A proteomic approach to the identification of cytochrome P450 isoforms in male and female rat liver by nanoscale liquid chromatography-electrospray ionization-tandem mass spectrometry.

Nanoscale reversed-phase liquid chromatography (LC) combined with electrospray ionization-tandem mass spectrometry (ESI-MS/MS) has been used as a method for the direct identification of multiple cytochrome P450 (P450) isoforms found in male and female rat liver. In this targeted proteomic approach, rat liver microsomes were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by in-gel tryptic digestion of the proteins present in the 48- to 62-kDa bands. The resultant peptides were extracted and analyzed by LC-ESI-MS/MS. P450 identifications were made by searching the MS/MS data against a rat protein database containing 21,576 entries including 47 P450s using Sequest software (Thermo Electron, Hemel Hempstead, UK). Twenty-four P450 isoforms from the subfamilies 1A, 2A, 2B, 2C, 2D, 2E, 3A, 4A, 4F, CYP17, and CYP19 were positively identified in rat liver.

Cloning of dog heart PDE1A - a first detailed characterization at the molecular level in this species.

The dog, as a model for cardiovascular function, has been widely used in the pharmacological analysis of PDE inhibitors, particularly those thought to target the heart. However biochemical analyses of dog heart PDE have been largely performed on mixed enzyme populations, sequence information is lacking and no PDE from dog heart has been cloned. We have characterized a completely purified PDE1 enzyme from dog heart using dye-affinity, Mono-Q and calmodulin-affinity chromatography. The enzyme was stimulated 3-4-fold by calmodulin ([S]=0.5 microM) and, in the absence of calmodulin, exhibited biphasic kinetics with a low K(m) of 1.2 microM and 0.53 microM for cAMP and cGMP, with respective V(max) values of 283 and 146 nmoles min(-1) mg(-1). Internal peptides from this enzyme were used to design degenerate PCR primers. Subsequent 3'-RACE, 5'-RACE and high fidelity PCR were then used to produce a full length gene identified as PDE1A1 by sequence identity to human and bovine sequences. Northern analysis using the dog heart cDNA as a probe suggested the presence of an additional form of PDE1, in heart only, separate from the PDE1A group which was present in both heart and skeletal muscle. Multiple forms of human PDE1A are known to exist and PDE1B is present in human heart muscle. The findings here extend the PDE1 data to the dog and contribute to our understanding of the molecular biology of PDE1A in this species.

DNA transfection and transfected cell viability using amphipathic asymmetric dendrimers.

Amphipathic asymmetric dendrimers have been investigated for use in delivery of genes into cells, with the objective of optimising transfection efficiency and maintaining cell viability. We have synthesised amphipathic asymmetric dendrimers by solid phase methods. The ability of two of these to transfect BHK cells in culture with beta-galactosidase gene was determined by X-gal staining. Cell viability was measured by the MTT assay for BHK cells, and by spectroscopy for lysis of erythrocytes. Interactions between dendrimer and DNA were investigated by agarose gel electrophoresis. BHK cells were optimally transfected at 5:1 +/- charge ratio yielding 20% cells receiving at least one copy of the plasmid. Cell viability decreased when the dendrimer to DNA ratio exceeded 5:1. Raising the pH significantly affected the electrophoretic mobility of complexes of dendrimer and DNA. We conclude that amphipathic asymmetric dendrimers enable efficient plasmid DNA uptake into BHK cells. Cell viability is maintained at high concentrations of dendrimer when complexed with DNA at a 5:1 +/- charge ratio. Efficiency of transfection and cell viability suggest the system may be suitable for gene delivery in vivo.

Alternative native flap conformation revealed by 2.3 A resolution structure of SIV proteinase.

A large conformational change is observed between HIV-1 proteinase in the ligand-free state and in complexes with transition-state inhibitors. Crystal structures of this enzyme have either the flaps open for the native or ligand-free enzyme or the flaps closed for peptidomimetic ligand-bound enzyme. We describe the structure of native recombinant SIV proteinase which like other retroviral proteinases crystallizes as a perfect 2-fold symmetric dimer but in a different crystal packing arrangement. In contrast to HIV-1 PR we show that SIV proteinase in the ligand-free state adopts the closed flaps conformation, demonstrating that ligand binding is not a prerequisite for the closed flaps conformation. The catalytic water was clearly observed between the two aspartates which were not perfectly co-planar, and in this structure the active site cleft is more restricted than for either inhibitor bound or ligand-free HIV-1 proteinase. Accommodation of two bulkier side-chains in the simian enzyme core has resulted in a more exposed N terminus than for HIV-1 PR which we predict could enhance autocatalytic cleavage at the N terminus.

Purification of crystallizable recombinant SIVmac251-32H proteinase.

