Étude structurale conformationnelle des toxines de l’anthrax par cryo-microscopie et dynamique moléculaire

Les toxines de l’anthrax font partie de la famille des toxines A-B dans laquelle la moitié B se fixe à la membrane de la cellule permettant par la suite la translocation de la moitié A. Dans le cas de l’anthrax, la moitié B est représentée par le Protective Antigen (PA) et la moitié A par les deux protéines Edema Factor (EF) et Lethal Factor (LF). Après le recrutement par les récepteurs cellulaires (CMG2 et TEM8), PA s’organise en heptamère. Il peut fixer jusqu'à 3 ligands (EF et LF) avant d'être endocyté. Les modèles actuels de PA suggèrent que la baisse de pH à l’intérieur des endosomes permet un changement de conformation de la forme pré-pore vers la forme pore et que les ligands EF et LF passeraient au travers le pore pour entrer dans le cytoplasme. Cependant, le diamètre du pore est environ dix fois inférieur à celui des ligands (10 Å contre 100 Å). Un processus de folding/unfolding a été proposé mais demeure controversé. Afin d'identifier le processus de passage des facteurs EF et LF dans le cytoplasme, nous avons déterminé par cryo-microscopie électronique combinée avec l’analyse d’image les structures tridimensionnelles des complexes formés par PA et LF aux étapes prépore et pore. Par la suite, une étude complémentaire par dynamique moléculaire nous a permis de modéliser à haute résolution les différentes interactions qui ont lieu au sein du complexe. La structure 3D du complexe prépore combiné à 3 LF a été déterminée à une résolution de 14 Å. Nous avons aussi calculé une structure préliminaire du complexe pore également combiné à 3 LF Celles-ci n’ont jamais été résolues auparavant et leur connaissance permet d’envisager l’étude en profondeur du mécanisme infectieux de l’Anthrax in vivo.

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

An alkaline protease gene (Eap) was isolated for the first time from a marine fungus, Engyodontium album. Eap consists of an open reading frame of 1,161 bp encoding a prepropeptide consisting of 387 amino acids with a calculated molecular mass of 40.923 kDa. Homology comparison of the deduced amino acid sequence of Eap with other known proteins indicated that Eap encode an extracellular protease that belongs to the subtilase family of serine protease (Family S8). A comparative homology model of the Engyodontium album protease (EAP) was developed using the crystal structure of proteinase K. The model revealed that EAP has broad substrate specificity similar to Proteinase K with preference for bulky hydrophobic residues at P1 and P4. Also, EAP is suggested to have two disulfide bonds and more than two Ca2? binding sites in its 3D structure; both of which are assumed to contribute to the thermostable nature of the protein.

Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

An alkaline protease gene (Eap) was isolated for the first time from a marine fungus, Engyodontium album. Eap consists of an open reading frame of 1,161 bp encoding a prepropeptide consisting of 387 amino acids with a calculated molecular mass of 40.923 kDa. Homology comparison of the deduced amino acid sequence of Eap with other known proteins indicated that Eap encode an extracellular protease that belongs to the subtilase family of serine protease (Family S8). A comparative homology model of the Engyodontium album protease (EAP) was developed using the crystal structure of proteinase K. The model revealed that EAP has broad substrate specificity similar to Proteinase K with preference for bulky hydrophobic residues at P1 and P4. Also, EAP is suggested to have two disulfide bonds and more than two Ca2? binding sites in its 3D structure; both of which are assumed to contribute to the thermostable nature of the protein.

Image-Based View Synthesis

We present a new method for rendering novel images of flexible 3D objects from a small number of example images in correspondence. The strength of the method is the ability to synthesize images whose viewing position is significantly far away from the viewing cone of the example images ("view extrapolation"), yet without ever modeling the 3D structure of the scene. The method relies on synthesizing a chain of "trilinear tensors" that governs the warping function from the example images to the novel image, together with a multi-dimensional interpolation function that synthesizes the non-rigid motions of the viewed object from the virtual camera position. We show that two closely spaced example images alone are sufficient in practice to synthesize a significant viewing cone, thus demonstrating the ability of representing an object by a relatively small number of model images --- for the purpose of cheap and fast viewers that can run on standard hardware.

Two new Ni-II complexes with mu(1.5)-dicyanamide as bridging ligand

One 3D and one 2D mu(1,5)-dicyanamide bridged Ni-II complexes having molecular formula [Ni(L1)(dca)(2)] (1) and [Ni-2(L-2)(2)(dca)(4)] (.) 0.5H(2)O (2) (L1 = 4-(2-aminoethyl)-morpholine, L2 = 1-(2-aminoethyl)-piperidine and dca = dicyanamide dianion) have been synthesized. X-ray single crystal analyses and low temperature magnetic measurements were used to characterize the complexes. Complex 1 represents a 3D structure where each metal ion is chelated by morpholine ligand (L1) and connected by four mu(1,5)-dca. Whereas complex 2 shows an undulated 2D structure with grid of (4,4) topology having two crystallographically independent Ni-II centers in similar octahedral environment where each metal center is chelated by one piperidine ligand (L2) and coordinated by four mu(1,5)-dca. Magnetic measurements of both the complexes indicate weak antiferromagnetic interactions through the mu-(1,5)-dca bridging ligands. (c) 2004 Elsevier B.V. All rights reserved.

