Cloning, expression, purification and preliminary X-ray diffraction studies of a putative Mycobacterium smegmatis thiolase

Thiolases are important in fatty-acid degradation and biosynthetic pathways. Analysis of the genomic sequence of Mycobacterium smegmatis suggests the presence of several putative thiolase genes. One of these genes appears to code for an SCP-x protein. Human SCP-x consists of an N-terminal domain (referred to as SCP2 thiolase) and a C-terminal domain (referred as sterol carrier protein 2). Here, the cloning, expression, purification and crystallization of this putative SCP-x protein from M. smegmatis are reported. The crystals diffracted X-rays to 2.5 angstrom resolution and belonged to the triclinic space group P1. Calculation of rotation functions using X-ray diffraction data suggests that the protein is likely to possess a hexameric oligomerization with 32 symmetry which has not been observed in the other six known classes of this enzyme.

Structure of tandem and its implication for bifunctional intercalation into dna

Quinoxaline antibiotics (Fig. 1a, b) form a useful group of compounds for the study of drug–nucleic acid interactions1,2. They consist of a cross-bridged cyclic octadepsipeptide, variously modified, bearing two quinoxaline chromophores. These antibiotics intercalate bifunctionally into DNA2,3 probably via the narrow groove, forming a complex in which, most probably, two base pairs are sandwiched between the chromophores4,5. Depending on the nature of their sulphur-containing cross-bridge and modifications to their amino acid side chains, they display characteristic patterns of nucleotide sequence selectivity when binding to DNAs of different base composition and to synthetic polydeoxynucleotides4,6,7. This specificity has been tentatively ascribed to specific hydrogen-bonding interactions between functional groups in the DNA and complementary moieties on the peptide ring2,4,5. Variations in selectivity have been attributed both to changes in the conformation of the peptide backbone6 and no modifications of the cross-bridge7. These suggestions were made, however, in the absence of firm knowledge about the three-dimensional structure and conformation of the antibiotic molecules. We now report the X-ray structure analysis of the synthetic analogue of the antibiotic triostin A, TANDEM (des-N-tetramethyl triostin A) (Fig. 1c), which binds preferentially to alternating adenine-thymine sequences7. The X-ray structure provides a starting point for exploring the origin of this specificity and suggests possible models for the binding of other members of the quinoxaline series.

Insights into differential modulation of receptor function by hinge region using novel agonistic lutropin receptor and inverse agonistic thyrotropin receptor antibodies

We report two antibodies, scFv 13B1 and MAb PD1.37, against the hinge regions of LHR and TSHR, respectively, which have similar epitopes but different effects on receptor function. While neither of them affected hormone binding, with marginal effects on hormone response, scFv 13B1 stimulated LHR in a dose-dependent manner, whereas MAb PD1.37 acted as an inverse agonist of TSHR. Moreover, PD1.37 could decrease the basal activity of hinge region CAMs, but had varied effects on those present in ECLs, whereas 13B1 was refractory to any CAMs in LHR. Using truncation mutants and peptide phage display, we compared the differential roles of the hinge region cysteine box-2/3 as well as the exoloops in the activation of these two homologus receptors. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Phylogeny of the Asian Eutropis (Squamata: Scincidae) reveals an `into India' endemic Indian radiation

Recent generic rearrangement of the circumtropical distributed skink genus `Mabuya' has raised a lot of debate. According to this molecular phylogeny based rearrangement, the tropical Asian members of this genus have been assigned to Eutropis. However, in these studies the Asian members of `Mabuya' were largely sampled from Southeast (SE) Asia with very few species from Indian subcontinent. To test the validity of this assignment and to determine the evolutionary origin of Indian members of this group we sequenced one nuclear and two mitochondrial genes from most of the species from the Indian subregion. The nuclear and mitochondrial trees generated from these sequences confirmed the monophyly of the tropical Asian Eutropis. Furthermore, in the tree based on the combined mitochondrial and nuclear dataset an endemic Indian radiation was revealed that was nested within a larger Asian clade. Results of dispersal-vicariance analysis and molecular dating suggested an initial dispersal of Eutropis from SE Asia into India around 5.5-17 million years ago, giving rise to the extant members of the endemic Indian radiation. This initial dispersal was followed by two back dispersals from India into SE Asia. We also discuss the relationships within the endemic Indian radiation and its taxonomic implications. (c) 2012 Elsevier Inc. All rights reserved.

