Docking and small angle X-ray scattering studies of purine nucleoside phosphorylase

Docking simulations have been used to assess protein complexes with some success. Small angle X-ray scattering (SAXS) is a well-established technique to investigate protein spatial configuration. This work describes the integration of geometric docking with SAXS to investigate the quaternary structure of recombinant human purine nucleoside phosphorylase (PNP). This enzyme catalyzes the reversible phosphorolysis of N-ribosidic bonds of purine nucleosides and deoxynucleosides. A genetic deficiency due to mutations in the gene encoding for PNP causes gradual decrease in T-cell immunity. Inappropriate activation of T-cells has been implicated in several clinically relevant human conditions such as transplant rejection, rheumatoid arthritis, lupus, and T-cell lymphomas. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. The present analysis confirms the trimeric structure observed in the crystal. The potential application of the present procedure to other systems is discussed. (C) 2003 Elsevier B.V. All rights reserved.

The X-ray crystallographic structure of the angiogenesis inhibitor angiostatin

Angiogenesis inhibitors have gained much public attention recently as anti-cancer agents and several are currently in clinical trials, including angiostatin (Phase I, Thomas Jefferson University Hospital, Philadelphia, PA). We report here the bowl-shaped structure of angiostatin kringles 1-3, the first multi-kringle structure to be determined. All three kringle lysine-binding sites contain a bound bicine molecule of crystallization while the former of kringle 2 and kringle 3 are cofacial. Moreover, the separation of the kringle 2 and kringle 3 lysiner binding sites is sufficient to accommodate the a-helix of the 30 residue pepticle VEK-30 found in the kringle 2/VEK-30 complex. Together the three kringles produce a central cavity suggestive of a unique domain where they may function in concert. (C) 2002 Elsevier B.V. Ltd. All rights reserved.

Crystallization and preliminary X-ray diffraction analysis of a Lys49-PLA(2) homologue from Cerrophidion godmani venom.

Lys49-phospholipase A(2) (Lys49-PLA(2)) homologues damage membranes by a Ca2+-independent mechanism which does not involve catalytic activity. The myotoxic Lys-49 phospholipase myotoxin II from Cerrophidion (Bothrops) godmani has been crystallized, and X-ray diffraction data were collected to 2.8 Angstrom resolution. Preliminary analysis reveals the presence of one molecule in the asymmetric unit.

Crystallization and preliminary X-ray crystallographic studies of Protac (R), a commercial protein C activator isolated from Agkistrodon contortrix contortrix venom

The protein C pathway plays an important role in the control and regulation of the blood coagulation cascade and prevents the propagation of the clotting process on the endothelium surface. In physiological systems, protein C activation is catalyzed by thrombin, which requires thrombomodulin as a cofactor. The protein C activator from Agkistrodon contortrix contortrix acts directly on the zymogen of protein C converting it into the active form, independently of thrombomodulin. Suitable crystals of the protein C activator from Agkistrodon contortrix contortrix were obtained from a solution containing 2 M ammonium sulfate as the precipitant and these crystals diffracted to 1.95 angstrom resolution at a synchrotron beamline. The crystalline array belongs to the monoclinic space group C2 with unit cell dimensions a=80.4, b = 63.3 and c = 48.2 angstrom, alpha = gamma = 90.0 degrees and beta = 90.8 degrees. (C) 2005 Elsevier B.V. All rights reserved.

Crystallization and preliminary X-ray diffraction analysis of the catalytic subunit of ADP-glucose pyrophosphorylase from potato tuber

ADP-glucose pyrophosphorylase is the key regulatory enzyme in the biosynthesis of starch in plants and glycogen in bacteria. The enzyme from potato tuber is comprised of a regulatory subunit and a catalytic subunit and is present as a heterotetramer (alpha(2)beta(2)) the catalytic subunit from potato tuber (50 kDa) was crystallized in four different forms, two of which are suitable for structural studies. A tetragonal crystal form obtained in the presence of the substrate analog Cr-ATP diffracted to 2.2 Angstrom and belongs to space group P4(1) (or its enantiomorph), with unit-cell parameters a = b = 110.57, c = 190.14 Angstrom. A second crystal form obtained diffracted to 2.8 Angstrom and belongs to space group PZ, with unit-eel parameters a = 80.06, b = 138.84, c = 92.20 Angstrom, beta = 112.40 degrees. As this protein displays no significant homology to any currently known protein structure, a search for heavy-atom derivatives has been initiated.