Sequencing of Spodoptera frugiperda midgut trehalases and demonstration of secretion of soluble trehalase by midgut columnar cells

Both soluble (SfTre1) and membrane-bound (SfTre2) trehalases occur along the midgut of Spodoptera frugiperda larvae. Released SfTre2 was purified as a 67 kDa protein. Its K(m) (1.6 mM) and thermal stability (half life 10 min at 62 degrees C) are different from the previously isolated soluble trehalase (K(m) = 0.47 mM; 100% stable at 62 degrees C). Two cDNAs coding for S. frugiperda trehalases have been cloned using primers based on consensus sequences of trehalases and having as templates a cDNA library prepared from total polyA-containing RNA extracted from midguts. One cDNA codes for a trehalase that has a predicted transmembrane sequence and was defined as SfTre2. The other, after being cloned and expressed, results in a recombinant trehalase with a K(m) value and thermal stability like those of native soluble trehalase. This enzyme was defined as SfTre1 and, after it was used to generate antibodies, it was immunolocalized at the secretory vesicles and at the glycocalyx of columnar cells. Escherichia coli trehalase 3D structure and sequence alignment with SfTre1 support a proposal regarding the residue modulating the pKa value of the proton donor.

Protein Hydrolysis by Immobilized and Stabilized Trypsin

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Hydrogen/deuterium exchange mass spectrometry for characterizing phosphoenolpyruvate-induced structural transitions in Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.1)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Genetic variability of porcine parvovirus isolates revealed by analysis of partial sequences of the structural coding gene VP2

The 3'-terminal 853 nt (and the putative 283 aa) sequence of the VP2-encoding gene from 29 field strains of porcine parvovirus (PPV) were determined and compared both to each other and with other published sequences. Sequences were examined using maximum-parsimony and statistical analyses for nucleotide diversity and sequence variability. Among the nucleotide sequences of the PPV field strains, 26 polymorphic sites were encountered; 22 polymorphic sites were detected in the putative amino acid sequence. Mapping polymorphic sites of protein data onto the three-dimensional (3D) structure of PPV VP2 revealed that almost all substitutions were located on the external surface of the viral capsid. Mapping amino acid substitutions to the alignment between PPV VP2 sequences and the 3D structure of canine parvovirus (CPV) capsid, many PPV substitutions were observed to map to regions of recognized antigenicity and/or to contain phenotypically important residues for CPV and other parvoviruses. In spite of the high sequence similarity, genetic analysis has shown the existence of at least two virus lineages among the samples. In conclusion, these results highlight the need for close surveillance on PPV genetic drift, with an assessment of its potential ability to modify the antigenic make-up of the virus.

Bioinformática estrutural aplicada ao estudo de proteínas alvo do genoma do Mycobacterium tuberculosis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Comparação dos efeitos do eletrojato equatorial nos dados magnetotelúricos bi e tridimensionais

Este trabalho trata da comparação dos efeitos do eletrojato equatorial nos dados magnetotelúricos bi e tridimensionais. Ele compõe-se fundamentalmente de duas partes: Na primeira, que consiste na comparação dos efeitos dos modelos bi e tridimensionais (linha de corrente e eletrojato gaussiano), determinamos as dimensões que deve apresentar uma estrutura tridimensional para que a resposta magnetotelúrica proveniente dessa estrutura, nas polarizações YX e XY, possa ser substituída pela resposta magnetotelúrica proveniente de uma estrutura bidimensional nos modos TE e TM respectivamente, para a resistividade aparente e fase. Os resultados mostram, para um embasamento condutivo ou resistivo, que é necessário aumentar a dimensão da estrutura tridimensional na direção principal acima de dezesseis vezes, em relação à dimensão inicial, para que a resposta magnetotelúrica proveniente dessa estrutura na polarização YX, possa ser substituída pela resposta magnetotelúrica proveniente de uma estrutura bidimensional no modo TE; no caso da polarização ser XY, essa substituição ocorrerá, no modo TM bidimensional, se aumentarmos a dimensão da estrutura tridimensional na direção principal acima de vinte e seis vezes em relação à dimensão inicial. Na segunda parte, que consiste na determinação dos efeitos do eletrojato equatorial Onwumechilliano, posicionamos a estrutura tridimensional a 10 km, 100 km, 300 km, 500 km, 1000 km e 1500 km, respectivamente, de distância do eletrojato. Dessa forma, determinamos a distância na qual os efeitos do eletrojato equatorial Onwumechilliano sobre as sondagens magnetotelúricas são praticamente desprezíveis. Verificamos que, posicionando a estrutura tridimensional a 1500 km de distância da fonte, para embasamento condutivo, o eletrojato não afeta as sondagens magnetotelúricas. Quando o embasamento é resistivo, o eletrojato afeta as sondagens magnetotelúricas, mesmo posicionando-se a estrutura tridimensional a 1500 km de distância da fonte. De um modo geral, constatamos que o eletrojato equatorial afeta as sondagens magnetotelúricas para freqüências inferiores a 10^-2 Hz, tanto na resistividade aparente quanto na fase e em ambas as polarizações, principalmente, quando o embasamento é resistivo. Observamos também que o efeito galvânico é mais pronunciado na polarização YX que na XY.

