of 8Li were not observed is fully consistent with Shell-Model calculations carried out for the 10Be g.\,s. and 8Li level structure applying momentum selection rules

Common Genetic Denominators for Ca++-Based Skeleton in Metazoa: Role of Osteoclast-Stimulating Factor and of Carbonic Anhydrase in a Calcareous Sponge

Calcium-based matrices serve predominantly as inorganic, hard skeletal systems in Metazoa from calcareous sponges [phylum Porifera; class Calcarea] to proto- and deuterostomian multicellular animals. The calcareous sponges form their skeletal elements, the spicules, from amorphous calcium carbonate (ACC). Treatment of spicules from Sycon raphanus with sodium hypochlorite (NaOCl) results in the disintegration of the ACC in those skeletal elements. Until now a distinct protein/enzyme involved in ACC metabolism could not been identified in those animals. We applied the technique of phage display combinatorial libraries to identify oligopeptides that bind to NaOCl-treated spicules: those oligopeptides allowed us to detect proteins that bind to those spicules. Two molecules have been identified, the (putative) enzyme carbonic anhydrase and the (putative) osteoclast-stimulating factor (OSTF), that are involved in the catabolism of ACC. The complete cDNAs were isolated and the recombinant proteins were prepared to raise antibodies. In turn, immunofluorescence staining of tissue slices and qPCR analyses have been performed. The data show that sponges, cultivated under standard condition (10 mM CaCl2) show low levels of transcripts/proteins for carbonic anhydrase or OSTF, compared to those animals that had been cultivated under Ca2+-depletion condition (1 mM CaCl2). Our data identify with the carbonic anhydrase and the OSTF the first two molecules which remain conserved in cells, potentially involved in Ca-based skeletal dissolution, from sponges (sclerocytes) to human (osteoclast)

Problems of exploitation of the lower Vistula River

W pracy omówiono historię i aktualny stan zagospodarowania dolnej Wisły oraz najistotniejsze argumenty na rzecz gospodarczego wykorzystania jej potencjału. Wskazano, że najlepszym sposobem kompleksowego i integralnego rozwiązania problemów związanych z zagrożeniem niesionym przez dolną Wisłę i wykorzystaniem istniejących możliwości jest powrót do idei budowy kaskady stopni wodnych. Takie podejście umożliwi kompleksowe rozwiązanie problemów zagrożenia powodzią, produkcji energii, transportu wodnego, zaopatrzenia w wodę, retencji wód opadowych oraz sportu i rekreacji. Dla porównania przedstawiono stan rozwoju infrastruktury hydrotechnicznej w Europie i na świecie.In the paper the history and current situation dealing with the possibilities of making use of the lower Vistula River potential are presented and discussed. Taking into account the hydrological characteristics and the remarkable various possibilities represented by the Vistula River, it is shown that building of a cascade of reservoirs could be probably the best solution. This investment will make possible to solve simultaneously such problems as production of hydro-energy, water transport, flood protection, supplying of water for agriculture and industry, development of sports and recreation, increasing of stored water capacity etc. Application of the modern solutions and technologies should limit negative impact of the hydraulic structures on the natural environment of the Vistula valley. For comparison similar projects carried out in many other countries in the past and currently realized are also presented

The pollutant transport equation for a steady, gradually varied flow in an open channel network: a solution of high accuracy

The paper is concerned with solving the transport pollutant problem for a steady, gradually varied flow in an open channel network. The 1D advective-diffusive transport equation is solved using the splitting technique. An analytical solution of the linear advective-diffusive equation in the form of an impulse response function is used to solve the advection-diffusion part of the governing equation. This approach, previously applied in solutions of the advection-diffusion equation for a single channel, is extended to a channel network. Numerical calculations are only required to compute the integral of convolution. The finite difference method is used to solve the second part of the governing equation, containing the source term. The applied approach has considerable advantages, especially appreciable in the case of advection-dominated transport with large gradients of concentration, since it generates no numerical dissipation or dispersion. The flow parameters are obtained via solution of the steady, gradually varied flow equation. In the final non-linear system of algebraic equations obtained through approximation of the ordinary differential equation, the depths at each cross-section of channels and the discharge at each branch of the network are considered as unknowns. The system is solved using the modified Picard iteration, which ensures convergence of the iterative process for a steady, gradually varied flow solved for both looped and tree-type open channel networks