Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.

BackgroundEvery genome contains a large number of uncharacterized proteins that may encode entirely novel biological systems. Many of these uncharacterized proteins fall into related sequence families. By applying sequence and structural analysis we hope to provide insight into novel biology.ResultsWe analyze a previously uncharacterized Pfam protein family called DUF4424 [Pfam:PF14415]. The recently solved three-dimensional structure of the protein lpg2210 from Legionella pneumophila provides the first structural information pertaining to this family. This protein additionally includes the first representative structure of another Pfam family called the YARHG domain [Pfam:PF13308]. The Pfam family DUF4424 adopts a 19-stranded beta-sandwich fold that shows similarity to the N-terminal domain of leukotriene A-4 hydrolase. The YARHG domain forms an all-helical domain at the C-terminus. Structure analysis allows us to recognize distant similarities between the DUF4424 domain and individual domains of M1 aminopeptidases and tricorn proteases, which form massive proteasome-like capsids in both archaea and bacteria.ConclusionsBased on our analyses we hypothesize that the DUF4424 domain may have a role in forming large, multi-component enzyme complexes. We suggest that the YARGH domain may play a role in binding a moiety in proximity with peptidoglycan, such as a hydrophobic outer membrane lipid or lipopolysaccharide

Activated biochars as sustainable and effective supports for hydrogenations

Activated biochars were obtained from pyrolysis and CO2-physical activation of four different biomasses including tannery shaving waste (T), vine wood waste (W), barley waste (B) and Sargassum, brown macroalgae of Venice lagoon (A). The potential of obtained carbonaceous materials as the supports of Ni,Al catalysts was investigated in levulinic acid (LA) conversion to γ-valerolactone (GVL) as a model hydrogenation reaction. Al-containing species as the Lewis acid sites for the dehydration step were incorporated to the supports using wet impregnation or precipitation. Ni as a hydrogenation active phase was added to the supports via wet impregnation. Biochar-based supports and catalysts were characterized by AAS, elemental analysis, FTIR, N2 physisorption, XRD, SEM, EDS, TEM, He-TPD, NH3-TPD and TPR techniques. The catalysts were tested for LA hydrogenation to GVL in a batch system and aqueous medium. The results showed that Ni supported on activated biochar was not active due to a lack of Lewis acid sites for dehydration. Precipitated Al-containing species on the biochar-based supports demonstrated a better catalytic performance in the reaction compared to impregnated one because of different interactions with the support and Ni species. Among different supports, the activated biochars obtained from T and W acted as the best ones. A higher catalytic efficiency was strongly influenced by the chemical (aromaticity and stability, presence of N,O-doped and functional groups), textural (the porous texture and surface area), and morphological (higher dispersion of active phases) properties of activated biochars obtained from different biomasses with different natures

Environmental risk to health of the population

Researches of the last years in the field of ecological epidemiology and the analysis of risk for health allow to claim with confidence that the polluted environment is one of the important factors defining changes of a state of health of the population. Expert opinions on the scale of this influence differ considerably now. These estimations vary from small shares of percent to several percent, reaching in some cases 30-50%. An attempt to elaborate economic approaches to a risk assessment to health of the population has been made in this work. The main reason which demands development of special approaches for an assessment of an environmental risk is that quantitative estimation of risk for health from environmental pollution is difficult to be realized. As a rule, population is affected by the whole set of the polluting substances from the atmosphere, drinking water, food, etc. For effective risk management it is necessary to assess and compare diverse risks caused by action of various pollutants coming to an organism in different ways. The stated methodical materials give an idea of possibility of the stage-by-stage multilevel risk analysis at the solution of environmental problems. Further comparative analysis connected with definition and comparison of various dangers can be done by means of the results received at a risk evaluation stage. © 2016 Anopchenko et al

In-plane magnetic field-induced spin polarization and transition to insulating behavior in two-dimensional hole systems