Selenium in Diketopyrrolopyrrole-based Polymers: Influence on Electronic Properties and Charge Carrier Mobilities

Diketopyrrolopyrrole (DPP)-based pi-conjugated copolymers with thiophene have exceptionally high electron mobilities. This paper investigates electronic properties and charge carrier mobilities of selenophene containing analogues. Two new copolymers, with alternating thiophene DPP (TDPP) and selenophene DPP (SeDPP) units, were synthesized. Two side-chains, hexyl (Hex) and triethylene glycol (TEG) were employed, yielding polymers designated as PTDPPSeDPP-Hex and PTDPPSeDPP-TEG. Selenophene systems have smaller band gaps, with concomitant enhancement of the stability of the reduced state. For both polymers, ambipolar mobilities were observed in organic field-effect transistors (OFET). Grazing incidence X-ray diffraction (GIXD) data indicates preferential edge-on orientation of PTDPPSeDPP-TEG, which leads to superior charge transport properties of the TEG substituted polymer, as compared to its Hex analogue. Time-dependent-density functional theory (TDDFT) calculations corroborate the decrease in the optical band gap with the inclusion of selenophene. Ambipolar charge transport is rationalized by exceptionally wide conduction bands. Delta SCF calculations confirm the larger electron affinity, and therefore the greater stability, of the reduced form of the selenophene-containing DPP polymer in presence of chloroform.

Space-Vector-Based Hybrid PWM Technique to Reduce Peak-to-Peak Torque Ripple in Induction Motor Drives

Special switching sequences involving division of active state time are used in space-vector-based generation of pulse width modulation (PWM) waveforms. This paper proposes a hybrid PWM technique which is a combination of the conventional and special switching sequences. The proposed hybrid PWM technique reduces the peak-to-peak torque ripple at high speeds of an induction motor drive. Supporting simulation and experimental results are presented from a closed-loop controlled motor drive.

Thermocapillary flow in an annular liquid layer painted on a moving fiber

In the present paper, a theoretical model is studied on the flow in the liquid annular film, which is ejected from a vessel with relatively higher temperature and painted on the moving solid fiber. A temperature gradient, driving a thermocapillary flow, is formed on the free surface because of the heat transfer from the liquid with relatively higher temperature to the environmental gas with relatively lower temperature. The thermocapillary flow may change the radii profile of the liquid film. This process analyzed is based on the approximations of lubrication theory and perturbation theory, and the equation of the liquid layer radii and the process of thermal hydrodynamics in the liquid layer are solved for a temperature distribution on the solid fiber.

Simulation-based optimal sensor scheduling with application to observer trajectory planning

The sensor scheduling problem can be formulated as a controlled hidden Markov model and this paper solves the problem when the state, observation and action spaces are continuous. This general case is important as it is the natural framework for many applications. The aim is to minimise the variance of the estimation error of the hidden state w.r.t. the action sequence. We present a novel simulation-based method that uses a stochastic gradient algorithm to find optimal actions. © 2007 Elsevier Ltd. All rights reserved.

Evaluación de la producción de forraje de Cnidoscolus aconitifolium(Mill) L.M. Johnst, Moringa oleifera (Lam) y Leucaena leucocephala (Lam) de Wit, para banco protéico en Pacora, San Francisco Libre, Nicaragua

El presente trabajo se realizo en la comunidad de Pacora, San Francisco Libre, Managua, donde los habitantes tradicionalmente, han utilizado la crianza de ganado menor (cerdos, cabras, gallinas, patos, Peliguey y otros) para satisfacer en cierta medida sus necesidades alimenticias y económicas por la pobreza que caracteriza la comunidad. Con este estudio se presenta una opción de utilizar las tierras que no pueden ser aprovechadas con cultivos tradicionales, empleando especies forestales cuyo sistema radicular y funciones fisiológicas son muy diferente a los cultivos tradicionales, permitiendo su sobrevivencia, calidad nutritiva, el manejo agronómico y el potencial de incorporar estos forrajes en la dieta de animales domésticos. Se evalúa la producción de biomasa total y comestible, la sobrevivencia y los agentes biológicos que afectan a las especies de Quelite ( Cnidoscolus aconitifolium (Mill) L.M.Johnst), m arango (Moringa oleífera) Lam, y Leucaena (Leucaena leucocephala (Lam) de wit), estableciéndose en parcelas de 10.5 m 2 La mayor producción de biomasa verde total la obtuvo Moringa oleífera (Lam) con 15,991 kg ha -1 en la primera poda (7 meses de establecido el ensayo) y en la segunda poda (12 meses de establecido el ensayo) con 34,873 kg ha -1 . Esta misma especie mostró los mejores rendimientos de biomasa seca total en la primera poda con 4,181 kg ha -1 , pero en la segunda poda fue superada por la especie Leucaena leucocephala (Lam) de wit, con 6,782 kg ha -1 . La mayor producción de biomasa verde comestible en la primera poda la obtuvo Cnidoscolus aconitifolium (Mill) L. M.Johnst con 9,491 kg ha -1 y en la segunda poda con 25,553 kg ha -1 , Esta misma especie mostró los mayores rendimientos en biomasa seca comestible con 1,790 kg ha -1 en la primera poda y 5,817 kg ha -1 en la segunda poda. Los mayores porcentajes de sobrevivencia (100%), en la primera poda fueron obtenidos por la especie Leucaena leucocephala (Lam) de wit , Cinco meses después esta misma especie mostró rendimientos de 100% de sobrevivencia. Los agentes biológicos (insectos) encontrados en el ensayo no ocasionaron daños a las plantas que incurrieran en la producción y la calidad de la biomasa obtenida en el estudio.

