An alternative mechanism for amidase signature enzymes

The peptide amidase from Stenotrophomonas maltophilia catalyses predominantly the hydrolysis of the C-terminal amide bond in peptide amides. Peptide bonds or amide functions in amino acid side-chains are not hydrolysed. This specificity makes peptide amidase (Pam) interesting for different biotechnological applications. Pam belongs to the amidase signature (AS) family. It is the first protein within this family whose tertiary structure has been solved. The structure of the native Pam has been determined with a resolution of 1.4A and in complex with the competitive inhibitor chymostatin at a resolution of 1.8A. Chymostatin, which forms acyl adducts with many serine proteases, binds non-covalently to this enzyme.Pam folds as a very compact single-domain protein. The AS sequence represents a core domain that is covered by alpha-helices. This AS domain contains the catalytic residues. It is topologically homologous to the phosphoinositol phosphatase domain.The structural data do not support the recently proposed Ser-Lys catalytic dyad mechanism for AS enzymes. Our results are in agreement with the role of Ser226 as the primary nucleophile but differ concerning the roles of Ser202 and Lys123: Ser202, with direct contact both to the substrate molecule and to Ser226, presumably serves as an acid/bases catalyst. Lys123, with direct contact to Ser202 but no contact to Ser226 or the substrate molecule, most likely acts as an acid catalyst.     

Refinement of Pig Retroperfusion Technique: Global Retroperfusion with Ligation of the Azygos Connection Preserves Hemodynamic Function in an Acute Infarction Model in Pigs (Sus scrofa domestica)

In ischemic hearts, venous retroperfusion is a potential myocardial revascularization strategy. This study aimed to refine the technical and functional aspects of a pig model of acute myocardial infarction and retroperfusion with respect to the azygos connection. Global retroperfusion after ligation of the ramus interventricularis paraconalis (equivalent to the left anterior descending artery in humans) was performed in 16 Landrace pigs (Sus scrofa domestica). Coronary sinus perfusion was performed in 8 pigs (P+) but not in the other 8 (P–), and the azygos vein was ligated (L+) 4 of the 8 pigs in each of these groups but left open (L–) in the remaining animals. Hemodynamic performance (for example, cardiac output, stroke volume) was significantly better in P+L+ pigs that underwent coronary sinus perfusion with ligation of the azygos vein compared with all other animals. In addition, troponin I release was significant lower in P+L+ pigs (1.7 ± 1.3 ng/mL) than in P–L– (5.47 ± 2.1 ng/mL), P–L+ (6.63 ± 2.4 ng/mL), and P+L– (4.81 ± 2.3 ng/mL) pigs. Effective retrograde flow and thus hemodynamic stability was achieved by ligation of the azygos vein. Therefore, experiments focusing on global retroperfusion will benefit from effective inhibition of the blood flow through the azygos vein.Abbreviations: ACS, aorta-to-coronary–sinus shunt, CS, coronary sinus, L, ligation, LAD, left anterior descending artery, P, perfusionAnimal models are used frequently to investigate myocardial revascularization techniques, and researchers have studied global or selective venous retroperfusion in dogs,²² pigs,⁹ and sheep.³³ The goal underlying retrograde coronary sinus (CS) perfusion is perfusion of the ischemic myocardium proximal to the occlusion or stenosis. This method frequently is used for delivering cardioplegic solutions during cardiac surgery. In addition, both clinical^{2,3,6,16,28,30} and experimental ^{11,21,25,34,37,42} studies have validated the efficiency of CS retroperfusion.Interpreting the results from experimental animal models and follow-up examinations of patients who have undergone venous revascularization has led to controversy.^9,37 In particular, technical problems with some studies have been identified. Previous animal studies on interspecies anatomic differences in mammals^4,7,19 have concentrated on the venous connections of the vessels draining the myocardium and have demonstrated a need for further feasibility studies of the pig model (German Landrace pigs, Sus scrofa domestica) that focus on hemodynamic performance.We wanted to characterize in detail the contribution of the azygos vein connection in swine during retroperfusion after myocardial infarction and hypothesized that ligation of the azygos vein would preserve hemodynamic function after ligation of the left anterior descending artery (LAD) in a global retroperfusion model in pigs.     

