Crystallographic structure of PNP from Mycobacterium tuberculosis at 1.9 angstrom resolution

Even being a bacterial purine nucleoside phosphorylase (PNP), which normally shows hexameric folding, the Mycobacterium tuberculosis PNP (MtPNP) resembles the mammalian trimeric structure. The crystal structure of the MtPNP apoenzyme was solved at 1.9 Angstrom resolution. The present work describes the first structure of MtPNP in complex with phosphate. In order to develop new insights into the rational drug design, conformational changes were profoundly analyzed and discussed. Comparisons over the binding sites were specially studied to improve the discussion about the selectivity of potential new drugs. (C) 2004 Elsevier B.V. All rights reserved.

Crystal structure of human PNP complexed with hypoxanthine and sulfate ion

Purine nucleoside phosphorylase (PNP) is a ubiquitous enzyme, which plays a key role in the purine salvage pathway, and PNP deficiency in humans leads to an impairment of T-cell function, usually with no apparent effects on B-cell function. Human PNP has been submitted to intensive structure-based design of inhibitors, most of them using low-resolution structures of human PNP. Here we report the crystal structure of human PNP in complex with hypoxanthine, refined to 2.6 Angstrom resolution. The intermolecular interaction between ligand and PNP is discussed. (C) 2004 Elsevier B.V. All rights reserved.

Crystal structure of human purine nucleoside phosphorylase at 2.3 angstrom resolution

Purine nucleoside phosphorylase (PNP) catalyzes the phosphorolysis of the N-ribosidic bonds of purine nucleosides and deoxynucleosides. In human, PNP is the only route for degradation of deoxyguanosine and genetic deficiency of this enzyme leads to profound T-cell mediated immunosuppression. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and its low resolution structure has been used for drug design. Here we report the structure of human PNP solved to 2.3 Angstrom resolution using synchrotron radiation and cryocrystallographic techniques. This structure allowed a more precise analysis of the active site, generating a more reliable model for substrate binding. The higher resolution data allowed the identification of water molecules in the active site, which suggests binding partners for potential ligands. Furthermore, the present structure may be used in the new structure-based design of PNP inhibitors. (C) 2003 Published by Elsevier B.V.

Ultra-structure and histochemistry of digestive cells of Podisus nigrispinus (Hemiptera: Pentatomidae) fed with prey reared on bt-cotton

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Differential distribution of some extracellular matrix fibers in an experimentally denervated rat megaileum

Absence of enteric neurons is associated with thickening of the intestinal muscularis externa in Chagas' disease. The thickening is due to hyperplasia and hypertrophy of the smooth muscle cells and increased extracellular matrix components. The influence of the nervous system on the structure of the smooth muscle cells and its associated matrix has been poorly investigated. An experimental model of denervation of the ileum in rats was performed by application of the surfactant agent benzalkonium chloride that selectively destroys the myenteric plexus. Three months later, ileal tissue samples were obtained and studied by histochemistry and transmission electron microsocopy. Sham operated rats were used as controls. The diameter of collagen fibrils was evaluated in electron micrographs. The histopathological analysis showed thickening of the muscular layer. The thin and weakly arranged collagen and reticulin fibers surrounding the smooth muscle cells, observed in control cases by Picrosirius polarization (PSP) stain method, corresponded to a population of loosely packed thin collagen fibrils of uniform diameters (mean = 29.16 nm) at the ultrastructural level. In contrast, the thick and strongly birefringent fibers around the muscle cells, observed in the treated group, stained by PSP, corresponded to densely packed thicker fibrils with large variation in diameter (mean = 39.41 nm). Comparison of the data demonstrated statistically significant difference between the groups suggesting that the replacement of loosely arranged reticulin fibers by fibrous tissue (with typical collagen fiber), may alter the biomechanical function resulting in impairment of muscular contraction. (c) 2007 Elsevier Ltd. All rights reserved.

Implications of obesity for tendon structure, ultrastructure and biochemistry: A study on Zucker rats

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

Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities

BaP1 is a 22.7-kD P-I-type zinc-dependent metalloproteinase isolated from the venom of the snake Bothrops asper, a medically relevant species in Central America. This enzyme exerts multiple tissue-damaging activities, including hemorrhage, myonecrosis, dermonecrosis, blistering, and edema. BaP1 is a single chain of 202 amino acids that shows highest sequence identity with metalloproteinases isolated front the venoms of snakes of the subfamily Crotalinae. It has six Cys residues involved in three disulfide bridges (Cys 117-Cys 197, Cys 159-Cys 181, Cys 157-Cys 164). It has the consensus sequence H(142)E(143)XXH(146)XXGXXH(152), as well as the sequence C164I165M166, which characterize the metzincin superfamily of metalloproteinases. The active-site cleft separates a major subdomain (residues 1-152), comprising four a-helices and a five-stranded beta-sheet, from the minor subdomain, which is formed by a single a-helix and several loops. The catalytic zinc ion is coordinated by the N-epsilon2 nitrogen atoms of His 142, His 146, and His 152, in addition to a solvent water molecule, which in turn is bound to Glu 143. Several conserved residues contribute to the formation of the hydrophobic pocket, and Met 166 serves as a hydrophobic base for the active-site groups. Sequence and structural comparisons of hemorrhagic and nonhemorrhagic P-I metalloproteinases from snake venoms revealed differences in several regions. In particular, the loop comprising residues 153 to 176 has marked structural differences between metalloproteinases with very different hemorrhagic activities. Because this region lies in close proximity to the active-site microenvironment, it may influence the interaction of these enzymes with physiologically relevant substrates in the extracellular matrix.

