Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations

Background: Protein/receptor explicit flexibility has recently become an important feature of molecular docking simulations. Taking the flexibility into account brings the docking simulation closer to the receptors’ real behaviour in its natural environment. Several approaches have been developed to address this problem. Among them, modelling the full flexibility as an ensemble of snapshots derived from a molecular dynamics simulation (MD) of the receptor has proved very promising. Despite its potential, however, only a few studies have employed this method to probe its effect in molecular docking simulations. We hereby use ensembles of snapshots obtained from three different MD simulations of the InhA enzyme from M. tuberculosis (Mtb), the wild-type (InhA_wt), InhA_I16T, and InhA_I21V mutants to model their explicit flexibility, and to systematically explore their effect in docking simulations with three different InhA inhibitors, namely, ethionamide (ETH), triclosan (TCL), and pentacyano (isoniazid)ferrate(II) (PIF). Results: The use of fully-flexible receptor (FFR) models of InhA_wt, InhA_I16T, and InhA_I21V mutants in docking simulation with the inhibitors ETH, TCL, and PIF revealed significant differences in the way they interact as compared to the rigid, InhA crystal structure (PDB ID: 1ENY). In the latter, only up to five receptor residues interact with the three different ligands. Conversely, in the FFR models this number grows up to an astonishing 80 different residues. The comparison between the rigid crystal structure and the FFR models showed that the inclusion of explicit flexibility, despite the limitations of the FFR models employed in this study, accounts in a substantial manner to the induced fit expected when a protein/receptor and ligand approach each other to interact in the most favourable manner. Conclusions: Protein/receptor explicit flexibility, or FFR models, represented as an ensemble of MD simulation snapshots, can lead to a more realistic representation of the induced fit effect expected in the encounter and proper docking of receptors to ligands. The FFR models of InhA explicitly characterizes the overall movements of the amino acid residues in helices, strands, loops, and turns, allowing the ligand to properly accommodate itself in the receptor’s binding site. Utilization of the intrinsic flexibility of Mtb’s InhA enzyme and its mutants in virtual screening via molecular docking simulation may provide a novel platform to guide the rational or dynamicalstructure-based drug design of novel inhibitors for Mtb’s InhA. We have produced a short video sequence of each ligand (ETH, TCL and PIF) docked to the FFR models of InhA_wt. These videos are available at http://www.inf.pucrs. br/~osmarns/LABIO/Videos_Cohen_et_al_19_07_2011.htm

In vitro determination of extracellular proteins from xylella fastidiosa

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)The phytopathogen Xylella fastidiosa causes economic losses in important agricultural crops. Xylem vessel occlusion caused by biofilm formation is the major mechanism underlying the pathogenicity of distinct strains of X. fastidiosa. Here, we provide a detailed in vitro characterization of the extracellular proteins of X. fastidiosa. Based on the results, we performed a comparison with a strain J1a12, which cannot induce citrus variegated chlorosis symptoms when inoculated into citrus plants. We then extend this approach to analyze the extracellular proteins of X. fastidiosa in media supplemented with calcium. We verified increases in extracellular proteins concomitant with the days of growth and, consequently, biofilm development (330 days). Outer membrane vesicles carrying toxins were identified beginning at 10 days of growth in the 9a5c strain. In addition, a decrease in extracellular proteins in media supplemented with calcium was observed in both strains. Using mass spectrometry, 71 different proteins were identified during 30 days of X. fastidiosa biofilm development, including proteases, quorum-sensing proteins, biofilm formation proteins, hypothetical proteins, phage-related proteins, chaperones, toxins, antitoxins, and extracellular vesicle membrane components.The phytopathogen Xylella fastidiosa causes economic losses in important agricultural crops. Xylem vessel occlusion caused by biofilm formation is the major mechanism underlying the pathogenicity of distinct strains of X. fastidiosa. Here, we provide a de7Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2001/07533-7, 2012/51580-4]Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES, Computational Biology Program)CAPESFAPESP [2011/50268-4]CAPES (Computational Biology Program)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Effective Action for QED with Fermion Self-Interaction in D=2 and D=3 Dimensions

In this work we discuss the effect of the quartic fermion self-interaction of Thirring type in QED in D=2 and D=3 dimensions. This is done through the computation of the effective action up to quadratic terms in the photon field. We analyze the corresponding nonlocal photon propagators nonperturbatively in % \frac{k}{m}, where k is the photon momentum and m the fermion mass. The poles of the propagators were determined numerically by using the Mathematica software. In D=2 there is always a massless pole whereas for strong enough Thirring coupling a massive pole may appear . For D=3 there are three regions in parameters space. We may have one or two massive poles or even no pole at all. The inter-quark static potential is computed analytically in D=2. We notice that the Thirring interaction contributes with a screening term to the confining linear potential of massive QED_{2}. In D=3 the static potential must be calculated numerically. The screening nature of the massive QED$_{3}$ prevails at any distance, indicating that this is a universal feature of % D=3 electromagnetic interaction. Our results become exact for an infinite number of fermion flavors.Comment: Latex, 13 pages, 3 figure

Perilipin regulates the thermogenic actions of norepinephrine in brown adipose tissue

