Spatial structure of an individual Mn acceptor in GaAs

The wave function of a hole bound to an individual Mn acceptor in GaAs is spatially mapped by scanning tunneling microscopy at room temperature and an anisotropic, cross-like shape is observed. The spatial structure is compared with that from an envelope-function, effective mass model, and from a tight-binding model. This demonstrates that anisotropy arising from the cubic symmetry of the GaAs crystal produces the cross-like shape for the hole wave-function. Thus the coupling between Mn dopants in GaMnAs mediated by such holes will be highly anisotropic.Comment: 3 figures, submitted to PR

Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi

Gene sequences annotated as proteins of unknown or non-specific function and hypothetical proteins account for a large fraction of most genomes. In the strictly anaerobic and organohalide respiring Dehalococcoides mccartyi, this lack of annotation plagues almost half the genome. Using a combination of bioinformatics analyses and genome-wide metabolic modelling, new or more specific annotations were proposed for about 80 of these poorly annotated genes in previous investigations of D. mccartyi metabolism. Herein, we report the experimental validation of the proposed reannotations for two such genes (KB1_0495 and KB1_0553) from D. mccartyi strains in the KB-1 community. KB1_0495 or DmIDH was originally annotated as an NAD[superscript +]-dependent isocitrate dehydrogenase, but biochemical assays revealed its activity primarily with NADP[superscript +] as a cofactor. KB1_0553, also denoted as DmPMI, was originally annotated as a hypothetical protein/sugar isomerase domain protein. We previously proposed that it was a bifunctional phosphoglucose isomerase/phosphomannose isomerase, but only phosphomannose isomerase activity was identified and confirmed experimentally. Further bioinformatics analyses of these two protein sequences suggest their affiliation to potentially novel enzyme families within their respective larger enzyme super families.University of TorontoNatural Sciences and Engineering Research Council of CanadaGenome Canada (Firm) (Ontario Genomics Institute 2009-OGI-ABC-1405)United States. Dept. of Defense. Strategic Environmental Research and Development Progra

Combined approach of density functional theory and quantum Monte Carlo method to electron correlation in dilute magnetic semiconductors

We present a realistic study for electronic and magnetic properties in dilute magnetic semiconductor (Ga,Mn)As. A multi-orbital Haldane-Anderson model parameterized by density-functional calculations is presented and solved with the Hirsch-Fye quantum Monte Carlo algorithm. Results well reproduce experimental results in the dilute limit. When the chemical potential is located between the top of the valence band and an impurity bound state, a long-range ferromagnetic correlations between the impurities, mediated by antiferromagnetic impurity-host couplings, are drastically developed. We observe an anisotropic character in local density of states at the impurity-bound-state energy, which is consistent with the STM measurements. The presented combined approach thus offers a firm starting point for realistic calculations of the various family of dilute magnetic semiconductors.Comment: 5 pages, 4 figure

Assessing the impact of high environmental temperatures on the frequency and structural characteristics of violations of traffic rules

In the hot season, there is a positive relationship between the number of accidents per thousand registered vehicles and air temperature, due to the fact that high temperatures and solar activity can have a significant negative impact on the condition of drivers. As a rule, the creation of an emergency is preceded by a violation of traffic rules. Therefore, the identification of the type and number of violations committed by drivers at high ambient temperatures is relevant. The purpose of the work is to assess the impact of high ambient temperatures on the structure and frequency of traffic violations. Based on a literature review, the article states that at present there is no methodology for assessing the impact of high ambient temperatures on the characteristics of traffic violations. As an information platform, data from the Wialon — GPS/Glonass system are used, which allow you to objectively assess the characteristics of driving activity and the number of traffic violations. The work uses methods of mathematical statistics. The main result of the work, which constitutes the scientific novelty of the study, is the revealed increasing dependence of the total number of traffic violations on the average monthly ambient temperature. The structure of such violations is determined. The most significant, based on the impact on the accident rate, violations are: exceeding the speed limit and abrupt and dangerous maneuvers. It has been found that the total number of violations of the rules increases during periods with high ambient temperatures by 94% compared to months with moderate temperatures. The largest number of violations consists in exceeding the speed limit — 97.8% of their total number. The practical significance of the work consists in obtaining objective information about accidents at high ambient temperatures, on the basis of which it becomes possible to develop organizational and technological measures aimed at improving road safety. The areas of further research are related to the creation of an information platform for theoretical and methodological tools aimed at preventing high accidents of road transport in the hot season

