The Intriguing Phospholipases A(2) Homologues: Relevant Structural Features on Myotoxicity and Catalytic Inactivity

Phospholipases A(2) homologues are found in the venom of Crotalinae snakes, being their main action related to myonecrosis induction. Although many studies on these toxins had already been performed, their mechanism of action remains unclear. Here, important aspects about these toxins are reviewed, including their correct biological assembly and how essential is the natural substitution D49K for their catalytic inactivity.

Probing the Specificity of Binding to the Major Nuclear Localization Sequence-binding Site of Importin-alpha Using Oriented Peptide Library Screening

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

Host specificity of sheep and cattle nematodes in São Paulo state, Brazil

The trial was carried out to investigate parasite host specificity and to analyse the dynamics of infection with nematodes parasitizing sheep and catt:le raised together or separately in São Paulo state, Brazil, and, also to clarify doubts about the systematics of species of the genus Haemonchus on the basis of cytological and morphological studies. Ten steers and 32 ewes were randomly assigned to three paddocks (P), as follows: P1, 5 steers; P2, 5 steers and 16 ewes; and P3, 16 ewes. The animals remained on these paddocks in continuous grazing throughout the trial (1-yr period). Faecal exams and larvae counting on pasture were performed fortnightly. Once a month two tracer lambs were placed in each paddock, while two tracer calves were also placed, but only in the eighth month of the trial. All these animals were slaughtered for worm identification and counting. At the end of the trial, one steer and one ewe from P2, which showed high faecal egg counts, were also slaughtered for the same purpose. Nematodes identified cytogenetically as H. placei presented spicule hooks longer than those identified as H. contortus. The following distribution of parasites in cattle and sheep was observed: Bunostomum phlebotomum, H. similis, Mammomonogamus laryngeus strongly adapted to cattle, H. placei and Cooperia punctata more adapted to cattle than to sheep, Trichostrongylus axel and C. spatulata apparently more adapted to cattle, T. colubriformis strongly adapted to sheep, H. contortus more adapted to sheep than to cattle and C. curticei apparently more adapted to sheep. Cross-infection was shown to occur involving some species, however, with time the animals apparently eliminate the species that are not well adapted to them. Therefore, grazing management systems using cattle and sheep appear to be promising for worm control in southeastern Brazil. (C) 1997 Elsevier B.V. B.V.

V(2)O(5)/TiO(2) catalytic xerogels raman and EPR studies

Raman spectroscopy and Electron Paramagnetic Resonance (EPR) studies were performed on a series of V(2)O(5)/TiO(2) catalysts prepared by a modified sol-gel method in order to identify the vanadium species. Two species of surface vanadium were identified by Raman measurements, monomeric vanadyls and polymeric vanadates. Monomeric vanadyls are characterized by a narrow Raman band at 1030 cm(-1) and polymeric vanadates by two broad bands in the region from 900 to 960 cm(-1) and 770 to 850 cm(-1). The Raman spectra do not exhibit characteristic peaks of crystalline V(2)O(5). These results are in agreement with those of X-ray Diffractometry (XRD) and Fourier Transform Infrared (FT-IR) previously reported (C.B. Rodella et al., J. Sol-Gel Sci. Techn., submitted). At least three families of V(4+) ions were identified by EPR investigations. The analysis of the EPR spectra suggests that isolated V(4+) ions are located in sites with octahedral symmetry substituting for Ti(4+) ions in the rutile structure. Magnetically interacting V(4+) ions are also present as pairs or clusters giving rise to a broad and structureless EPR line. At higher concentration of V(2)O(5), a partial oxidation of V(4+) to V(5+) is apparent from the EPR results.

Surface characterisation of V(2)O(5)/TiO(2) catalytic system

Samples of the V(2)O(5)/TiO(2) system were prepared by the sol-gel method and calcined at different temperatures. Surface species of vanadium, their dispersion, as well as the structural evolution of the system were analysed by XRD, Raman, EPR, and XPS techniques. The results of XRD showed the evolution of TiO(2) from anatase phase to rutile. phase. The Raman spectra for calcination temperatures up to 500 degreesC showed a good dispersion of vanadium over titania in the form of monomeric vanadyl groups (V(4+)) and polymeric vanadates (V(5+)). At least three families of V4+ ions were identified by EPR investigations. Two kinds of isolated V(4+) species are placed in sites of octahedral symmetry, substituting Ti(4+) in the rutile phase. The third is formed by pairs of V(4+) species on the surface of titania. Above 500 degreesC part of superficial V(4+) is inserted into the,matrix of titania and part is oxidized to V(5+). The XPS results showed that the V/Ti ratio rises with increasing calcination temperature, indicating a smaller dispersion of vanadium.

New catalytic mechanism for human purine nucleoside phosphorylase

Human purine nucleoside phosphorylase has been submitted to intensive structure-based design of inhibitors, most of them using low-resolution structures of human PNP. Recently, several structures of human PNP have been reported, which allowed redefinition of the active site and understanding of the structural basis for inhibition of PNP by acyclovir and immucillin-H. Based on previously solved human PNP structures, we proposed here a new catalytic mechanism for human PNP, which is supported by crystallographic studies and explains previously determined kinetic data. (C) 2004 Elsevier B.V. All rights reserved.