We have cloned a simian immunodeficiency virus (SIV) proteinase gene directly from proviral DNA of the infectious viral stock SIVmac251-32H (11/88 pool). The deduced amino acid sequence from this proteinase gene is similar to that for the published SIVmac239 molecular clone. SIVmac251-32H proteinase (SIV PR) and its flanking pol sequences were expressed in Escherichia coli as a fusion protein with most of the T7 bacteriophage gene 10 protein. The expressed protein formed cytoplasmic inclusion bodies which were solubilized in 8 M urea, and the recombinant SIV PR was refolded, yielding active, self-processed enzyme. The SIV PR was purified to homogeneity using a single pepstatin A affinity chromatography step, and had a specific peptidolytic activity of 20 mumol/min/mg. Enzymatic characteristics similar to those previously documented for other immunodeficiency virus proteinases (EC 3.4.23) were observed. These include an acidic pH optimum (pH 5.3), sensitivity to sodium chloride concentration, and complete inhibition by pepstatin A. In addition to these properties we have observed quantitative crystallization from low protein concentrations. We describe the first crystal habit for the proteinase from the HIV-2/SIV class of immunodeficiency virus, which is distinctly different from that for HIV-1 proteinase crystals.

Crystallization and preliminary X-ray investigation of recombinant simian immunodeficiency virus proteinase.

Simian immunodeficiency virus (SIV) proteinase has been crystallized from sodium acetate buffer with sodium chloride as precipitant. The crystals are orthorhombic and the space group is C222(1) with unit cell dimensions a = 32.18 A, b = 62.52 A, c = 95.76 A, alpha = beta = gamma = 90 degrees, indicating a single monomer of 10 kDa in the asymmetric unit. The crystals grow to dimensions of 0.2 mm x 0.2 mm x 0.07 mm within a week and are stable in the X-ray beam for at least 50 hours. A different crystal lattice was observed for SIV proteinase crystallized in the presence of pepstatin. The space group was P2(1)2(1)2(1) with cell dimensions of a = 35.26 A, b = 58.59 A, c = 93.95 A, alpha = beta = gamma = 90 degrees. Diffraction beyond 1.7 A was observed, indicating that a high resolution structure analysis is feasible.

A pyruvate-stimulated adenylate cyclase has a sequence related to the fes/fps oncogenes and to eukaryotic cyclases.

The pyruvate-stimulated adenylate cyclase from Brevibacterium liquefaciens produces up to 450 microM cyclic AMP in the culture medium when the bacterium is grown on glucose and alanine. In this paper we report the cloning, expression and sequencing of the gene for this enzyme. Residues were identified, within the C-terminal domain, which are conserved in adenylate and guanylate cyclase sequences from eukaryotes and in the adenylate cyclase of the prokaryote Rhizobium meliloti. We have also identified a sequence of 30 residues near the N-terminus of the protein which is homologous to part of the regulatory domain of the cellular homologues of the oncogenes fes and fps; this sequence is also present in the avian Fujinami sarcoma virus fps gene.

The 3-D structure of HIV-1 proteinase and the design of antiviral agents for the treatment of AIDS.

A proteinase is essential for replication of HIV. Cloning and chemical synthesis have provided a sufficient supply of HIV-1 proteinase for the determination of its three-dimensional structure. Analogies between the structures of HIV-1 proteinase and the mammalian enzyme renin, which is involved in the control of blood pressure, have given important clues concerning the design of specific inhibitors that have antiviral activity.

Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase does not conform to the 'hotspot' topogenic signal model.

The genes which encode glycosomal glyceraldehyde-phosphate dehydrogenase (gGAPDH) of Trypanosoma cruzi are arranged as a tandemly repeated pair on a single chromosome and are identical at the level of nucleotide sequence. They are separated by an intergenic region which contains a 317 base pair sequence with the properties of a retroposon. The genes express a 1.5 kb mRNA and a 38 kd protein. The amino acid sequence contains features characteristic of glycosomal enzymes such as peptide insertions and a C-terminal extension. However, T. cruzi gGAPDH lacks one of the positively charged 'hotspot' motifs which have been proposed as topogenic signals for import into the glycosome, a unique microbody-like organelle. Molecular modelling of the T. cruzi and T. brucei enzymes suggests that neither structure would fulfil the requirements of the 'hotspot' glycosomal import model.

The reaction of fluorescein isothiocyanate with thiols: a method for assay of isothiocyanates.

The reversible formation of dithiourethanes from fluorescein isothiocyanate and mercaptoethanol or mercaptoethylamine has been studied. It is shown that it is possible to use the reaction as the basis for a spectrophotometric titration of a number of isothiocyanates with mercaptoethanol.

Identification of a labelled peptide after stoicheiometric reaction of fluorescein isothiocyanate with the Ca2+ -dependent adenosine triphosphatase of sarcoplasmic reticulum.

Incorporation of 4.5 nmol fluorescein isothiocyanate/mg rabbit sarcoplasmic reticulum, or of 7.4 nmol/mg purified ATPase, was sufficient to inhibit the activity completely. These results are not consistent with the suggestion (Pick, U. and Karlish, S.J.D. (1980) Biochim. Biophys. Acta 626, 255-261) that 2 mol ATPase were inhibited by each mole of reagent incorporated. A single labelled peptide was purified from the inhibited ATPase and it was shown that Lys 3/190, 10 residues from the N-terminus of tryptic fragment B, was the reactive lysine residue. This site is close to a potential nucleotide-binding fold in the ATPase sequence. A similar peptide showing only 2 conservative replacements was isolated from the sarcoplasmic reticulum of the lobster.