Bornyl (3,4,5-trihydroxy)-cinnamate--an optimized human neutrophil elastase inhibitor designed by free energy calculations

Human neutrophil elastase (HNE), a serine protease, is involved in the regulation of inflammatory processes and controlled by endogenous proteinase inhibitors. Abnormally high levels of HNE can cause degradation of healthy tissues contributing to inflammatory diseases such as rheumatoid arthritis, and also psoriasis and delayed wound healing. In continuation of our research on HNE inhibitors we have used the recently developed binding mode model for a group of cinnamic acid derivative elastase inhibitors and created bornyl (3,4,5-trihydroxy)-cinnamate. This ligand exhibited improved binding affinity predicted by means of free energy calculations. An organic synthesis scheme for the ligand was developed and its inhibitory activity was tested toward the isolated enzyme. Its IC(50) value was found to be three times lower than that of similar compounds, which is in line with the computational result showing the high potential of free energy calculations as a tool in drug development.     

Structure of the puf operon of the obligately aerobic, bacteriochlorophyll alpha-containing bacterium Roseobacter denitrificans OCh114 and its expression in a Rhodobacter capsulatus puf puc deletion mutant.

Roseobacter denitrificans (Erythrobacter species strain OCh114) synthesizes bacteriochlorophyll a (BChl) and the photosynthetic apparatus only in the presence of oxygen and is unable to carry out primary photosynthetic reactions and to grow photosynthetically under anoxic conditions. The puf operon of R. denitrificans has the same five genes in the same order as in many photosynthetic bacteria, i.e., pufBALMC. PufC, the tetraheme subunit of the reaction center (RC), consists of 352 amino acids (Mr, 39,043); 20 and 34% of the total amino acids are identical to those of PufC of Chloroflexus aurantiacus and Rubrivivax gelatinosus, respectively. The N-terminal hydrophobic domain is probably responsible for anchoring the subunit in the membrane. Four heme-binding domains are homologous to those of PufC in several purple bacteria. Sequences similar to pufQ and pufX of Rhodobacter capsulatus were not detected on the chromosome of R. denitrificans. The puf operon of R. denitrificans was expressed in trans in Escherichia coli, and all gene products were synthesized. The Roseobacter puf operon was also expressed in R. capsulatus CK11, a puf puc double-deletion mutant. For the first time, an RC/light-harvesting complex I core complex was heterologously synthesized. The strongest expression of the R. denitrificans puf operon was observed under the control of the R. capsulatus puf promoter, in the presence of pufQ and pufX and in the absence of pufC. Charge recombination between the primary donor P+ and the primary ubiquinone Q(A)- was observed in the transconjugant, showing that the M and L subunits of the RC were correctly assembled. The transconjugants did not grow photosynthetically under anoxic conditions.     

Sequence analysis reveals new membrane anchor of reaction centre-bound cytochromes possibly related to PufX

Most of the bacterial photosynthetic reaction centres known to date contain a cytochrome subunit with four covalently bound haem groups. In the case of Blastochloris viridis, this reaction centre subunit is anchored in the membrane by a lipid molecule covalently attached to the cysteine which forms the N-terminus of the mature protein after processing by a signal peptidase. We show that posttranslational N-terminal cleavage of the cytochrome subunit does not occur in the aerobic photosynthetic bacterium Roseobacter denitrificans. From sequence analysis of the resulting elongated N-terminus it follows that a transmembrane helix is anchoring the reaction centre-bound cytochrome in the membrane. Comparative sequence analysis strongly suggests that all cytochrome subunits lacking the lipid coupling cysteine share this structural feature. Comparison of the N-terminal segment of the cytochrome subunit of Roseobacter denitrificans with the sequences of the PufX proteins from Rhodobacter sphaeroides and Rhodobacter capsulatus suggests a phylogenetic relation.     

Geomicrobiological Changes in Two Ephemeral Desert Playa Lakes in the Western United States