跨声速激波边界层相互作用的被动控制

运用激波管风洞,在Re_∞/m=3×10~7,M_∞=0.732-0.817范围内,在厚度比为12％的圆弧翼型半模型和厚度比为14％的超临界翼型半模型上,对被动控制现象及其若干规律进行了实验研究。结果表明,不同空腔深度的开孔壁和导管连通壁均可对壁面激波与边界层的相互作用实现被动控制,使得沿以上两种模型表面的马赫数峰值、逆压力梯度和激波强度明显减小,这对于飞行器将起到减阻作用。对超、跨声速压气机内激波与边界层相互作用的控制,亦能提高其效率和工作的稳定性。

高速流动激光器的稳定振荡条件、模式结构与输出功率的一维改进和二、三维处理

本文对高速流动激光器,将文献[1]在几何光学近似下的一维一级近似处理改进为几何光学近似所容许的最精确处理,并进行了二、三维处理,导出了二、三维情况下的稳定振荡条件、输出功率公式以及几何光学近似下的模式表示式(用增益函数表示)。按本文理论对Gerry的典型实验进行了一维和二维计算,结果均与实验吻合很好。 本文还将文献[1]对Lee的稳定振荡条件的适用范围所加的限制进行了拓广;文中还给出了光腔中模式结构的几何光学近似的适用条件,指出这一条件与自由空间中几何光学适用条件的差异。

Two-time scales inner solutions and motion of a geostrophic vortex

Based on the authors' previous work, in this paper the systematical analyses on the motion and the inner solutions of a geostrophic vortex have been presented by means of thematched asymptotic expansion method with multiple time scales (S/gh001/2 and α S/gh001/2) and space scales. It has been shown that the leading inner solutions to the core structure in two-time scales analyses are identified with the results in normal one-time scale analyses. The time averages of the first-order solutions on short time variable τ are the same as the first-order solutions obtained in one normal time scale analyses. The geostrophic vortex induces an oscillatory motion in addition to moving with the background flow. The period, amplitude andthe deviation from the mean trajectory depend on the core structure and the initial conditions. The velocity of the motion of vortex center varies periodically and the time average of the velocity on short time variable τ is equal to the value of the local mean velocity.

Structure Prediction of G-Protein Coupled Receptors

G-protein coupled receptors (GPCRs) form a large family of proteins and are very important drug targets. They are membrane proteins, which makes computational prediction of their structure challenging. Homology modeling is further complicated by low sequence similarly of the GPCR superfamily.

In this dissertation, we analyze the conserved inter-helical contacts of recently solved crystal structures, and we develop a unified sequence-structural alignment of the GPCR superfamily. We use this method to align 817 human GPCRs, 399 of which are nonolfactory. This alignment can be used to generate high quality homology models for the 817 GPCRs.

To refine the provided GPCR homology models we developed the Trihelix sampling method. We use a multi-scale approach to simplify the problem by treating the transmembrane helices as rigid bodies. In contrast to Monte Carlo structure prediction methods, the Trihelix method does a complete local sampling using discretized coordinates for the transmembrane helices. We validate the method on existing structures and apply it to predict the structure of the lactate receptor, HCAR1. For this receptor, we also build extracellular loops by taking into account constraints from three disulfide bonds. Docking of lactate and 3,5-dihydroxybenzoic acid shows likely involvement of three Arg residues on different transmembrane helices in binding a single ligand molecule.

Protein structure prediction relies on accurate force fields. We next present an effort to improve the quality of charge assignment for large atomic models. In particular, we introduce the formalism of the polarizable charge equilibration scheme (PQEQ) and we describe its implementation in the molecular simulation package Lammps. PQEQ allows fast on the fly charge assignment even for reactive force fields.