In response to cold, norepinephrine (NE)-induced triacylglycerol hydrolysis (lipolysis) in adipocytes of brown adipose tissue (BAT) provides fatty acid substrates to mitochondria for heat generation (adaptive thermogenesis). NE-induced lipolysis is mediated by protein kinase A (PKA)-dependent phosphorylation of perilipin, a lipid droplet-associated protein that is the major regulator of lipolysis. We investigated the role of perilipin PKA phosphorylation in BAT NE-stimulated thermogenesis using a novel mouse model in which a mutant form of perilipin, lacking all six PKA phosphorylation sites, is expressed in adipocytes of perilipin knockout (Peri KO) mice. Here, we show that despite a normal mitochondrial respiratory capacity, NE-induced lipolysis is abrogated in the interscapular brown adipose tissue (IBAT) of these mice. This lipolytic constraint is accompanied by a dramatic blunting (∼70%) of the in vivo thermal response to NE. Thus, in the presence of perilipin, PKA-mediated perilipin phosphorylation is essential for NE-dependent lipolysis and full adaptive thermogenesis in BAT. In IBAT of Peri KO mice, increased basal lipolysis attributable to the absence of perilipin is sufficient to support a rapid NE-stimulated temperature increase (∼3.0°C) comparable to that in wild-type mice. This observation suggests that one or more NE-dependent mechanism downstream of perilipin phosphorylation is required to initiate and/or sustain the IBAT thermal response

Quadratic Effective Action for QED in D=2,3 Dimensions

We calculate the effective action for Quantum Electrodynamics (QED) in D=2,3 dimensions at the quadratic approximation in the gauge fields. We analyse the analytic structure of the corresponding nonlocal boson propagators nonperturbatively in k/m. In two dimensions for any nonzero fermion mass, we end up with one massless pole for the gauge boson . We also calculate in D=2 the effective potential between two static charges separated by a distance L and find it to be a linearly increasing function of L in agreement with the bosonized theory (massive Sine-Gordon model). In three dimensions we find nonperturbatively in k/m one massive pole in the effective bosonic action leading to screening. Fitting the numerical results we derive a simple expression for the functional dependence of the boson mass upon the dimensionless parameter e^{2}/m .Comment: 10 pages, 2 figure

Development of microsprinkler prototypes through rapid prototyping and mechanical lathing

Objetivou-se, com este trabalho, construir protótipos de microaspersores, com boa uniformidade de distribuição para irrigações com sobreposição em hortas agrícolas, utilizando-se os processos de prototipagem rápida e torneamento mecânico. O estudo foi conduzido na ESALQ/USP e no Centro de Tecnologia da Informação Renato Archer (CTI). Utilizou-se o coeficiente de uniformidade de Christiansen na avaliação do desempenho dos emissores. O PVC e o tecnyl foram os materiais que apresentaram mais facilidade na construção dos protótipos no processo de torneamento mecânico, porém o PVC foi o escolhido devido ao melhor acabamento. Os protótipos construídos com torneamento mecânico apresentaram resultados satisfatórios ressaltando tratar-se de um processo bastante artesanal e laborioso; já com a prototipagem rápida se construíram protótipos com melhores acabamentos e mais rapidez. A utilização da prototipagem rápida no desenvolvimento de equipamentos de irrigação é algo totalmente inovador e de caráter pioneiro, além de uma ferramenta de grande utilidade na área de inovação de produtos no setor de Engenharia Agrícola.The present study had the objective of developing prototypes of microsprinkler with good distribution uniformity to irrigate with overlap in vegetable crops, by rapid prototyping and mechanic tournament. The work was carried out in the Hydraulic Laboratory of the Escola Superior de Agricultura Luiz de Queiroz, University of Sao Paulo, Brazil, and in the Centro de Tecnologia da Informação Renato Archer (CTI). Two processes were tested in the development of the microsprinkler prototypes rapid prototype and mechanical lathing. Christiansen Uniformity Coefficient was used as indicator to evaluate the distribution uniformity. Among the tested materials, the PVC and the technyl showed more facility in the prototype development in the mechanical lathing process, however, the PVC was chosen due to better finishing. The prototypes built by mechanical lathing showed satisfactory results, but were hard work and handmade. On the other hand, with the rapid prototyping, prototypes were built with better finishing and were quicker. The utilization of rapid prototyping in the development of irrigation devices is something completely innovative and pioneering, besides being a tool of great utility in the product innovation in the Agricultural Engineering sector.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), pelo apoio financeiro a esta pesquisa, através do Instituto Nacional de Ciência e Tecnologia em Engenharia da Irrigação (INCTEI

Physics informed neural networks learning a two-qubit Hamiltonian

Machine learning techniques are employed to perform the full characterization of a quantum system. The particular artificial intelligence technique used to learn the Hamiltonian is called physics informed neural network (PINN). The idea behind PINN is the universal approximation theorem, which claims that any function can be approximate by a neural network if it contains enough complexity. Consequently, a neural network can be a solution of a physical model. Moreover, by means of extra data provided by the user, intrinsic physical parameters can be extracted from the approach called inverse-PINN. Here, we apply inverse-PINN with the goal of extracting all the physical parameters that constitutes a two qubit Hamiltonian. We find that this approach is very efficient. To probe the robustness of the inverse-PINN to learn the Hamiltonian of a two-qubit system, we use the IBM quantum computers as experimental platforms to obtain the data that is plugged in the PINN. We found that our method is able to predict the two-qubit parameters with 5% of accuracy on average.Comment: 5 pages, 4 figure

The Borborema Pegmatite Province, NE-Brazil revisited

Considering the internal structure, mineralogical distribution and geochemical data on K-feldspar, white micas, Nb-Taoxides, tourmalines, garnet and spinel, it becomes clear that the pegmatites classified as "heterogeneous" (Johnston 1945) include examples of several types and subtypes of LCT family, Rare Element Class pegmatites if the modern pegmatite classification models of Černý & Ercit 2005 are applied: at least examples of the beryl-columbite, beryl-columbite-phosphate and complex-spodumene,complex-lepidolite (±gemmologic elbaite)and albite (± cassiterite) pegmatite types and subtypes were ntatively identified. The impossibility to determine a granitelinked zoned regional distribution of these types may be the result of the fact that there is no single central source pluton but several smaller granitic intrusions in the province and the zoning around them may overlap each other