Crystallization and preliminary X-ray crystallographic analysis of the heterodimeric crotoxin complex and the isolated subunits crotapotin and phospholipase A(2)

Crotoxin, a potent neurotoxin from the venom of the South American rattlesnake Crotalus durissus terrificus, exists as a heterodimer formed between a phospholipase A(2) and a catalytically inactive acidic phospholipase A(2) analogue (crotapotin). Large single crystals of the crotoxin complex and of the isolated subunits have been obtained. The crotoxin complex crystal belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 38.2, b = 68.7, c = 84.2 angstrom, and diffracted to 1.75 angstrom resolution. The crystal of the phospholipase A(2) domain belongs to the hexagonal space group P6(1)22 (or its enantiomorph P6(5)22), with unit-cell parameters a = b = 38.7, c = 286.7 angstrom, and diffracted to 2.6 angstrom resolution. The crotapotin crystal diffracted to 2.3 angstrom resolution; however, the highly diffuse diffraction pattern did not permit unambiguous assignment of the unit-cell parameters.

Crystallization and preliminary X-ray diffraction analysis of a class II phospholipase D from Loxosceles intermedia venom

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

Production, purification, crystallization and preliminary X-ray diffraction studies of the nucleoside diphosphate kinase b from Leishmania major

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

Crystallization and preliminary X-ray diffraction analysis of an l-amino-acid oxidase from Bothrops jararacussu venom

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

Purification, crystallization and preliminary X-ray diffraction analysis of crotamine, a myotoxic polypeptide from the Brazilian snake Crotalus durissus terrificus

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

Crystallization, preliminary X-ray diffraction analysis and Patterson search of oxyhaemoglobin I from the wolf (Chrysocyon brachiurus)

Oxyhaemoglobin I isolated from the Brazilian wolf Chrysocyon brachiurus has been crystallized and X-ray diffraction data has been collected to 2.06 A resolution using a synchrotron-radiation source. Crystals were determined to belong to the space group P2(1)2(1)2(1) and preliminary structural analysis revealed the presence of one tetramer in the asymmetric unit. The structure was determined using standard molecular-replacement techniques and is currently being refined using maximum-likelihood protocols. This is the first haemoglobin isolated from a member of the Canidae family to be crystallized and it will provide further insights in the comparative biochemistry of vertebrate haemoglobins.

Microbiological or Chemical Models of Enamel Secondary Caries Compared by Polarized-Light Microscopy and Energy Dispersive X-ray Spectroscopy

Different secondary caries models may present different results. The purpose of this study was to compare different in vitro secondary caries models, evaluating the obtained results by polarized-light microscopy (PLM), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (EDS). Standardized human enamel specimens (n = 12) restored with different materials (Z250 conventional composite resin-CRZ, Freedom polyacid-modified composite resin-CRF, Vitremer resin-modified glass-ionomer-GIV, and Fuji IX conventional glass-ionomer cement-GIF) were submitted to microbiological (MM) or chemical caries models (CM). The control group was not submitted to any caries model. For MM, specimens were immersed firstly in sucrose broth inoculated with Streptococcus mutans ATCC 35688, incubated at 37 degrees C/5% CO(2) for 14 days and then in remineralizing solution for 14 days. For CM, specimens were submitted to chemical pH-cycling. Specimens were ground, submitted to PLM and then were dehydrated, gold-sputtered and submitted to SEM and EDS. Results were statistically analyzed by Kruskall-Wallis and Student-Newman-Keuls tests (alpha = 0.05). No differences between in vitro caries models were found. Morphological differences in enamel demineralization were found between composite resin and polyacid-modified composite resin (CRZ and CRF) and between the resin-modified glass-ionomer and the glass-ionomer cement (GIF and GIV). GIF showed higher calcium concentration and less demineralization, differing from the other materials. In conclusion, the glass-ionomer cement showed less caries formation under both in vitro caries models evaluated. (C) 2009 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 90B: 635-640, 2009

Analysis of Tooth Enamel After Excessive Bleaching: A Study Using Scanning Electron Microscopy and Energy Dispersive X-ray Spectroscopy

This study assessed alterations on bovine enamel after excessive bleaching. Coronal portions of bovine teeth (n = 30) were sectioned and divided into three groups (n = 10 per group). The coronal parts were further cut incisocervically into two halves. While one half received no bleaching (control), the other half was subjected to either one (group 1), three (group 2), or five bleaching sessions (group 3) with 35% hydrogen peroxide. The enamel surfaces were then analyzed using scanning electron microscopy and energy dispersive x-ray spectroscopy (EDS). Fxcessive bleaching affected the surface morphology and chemistry of the bovine enamel. EDS analysis showed the highest decrease in calcium ion percentages in groups 2 and 3 when compared to their nonbleached halves. Oxygen and phosphorus percentages were comparable on both the control and bleached enamel, regardless of the number of bleaching sessions. Consecutive bleaching sessions with 35% hydrogen peroxide may lead to morphologic and specific elemental changes when performed in a short period of time. Calcium ion percentages may decrease when this bleaching agent is used for more than one session. Int J Prosthodontics 2010;23:29-32.