Using fold recognition to search for useful proteins: Bayesian approach to fold recognition

The wealth of protein sequence and structure data is greater than ever, thanks to the ongoing Genomics and Structural Genomics projects. The information available through such efforts needs to be analysed by new methods that combine both databases. One important result of genomic sequence analysis is the inference of functional homology among proteins. Until recently sequence similarity comparison was the only method for homologue inference. The new fold recognition approach reviewed in this paper enhances sequence comparison methods by including structural information in the process of protein comparison. This additional information often allows for the detection of similarities that cannot be found by methods that only use sequence information.     

Adenovirus protein involved in virus internalization recruits ubiquitin-protein ligases

Adenovirus penton base protein is involved in virus internalization. Searching for the cellular partners of this protein, we used dodecahedra, adenovirus subviral particles composed of 12 bases, for screening a human lung expression library. This screen yielded three ubiquitin-protein ligases, WWP1, WWP2, and AIP4, all of which belong to the HECT family and contain multiple WW domains. The xPPxY motif, known to interact with WW domains in partner proteins occurs twice in the N-terminal part of the base polypeptide chain. The recruitment of three ubiquitin-protein ligases was shown for two distinct virus serotypes, Ad2 and Ad3. The first N-terminal xPPxY motif in the base protein sequence is indispensable for the interaction. The association in vitro was shown by the protein overlay technique and in vivo by cotransfection followed by immunoprecipitation. The binding parameters studied by surface plasmon resonance confirmed the interaction of base protein with three ubiquitin-protein ligases. In case of WWP1 when the saturation of binding was achieved, the apparent dissociation constant of 65nM was calculated. This is the first demonstration of the interaction of nonenveloped viruses with ubiquitin-protein ligases of host cells.     

Gene transfer of baculoviral p35 by adenoviral vector protects human cerebral neurons from apoptosis

Apoptosis plays an important role in neuronal cell death in both chronic and acute human neurological diseases, including ALS, Huntington's disease, cerebral ischemia, and HIV encephalopathy. We evaluated the ability of an extremely powerful antiapoptotic agent, baculoviral p35, to prevent apoptosis and cell death of human cerebral neurons that undergo severe neurotoxic changes in a culture system when treated with agents that are implicated in human neurological disorders, that is, tumor necrosis factor (TNFalpha) and the HIV proteins Tat and gp120. P35 is a potent broad-spectrum antiapoptotic protein derived from baculovirus, that inhibits nearly all caspases, and has other antiapoptotic actions as well. Adenoviral vectors expressing p35 (Ad. p35) or a control gene (lacZ) efficiently transduced human neurons. Treatment of control cultures with the toxic agents TNFalpha, TNFalpha plus Actinomycin D, or Tat and gp120, induced neurotoxicity and death of neurons. Transduction of neurons with Ad. p35 blocked apoptosis, and eliminated cell death due to TNFalpha, or Tat and gp120. Viral vector transfer of the p35 gene efficiently protects human neurons from TNFalpha, or Tat and gp120-induced apoptosis and cell death. These results suggest that p35 transduction of neurons by viral vectors could be therapeutically useful in the treatment of human neurodegenerative diseases.     

Stereoselectivity in formation of oxacephams from 1,3-alkylidene-threitols

The [2+2]cycloaddition of CSI to the (Z)-propenyl ethers derived from respective 1,3-methylidene- and 1,3-ethylidene-threitols, contrary to the corresponding erythritol derivatives, is characterized by a low stereoselectivity and a lack of stereospecificity. On the other hand, the alternative method of the oxacepham formation, based on the 4-vinyloxy-azetidinone, proceeds with an excellent stereoselectivity. The CD-spectroscopy offers an attractive tool for determination of the absolute configuration of the bridgehead carbon atom at the 5-oxacepham skeleton.     