Function inferences from a molecular structural model of bacterial ParE toxin

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

DNA-Interactive Properties of Crotamine, a Cell-Penetrating Polypeptide and a Potential Drug Carrier

Crotamine, a 42-residue polypeptide derived from the venom of the South American rattlesnake Crotalus durissus terrificus, has been shown to be a cell-penetrating protein that targets chromosomes, carries plasmid DNA into cells, and shows specificity for actively proliferating cells. Given this potential role as a nucleic acid-delivery vector, we have studied in detail the binding of crotamine to single- and double-stranded DNAs of different lengths and base compositions over a range of ionic conditions. Agarose gel electrophoresis and ultraviolet spectrophotometry analysis indicate that complexes of crotamine with long-chain DNAs readily aggregate and precipitate at low ionic strength. This aggregation, which may be important for cellular uptake of DNA, becomes less likely with shorter chain length. 25-mer oligonucleotides do not show any evidence of such aggregation, permitting the determination of affinities and size via fluorescence quenching experiments. The polypeptide binds non-cooperatively to DNA, covering about 5 nucleotide residues when it binds to single (ss) or (ds) double stranded molecules. The affinities of the protein for ss-vs. ds-DNA are comparable, and inversely proportional to salt levels. Analysis of the dependence of affinity on [NaCl] indicates that there are a maximum of,3 ionic interactions between the protein and DNA, with some of the binding affinity attributable to non-ionic interactions. Inspection of the three-dimensional structure of the protein suggests that residues 31 to 35, Arg-Trp-Arg-Trp-Lys, could serve as a potential DNA-binding site. A hexapeptide containing this sequence displayed a lower DNA binding affinity and salt dependence as compared to the full-length protein, likely indicative of a more suitable 3D structure and the presence of accessory binding sites in the native crotamine. Taken together, the data presented here describing crotamine-DNA interactions may lend support to the design of more effective nucleic acid drug delivery vehicles which take advantage of crotamine as a carrier with specificity for actively proliferating cells. Citation: Chen P-C, Hayashi MAF, Oliveira EB, Karpel RL (2012) DNA-Interactive Properties of Crotamine, a Cell-Penetrating Polypeptide and a Potential Drug Carrier. PLoS ONE 7(11): e48913. doi:10.1371/journal.pone.0048913

The Influence of Osteoblast Differentiation Stage on Bone Formation in Autogenously Implanted Cell-Based Poly(Lactide-Co-Glycolide) and Calcium Phosphate Constructs

We tested the hypothesis that the osteoblast differentiation status of bone marrow stem cells (BMSCs) combined with a three-dimensional (3D) structure modulates bone formation when autogenously implanted. Rat BMSCs were aspirated, expanded, and seeded into a 3D composite of poly(lactide-co-glycolide) and calcium phosphate (PLGA/CaP) to produce a hybrid biomaterial. Calvarial defects were implanted with (1) scaffold without cells (SC/NC), (2) scaffold and BMSCs (SC + BMSC), (3) scaffold and osteoblasts differentiated for 7 days (SC + OB7), and (4) for 14 days (SC + OB14). After 4 weeks, there was more bone formation in groups combining scaffold and cells, SC + BMSC and SC + OB7. A nonsignificant higher amount of bone formation was observed on SC + OB14 compared with SC/NC. Additionally, more blood vessels were counted within all hybrid biomaterials, without differences among them, than into SC/NC. These findings provide evidences that the cell differentiation status affects in vivo bone formation in autogenously implanted cell-based constructs. Undifferentiated BMSCs or osteoblasts in early stage of differentiation combined with PLGA/CaP scaffold favored bone formation compared with plain scaffold and that one associated with more mature osteoblasts.

A fragment-based approach for ligand binding affinity and selectivity for the liver X receptor beta

Selective modulation of liver X receptor beta (LXR beta) has been recognized as an important approach to prevent or reverse the atherosclerotic process. In the present work, we have developed robust conformation-independent fragment-based quantitative structure-activity and structure-selectivity relationship models for a series of quinolines and cinnolines as potent modulators of the two LXR sub-types. The generated models were then used to predict the potency of an external test set and the predicted values were in good agreement with the experimental results, indicating the potential of the models for untested compounds. The final 2D molecular recognition patterns obtained were integrated to 3D structure-based molecular modeling studies to provide useful insights into the chemical and structural determinants for increased LXR beta binding affinity and selectivity. (C) 2011 Elsevier Inc. All rights reserved.