The geochemistry and microbiology of two ephemeral playa lakes in the Western United States, Surprise Valley Alkali Lake (SVAL) and Eldorado Playa (EP), were examined over one wetting cycle, revealing dramatic temporal changes in suspended mineralogy, aqueous chemistry, and bacterial populations. In SVAL the predominant suspended mineral changed from smectite to vermiculite and clinoptilolite, which led to a depletion of soluble Mg²⁺. Nitrate became depleted in both playas as a result of biological nitrogen demand imparted by unusually dense microbial communities reaching ～1 × 10⁸ cultivable heterotrophs per ml of water. One hundred eighty eight bacterial isolates were obtained, representing sixty phylotypes and four phyla: Actinobacteria, Bacteroidetes, Proteobacteria, and Firmicutes. Phylogenetic analyses suggested that the microbial communities reflected different phases of succession, with SVAL changing from a diverse community with abundant Yonghaparkia to a less diverse late summer community with abundant Bacteroidetes and Proteobacteria such as Loktanella, Rhodobaca, Saccharospirillum, Flexibacter, and phylogenetically novel members of the Flexibacteriaceae. In EP, a diverse assemblage of bacteria often associated with soils was replaced very quickly by a much less even community dominated by Yonghaparkia, Sandarakinorhabdus, and relatives of Belliella baltica. Strikingly, the early summer microbial community from SVAL was not significantly different from the EP community that developed within one week of flooding, even though these playas are almost 1000 km apart, whereas sympatric communities in different phases of succession were different. To our knowledge, this is one of the first geomicrobiological studies of a recharge playa, the dominant playa type worldwide.     

Expression and Purification of Functional Human Mu Opioid Receptor from E.coli

N-terminally his-tagged human mu opioid receptor, a G protein-coupled receptor was produced in E.coli employing synthetic codon-usage optimized constructs. The receptor was expressed in inclusion bodies and membrane-inserted in different E.coli strains. By optimizing the expression conditions the expression level for the membrane-integrated receptor was raised to 0.3–0.5 mg per liter of culture. Milligram quantities of receptor could be enriched by affinity chromatography from IPTG induced cultures grown at 18°C. By size exclusion chromatography the protein fraction with the fraction of alpha-helical secondary structure expected for a 7-TM receptor was isolated, by CD-spectroscopy an alpha-helical content of ca. 45% was found for protein solubilised in the detergent Fos-12. Receptor in Fos-12 micelles was shown to bind endomorphin-1 with a K_D of 61 nM. A final yield of 0.17 mg functional protein per liter of culture was obtained.     

Production and comprehensive quality control of recombinant human Interleukin-1beta: a case study for a process development strategy

We describe an efficient strategy to produce high-quality proteins by using a single large IMAC chromatography column and enzymatic His-tag removal via the TAGZyme system in pilot scale. Numerous quality assays demonstrated a high purity of the final product, the human cytokine Interleukin-1beta (IL-1beta). The protein preparation was apparently free of host cell proteins, endotoxins, protease, and aggregates. The N-terminal amino acid sequence of IL-1beta was in full agreement with the natural mature form of IL-1beta. The homogeneity of the product was further shown by X-ray structure determination which confirmed the previously solved structure of the protein. We propose the applied workflow as a strategy for industrial production of protein-based biopharmaceuticals.     

Feasibility of the laryngeal tube airway for artificial ventilation in pigs and comparison with the laryngeal mask airway

Airway management in anesthetized pigs is known to be technically demanding, and the 'gold standard' technique of endotracheal intubation is particularly difficult to master. The authors investigated the feasibility of the laryngeal tube as an alternative technique for airway management in German Landrace pigs (n = 5). They compared this method with the laryngeal mask, which is considered to be an effective yet relatively straightforward tool for porcine airway management. One after the other, investigators attempted to establish an airway in each anesthetized, artificially ventilated pig using each device. The laryngeal tube was too short to intubate the largest pig (weighing 45 kg), and it took investigators slightly longer to insert this device compared with the laryngeal mask. With the laryngeal mask, there were several incidents of gastric insufflation. Despite these complications, all investigators were able to establish a secure airway and maintain oxygenation with the laryngeal tube, and all subjectively rated both devices as easy to use.     

Uni-site ATP synthesis in thylakoids

Uni-site ATP synthesis was measured with thylakoids. The membrane-bound ATP-synthase, CF0F1, was brought into the active, reduced state by illumination in the presence of thioredoxin, dithiothreitol and phosphate. This enzyme contains two tightly bound ATP per CF0F1. ATP was released from the enzyme when ADP was added in substoichiometric amounts during illumination. Experiments with [14C]ADP indicated that after binding the same nucleotide was phosphorylated and released as [14C]ATP, i.e. only one site is involved in ATP-synthesis ('uni-site ATP-synthesis'). The two tightly bound ATP are not involved in the catalytic turnover. The rate constant for ADP binding was (4 +/- 2) x 10(6) M-1s-1. Compared to deenergized conditions the rate constant for ADP binding and that for ATP-release were drastically increased, i.e. membrane energization increased the rate constants for the ATP-synthesis direction.