Inhibition by tributyltin of herring skeletal muscle lactate dehydrogenase activity

The activity of herring (Clupea harengus) skeletal muscle lactate dehydrogenase (EC 1.1.1.27) LDH-A4 isoenzyme was examined in the presence of tributyltin chloride (TBT). This paper reports the in vitro inhibition of LDH activity with increasing concentration of TBT. Bovine serum albumin (BSA) added to the LDH-A4 isoenzyme prior to the addition of TBT was able to protect enzyme activity against inhibition by this toxicant. The observed protection of LDH-A4 activity increased with increasing BSA concentration in the incubation medium. The results suggest that the presence of BSA could protect LDH activity from direct binding of TBT to LDH.     

Otubains: a new family of cysteine proteases in the ubiquitin pathway

The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes. Protein ubiquitylation is a dynamic and reversible process; attached Ub can be removed by deubiquitylating enzymes (DUBs), a heterogeneous group of cysteine proteases that cleave proteins precisely at the Ub–protein bond. Two families of DUBs have been identified previously. Here, we describe new, highly specific Ub iso-peptidases, that have no sequence homology to known DUBs, but which belong to the OTU (ovarian tumour) superfamily of proteins. Two novel proteins were isolated from HeLa cells by affinity purification using the DUB-specific inhibitor, Ub aldehyde (Ubal). We have named these proteins otubain 1 and otubain 2, for OTU-domain Ubal-binding protein. Functional analysis of otubains shows that the OTU domain contains an active cysteine protease site.     

Developing synthetic methods for bioactive phosphorus compounds using H-phosphonate chemistry: a progress report

In this paper a short account of our recent research concerning the development of new synthetic methods and reagents for the preparation of nucleotides and their analogues, is given.     

Analysis of <Emphasis Type="Italic">cry</Emphasis> Gene Profiles in <Emphasis Type="Italic">Bacillus Thuringiensis</Emphasis> Strains Isolated During Epizootics in <Emphasis Type="Italic">Cydia pomonella</Emphasis> L.

The crystal morphology and the profiles of genes encoding protein toxins (Cry and Cyt) were analyzed in 12 Bacillus thuringiensis strains isolated during epizootics in laboratory culture lines of Cydia pomonella, 2 isolates cultured from Leucoma salicis larvae, and 9 reference strains. Epizootic isolates produced crystals of the same bipyramidal shape; however, they revealed a variety of number and type of cry genes. Genes cry1I, cry2Ab, and cry9B were the most frequently observed in epizootic strains. Gene cry1I was noted in of 50% epizootic isolates. Eighty-three percent of them harbored gene cry2Ab. Gene cry9B was found for 42% of strains isolated during epizootics. Three isolates showed the largest number of cry genes and their variety; hence, they were chosen for the toxicity assay of their crystals and spores on C. pomonella larvae. One of them had approximately sixfold higher insecticidal activity than the reference strain B. thuringiensis subsp. kurstaki BTK STANDARD.     

Conjugal Transfer of Plasmid R6K γ <Emphasis Type="Italic">ori</Emphasis> Minireplicon Derivatives from <Emphasis Type="Italic">Escherichia coli</Emphasis> to Various Genera of Pathogenic Bacteria

Three R6K-derived γ ori minireplicons were successfully transferred by conjugation from Escherichia coli to several species of pathogenic bacteria. The pFL129 replicon encodes the wild-type initiation replication protein π, while plasmids pFL130 and pAG101 encode mutant forms of the π protein conferring the plasmid copy-up phenotype. Plasmids could be transferred to all recipient species tested, although high efficiency conjugal transfer was only obtained with genera of the Enterobacteriaceae. The efficiency of plasmid transfer to all recipients was lower for the copy-up derivatives, pFL130 and pAG101, than for pFL129. The three γ ori replicons were stably maintained in all transconjugants except pFL129 in Listeria monocytogenes. The two mutant plasmids retained their copy-up phenotype in the new bacterial hosts.