Using a novel technique, we make quantitative measurements of the spin polarization of dilute (3.4 to 6.8*10^{10} cm^{-2}) GaAs (311)A two-dimensional holes as a function of an in-plane magnetic field. As the field is increased the system gradually becomes spin polarized, with the degree of spin polarization depending on the orientation of the field relative to the crystal axes. Moreover, the behavior of the system turns from metallic to insulating \textit{before} it is fully spin polarized. The minority-spin population at the transition is ~8*10^{9} cm^{-2}, close to the density below which the system makes a transition to an insulating state in the absence of a magnetic field.Comment: 4 pages with figure

ThYme: a database for thioester-active enzymes

The ThYme (Thioester-active enzYme; http://www.enzyme.cbirc.iastate.edu) database has been constructed to bring together amino acid sequences and 3D (tertiary) structures of all the enzymes constituting the fatty acid synthesis and polyketide synthesis cycles. These enzymes are active on thioester-containing substrates, specifically those that are parts of the acyl-CoA synthase, acyl-CoA carboxylase, acyl transferase, ketoacyl synthase, ketoacyl reductase, hydroxyacyl dehydratase, enoyl reductase and thioesterase enzyme groups. These groups have been classified into families, members of which are similar in sequences, tertiary structures and catalytic mechanisms, implying common protein ancestry. ThYme is continually updated as sequences and tertiary structures become available

Interactions in high-mobility 2D electron and hole systems

Electron-electron interactions mediated by impurities are studied in several high-mobility two-dimensional (electron and hole) systems where the parameter $k_BT\tau /\hbar$ changes from 0.1 to 10 ($\tau$ is the momentum relaxation time). This range corresponds to the \textit{intermediate} and \textit {ballistic} regimes where only a few impurities are involved in electron-electron interactions. The interaction correction to the Drude conductivity is detected in the temperature dependence of the resistance and in the magnetoresistance in parallel and perpendicular magnetic fields. The effects are analysed in terms of the recent theories of electron interactions developed for the ballistic regime. It is shown that the character of the fluctuation potential (short-range or long-range) is an important factor in the manifestation of electron-electron interactions in high-mobility 2D systems.Comment: 22 pages, 11 figures; to appear in proceedings of conference "Fundamental Problems of Mesoscopic Physics", Granada, Spain, 6-11 September, 200

The nature of lithium perchlorate and gallium chloride salt effect in cycloaddition reactions

Comparing the acceleration effects of (4 + 2)-, (3 + 2)- and (2 + 2)-cycloaddition reactions in the presence of the salts of two types: gallium chloride in inert solvents and lithium perchlorate (LP) in diethyl ether (DE) it was observed that in the presence of GaCl3 the acceleration effect is approximately the same (104 times) for the studied reactions, while in LPDE medium for the same reactions strong increase (up to 104 times), weak increase or even decrease of the rate and equilibrium constants take place even with the common dienophile depending on the nature of the second reagent. it was suggested that the acceleration effect of cycloaddition reactions in the presence of such Lewis acids as aluminum, gallium or boron halides is due to the sharp increase of Π-acceptor properties of dienophiles and therefore increasing energy of orbital interaction, whereas LPDE medium demonstrates strong stabilization of static and/or dynamic polar forms and favors reactions with charge control

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/

Spin-valley phase diagram of the two-dimensional metal-insulator transition

Using symmetry breaking strain to tune the valley occupation of a two-dimensional (2D) electron system in an AlAs quantum well, together with an applied in-plane magnetic field to tune the spin polarization, we independently control the system's valley and spin degrees of freedom and map out a spin-valley phase diagram for the 2D metal-insulator transition. The insulating phase occurs in the quadrant where the system is both spin- and valley-polarized. This observation establishes the equivalent roles of spin and valley degrees of freedom in the 2D metal-insulator transition.Comment: 4 pages, 2 figure

Quantum Hall Effect in Three Dimensional Layered Systems

Using a mapping of a layered three-dimensional system with significant inter-layer tunneling onto a spin-Hamiltonian, the phase diagram in the strong magnetic field limit is obtained in the semi-classical approximation. This phase diagram, which exhibit a metallic phase for a finite range of energies and magnetic fields, and the calculated associated critical exponent, $\nu=4/3$, agree excellently with existing numerical calculations. The implication of this work for the quantum Hall effect in three dimensions is discussed.Comment: 4 pages + 4 figure