Structural and biochemical studies of novel Aldo-keto Reductases (AKRs) for the biocatalytic conversion of 3-hydroxybutanal to 1,3-butanediol

The non-natural alcohol 1,3-butanediol (1,3-BDO) is a valuable building block for the synthesis of various polymers. One of the potential pathways for the biosynthesis of 1,3-BDO includes the biotransformation of acetaldehyde to 1,3-BDO via 3-hydroxybutanal (3-HB) using aldolases and aldo-keto reductases. This pathway requires an aldo-keto reductase (AKR) selective for 3-HB, but inactive toward acetaldehyde, so it can be used for one pot synthesis. In this work, we screened over 20 purified uncharacterized AKRs for 3-HB reduction and identified 10 enzymes with significant activity and nine proteins with detectable activity. PA1127 from Pseudomonas aeruginosa showed the highest activity and was selected for comparative studies with STM2406 from Salmonella typhimurium, for which we have determined the crystal structure. Both AKRs used NADPH as cofactor, reduced a broad range of aldehydes, and showed low activity toward acetaldehyde. The crystal structures of STM2406 in complex with cacodylate or NADPH revealed the active site with bound molecules of a substrate mimic or cofactor. Site-directed mutagenesis of STM2406 and PA1127 identified the key residues important for activity against 3-HB and aromatic aldehydes, which include the residues of the substrate binding pocket and C-terminal loop. Our results revealed that the replacement of the STM2406 Asn65 by Met enhanced both activity and affinity of this protein toward 3-HB resulting in a seven-fold increase in kcat/Km. Our work provided further insights into the molecular mechanisms of substrate selectivity of AKRs and rational design of these enzymes towards new substrates. Importance In this study, we identified several aldo-keto reductases with significant activity in the reduction of 3-hydroxybutanal to 1,3-BDO, an important commodity chemical. Biochemical and structural studies of these enzymes revealed the key catalytic and substrate binding residues including the two structural determinants necessary for high activity in the biosynthesis of 1,3-BDO. This work expands our understanding of the molecular mechanisms of substrate selectivity of AKRs and the potential for protein engineering of these enzymes for applications in the biocatalytic production of 1,3-BDO and other valuable chemicals

Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi

Gene sequences annotated as proteins of unknown or non-specific function and hypothetical proteins account for a large fraction of most genomes. In the strictly anaerobic and organohalide respiring Dehalococcoides mccartyi, this lack of annotation plagues almost half the genome. Using a combination of bioinformatics analyses and genome-wide metabolic modelling, new or more specific annotations were proposed for about 80 of these poorly annotated genes in previous investigations of D. mccartyi metabolism. Herein, we report the experimental validation of the proposed reannotations for two such genes (KB1_0495 and KB1_0553) from D. mccartyi strains in the KB-1 community. KB1_0495 or DmIDH was originally annotated as an NAD+-dependent isocitrate dehydrogenase, but biochemical assays revealed its activity primarily with NADP+ as a cofactor. KB1_0553, also denoted as DmPMI, was originally annotated as a hypothetical protein/sugar isomerase domain protein. We previously proposed that it was a bifunctional phosphoglucose isomerase/phosphomannose isomerase, but only phosphomannose isomerase activity was identified and confirmed experimentally. Further bioinformatics analyses of these two protein sequences suggest their affiliation to potentially novel enzyme families within their respective larger enzyme super families