Using genetic algorithm to design protein sequence

In this work, genetic algorithms concepts along with a rotamer library for proteins side chains are used to optimize the tertiary structure of the hydrophobic core of Cytochrome b(562) starting from the known PDB structure of its backbone which is kept fixed while the side chains of the hydrophobic core are allowed to adopt the conformations present in the rotamer library. The atoms of the side chains forming the core interact via van der Waals energy. Besides the prediction of the native core structure, it is also suggested a set of different amino acid sequences for this core. Comparison between these new cores and the native are made in terms of their volumes, van der Waals energies values and the numbers of contacts made by the side chains forming the cores. This paper proves that genetic algorithms area efficient to design new sequence for the protein core. (C) 2007 Elsevier B.V. All rights reserved.

Design and synthesis of peptides from bacterial ParE toxin as inhibitors of topoisomerases

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

Design of hierarchical porous aluminas by using one-pot synthesis and different calcination temperatures

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Structure and genetic relationships between Brazilian naturalized and exotic purebred goat domestic goat (Capra hircus) breeds based on microsatellites

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

STRUCTURE OF THE RETE TESTIS OF THE CAT (FELIS-DOMESTICA, L)

The rete testis of the cat consists of 3 parts: a septal or interlobular part; a mediastinal part and a tunical part. The septal part contains the septal or transitory tubuli recti and the tubuli recti. The transitory tubules are formed as a confluence of the seminiferous tubules at the apex of the testicular lobules and the tubuli recti. The mediastinal rete is formed of long, straight channels which increase in size and become more irregular and anastomotic below the tunica albuginea at the cranial extremity of the testis. The end is characterized as the tunical part of the rete testis and communicates with the extratesticular rete testis. The channels all parts of the rete are lined by simple cuboidal or columnar epithelium. These epithelial channels are supported by a connective tissue containing smooth muscle cells. The framework tissue of the rete is more conspicuous at the cranial extremity of the testis, with a mio-connective matrix organization.

Visible PL phenomenon at room temperature in disordered structure of SrWO4 powder

The SrWO4 (SWO) powders were synthesized by the polymeric precursor method and annealed at different temperatures. The SWO structure was obtained by X-ray diffraction and the corresponding photoluminescence (PL) spectra was measured. The PL results reveal that the structural order-disorder degree in the SWO lattice influences in the PL emission intensity. Only the structurally order-disordered samples present broad and intense PL band in the visible range. To understand the origin of this phenomenon, we performed quantum-mechanical calculations with crystalline and order-disordered SWO periodic models. Their electronic structures were analyzed in terms of band structure. The appearance of localized levels in the band gap of the order-disordered structure was evidenced and is a favorable condition for the intense PL to occur.

THE CRYSTAL-STRUCTURE OF BENZOYL-HISTIDINE MONOHYDRATE

The crystal structure of benzoyl-histidine monohydrate (BYLH hereafter), C-13H-12N-3O-3. H2O was determined from three dimensional data of 3012 independent reflections measured on a Enraf-Nonius (CAD4) single crystal diffractometer. The compound crystallizes in the orthorhombic space group P2(1)2(1)2(1) with cell dimensions alpha = 7.102(1) angstrom, b = 13.783(3) angstrom, c = 14.160(4) angstrom, V = 1385.92 angstrom-3, F.W. = 277.28, F(000) = 584 Q(calc) = 1.32 g cm-3 and Z = 4.The structure was solved with direct methods. All positional and anisotropic thermal parameters were refined by full-matrix least-squares calculations. The final reliability factor was R = 0.040, while the weighted one was Rw = 0.034. The H atoms found in the difference Fourier map were refined isotropically.The compound consists of a histidine molecule bound to a benzoyl group. There is also a cocrystallized water molecule stabilized through a hydrogen bridge.The 5-membered ring of the histidine has its tautomeric form, after the transfer of the H atom from the N(delta) to the N(epsilon) atom of the ring. There is an sp2 conformation around C6 while the conformation around C3 is that of sp3. The histidine ring forms with the benzene ring a dihedral angle of 109.8(1)-degree.All angle values and bond distances agree very well with the expected values in the literature.

REDUCTION OF TODA LATTICE HIERARCHY TO GENERALIZED KDV HIERARCHIES AND THE 2-MATRIX MODEL

Toda lattice hierarchy and the associated matrix formulation of the 2M-boson KP hierarchies provide a framework for the Drinfeld-Sokolov reduction scheme realized through Hamiltonian action within the second KP Poisson bracket. By working with free currents, which Abelianize the second KP Hamiltonian structure, we are able to obtain a unified formalism for the reduced SL(M + 1, M - k) KdV hierarchies interpolating between the ordinary KP and KdV hierarchies. The corresponding Lax operators are given as superdeterminants of graded SL(M + 1, M - k) matrices in the diagonal gauge and we describe their bracket structure and field content. In particular, we provide explicit free field representations of the associated W(M, M - k) Poisson bracket algebras generalising the familiar nonlinear W-M+1 algebra. Discrete Backlund transformations for SL(M + 1, M - k) KdV are generated naturally from lattice translations in the underlying Toda-like hierarchy. As an application we demonstrate the equivalence of the two-matrix string model to the SL(M + 1, 1) KdV hierarchy.