Determining the structural basis for specificity of ligands using crystallographic screening

Crystallographic screening has been used to identify new inhibitors for potential target for drug development. Here, we describe the application of the crystallographic screening to assess the structural basis of specificity of ligands against a protein target. The method is efficient and results in detailed crystallographic information. The utility of the method is demonstrated in the study of the structural basis for specificity of ligands for human purine nucleoside phosphorylase (PNP). Purine nucleoside phosphorylase catalyzes the phosphorolysis of the N-ribosidic bonds of purine nucleosides and deoxynucleosides. This enzyme is a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. This methodology may help in the future development of a new generation of PNP inhibitors.

Development of an operational substrate for ZapA, a metalloprotease secreted by the bacterium Proteus mirabilis

The protease ZapA, secreted by Proteus mirabilis, has been considered to be a virulence factor of this opportunistic bacterium. The control of its expression requires the use of an appropriate methodology, which until now has not been developed. The present study focused on the replacement of azocasein with fluorogenic substrates, and on the definition of enzyme specificity. Eight fluorogenic substrates were tested, and the peptide Abz-Ala-Phe-Arg-Ser-Ala-Ala-Gln-EDDnp was found to be the most convenient for use as an operational substrate for ZapA. A single peptide bond (Arg-Ser) was cleaved with a Km of 4.6 µM, a k cat of 1.73 s-1, and a catalytic efficiency of 376 (mM s)-1. Another good substrate for ZapA was peptide 6 (Abz-Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg-Gln-EDDnp) which was cleaved at a single bond (Phe-Ser) with a Km of 13.6 µM, a k cat of 3.96 s-1 and a catalytic efficiency of 291 (mM s)-1. The properties of the amino acids flanking the scissile bonds were also evaluated, and no clear requirement for the amino acid residue at P1 was found, although the enzyme seems to have a preference for a hydrophobic residue at P2.

Purification and physicochemical properties of a ribonuclease produced by Aspergillus flavipes (IZ : 1501)

A RNase of Aspergillus flavipes (IZ:1501) was purified from culture medium by chromatography on DEAE-cellulose and Sephadex G50 columns, after 96 h of cultivation. The molecular weight of the RNase was estimated to be 15 kD by gel filtration using Sephadex G100, and the optimum pH and temperature were 4.0 and 55 degrees C, respectively. Catalytic activity was inhibited by Hg2+, Ag+, Fe3+, Co2+ and Zn2+. The enzyme showed guanosine specificity producing only 3'-GMP from yeast RNA.

Synergistic effect in the catalytic activity of lipase Rhizomucor miehei immobilized on zeolites for the production of biodiesel

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

Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1)

The 1.7 angstrom resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved P-sheets form the active-site and substrate-binding cleft. The onset of thermal denaturation of rXynA occurs at 328 K, in excellent agreement with the optimum catalytic temperature. Molecular dynamics simulations at temperatures of 298-328 K demonstrate that below the optimum temperature the thumb loop and palm domain adopt a closed conformation. However, at 328 K these two domains separate facilitating substrate access to the active-site pocket, thereby accounting for the optimum catalytic temperature of the rXynA. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Structural insights into the catalytic mechanism of sphingomyelinases D and evolutionary relationship to glycerophosphodiester phosphodiesterases

Spider venom sphingomyelinases D catalyze the hydrolysis of sphingomyelin via an Mg2+ ion-dependent acid-base catalytic mechanism which involves two histidines. In the crystal structure of the sulfate free enzyme determined at 1.85 angstrom resolution, the metal ion is tetrahedrally coordinated instead of the trigonal-bipyramidal coordination observed in the sulfate bound form. The observed hyperpolarized state of His47 requires a revision of the previously suggested catalytic mechanism. Molecular modeling indicates that the fundamental structural features important for catalysis are fully conserved in both classes of SMases D and that the Class II SMases D contain an additional intra-chain disulphide bridge (Cys53-Cys201). Structural analysis suggests that the highly homologous enzyme from Loxosceles bonetti is unable to hydrolyze sphingomyelin due to the 95G1y -> Asn and 134Pro -> Glu mutations that modify the local charge and hydrophobicity of the interfacial face. Structural and sequence comparisons confirm the evolutionary relationship between sphingomyelinases D and the glicerophosphodiester phosphoesterases which utilize a similar catalytic mechanism. (c) 2006 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.

Structural basis for metal ion coordination and the catalytic mechanism of sphingomyelinases D

Sphingomyelinases D (SMases D) from Loxosceles spider venom are the principal toxins responsible for the manifestation of dermonecrosis, intravascular hemolysis, and acute renal failure, which can result in death. These enzymes catalyze the hydrolysis of sphingomyelin, resulting in the formation of ceramide 1-phosphate and choline or the hydrolysis of lysophosphatidyl choline, generating the lipid mediator lysophosphatidic acid. This report represents the first crystal structure of a member of the sphingomyelinase D family from Loxosceles laeta (SMase I), which has been determined at 1.75-angstrom resolution using the quick cryo-soaking technique and phases obtained from a single iodine derivative and data collected from a conventional rotating anode x-ray source. SMase I folds as an (alpha/beta)(8) barrel, the interfacial and catalytic sites encompass hydrophobic loops and a negatively charged surface. Substrate binding and/or the transition state are stabilized by a Mg2+ ion, which is coordinated by Glu(32), Asp(34), Asp(91), and solvent molecules. In the proposed acid base catalytic mechanism, His(12) and His(47) play key roles and are supported by a network of hydrogen bonds between Asp(34), Asp(52), Trp(230), Asp(233), and Asn(252).