Riboneogenesis in Yeast

SummaryGlucose is catabolized in yeast via two fundamental routes, glycolysis and the oxidative pentose phosphate pathway, which produces NADPH and the essential nucleotide component ribose-5-phosphate. Here, we describe riboneogenesis, a thermodynamically driven pathway that converts glycolytic intermediates into ribose-5-phosphate without production of NADPH. Riboneogenesis begins with synthesis, by the combined action of transketolase and aldolase, of the seven-carbon bisphosphorylated sugar sedoheptulose-1,7-bisphosphate. In the pathway's committed step, sedoheptulose bisphosphate is hydrolyzed to sedoheptulose-7-phosphate by the enzyme sedoheptulose-1,7-bisphosphatase (SHB17), whose activity we identified based on metabolomic analysis of the corresponding knockout strain. The crystal structure of Shb17 in complex with sedoheptulose-1,7-bisphosphate reveals that the substrate binds in the closed furan form in the active site. Sedoheptulose-7-phosphate is ultimately converted by known enzymes of the nonoxidative pentose phosphate pathway to ribose-5-phosphate. Flux through SHB17 increases when ribose demand is high relative to demand for NADPH, including during ribosome biogenesis in metabolically synchronized yeast cells

Biochemical and structural insights into enzymatic depolymerization of polylactic acid and other polyesters by microbial carboxylesterases

Polylactic acid (PLA) is a biodegradable polyester derived from renewable resources, which is a leading candidate for the replacement of traditional petroleum-based polymers. Since the global production of PLA is quickly growing, there is an urgent need for the development of efficient recycling technologies, which will produce lactic acid instead of CO₂ as the final product. After screening 90 purified microbial α/β-hydrolases, we identified hydrolytic activity against emulsified PLA in two uncharacterized proteins, ABO2449 from <i>Alcanivorax borkumensis</i> and RPA1511 from <i>Rhodopseudomonas palustris</i>. Both enzymes were also active against emulsified polycaprolactone and other polyesters as well as against soluble α-naphthyl and <i>p</i>-nitrophenyl monoesters. In addition, both ABO2449 and RPA1511 catalyzed complete or extensive hydrolysis of solid PLA with the production of lactic acid monomers, dimers, and larger oligomers as products. The crystal structure of RPA1511 was determined at 2.2 Å resolution and revealed a classical α/β-hydrolase fold with a wide-open active site containing a molecule of polyethylene glycol bound near the catalytic triad Ser114-His270-Asp242. Site-directed mutagenesis of both proteins demonstrated that the catalytic triad residues are important for the hydrolysis of both monoester and polyester substrates. We also identified several residues in RPA1511 (Gln172, Leu212, Met215, Trp218, and Leu220) and ABO2449 (Phe38 and Leu152), which were not essential for activity against soluble monoesters but were found to be critical for the hydrolysis of PLA. Our results indicate that microbial carboxyl esterases can efficiently hydrolyze various polyesters making them attractive biocatalysts for plastics depolymerization and recycling

The key role of smooth impurity potential in formation of hole spectrum for p-Ge/Ge_{1-x}Si_x heterostructures in the quantum Hall regime

We have measured the temperature (0.1 <= T <= 15 K) and magnetic field (0 <= B <= 12 T) dependences of longitudinal and Hall resistivities for the p-Ge_0.93Si_0.07/Ge multilayers with different Ge layer widths 10 <= d_w <= 38 nm and hole densities p_s = (1-5)10^11 cm^-2. Two models for the long-range random impurity potential (the model with randomly distributed charged centers located outside the conducting layer and the model of the system with a spacer) are used for evaluation of the impurity potential fluctuation characteristics: the random potential amplitude, nonlinear screening length in vicinity of integer filling factors nu = 1 and nu = 2 and the background density of state (DOS). The described models are suitable for explanation of the unusually high value of DOS at nu = 1 and nu = 2, in contrast to the short-range impurity potential models. For half-integer filling factors the linear temperature dependence of the effective QHE plateau-to-plateau transition width nu_0(T) is observed in contrast to scaling behavior for systems with short-range disorder. The finite T -> 0 width of QHE transitions may be due to an effective low temperature screening of smooth random potential owing to Coulomb repulsion of electrons.Comment: Accepted for publication in Nanotechnolog