Barrier passage and protein dynamics in enzymatically catalyzed reactions.

This review describes studies of particular enzymatically catalyzed reactions to investigate the possibility that catalysis is mediated by protein dynamics. That is, evolution has crafted the protein backbone of the enzyme to direct vibrations in such a fashion to speed reaction. The review presents the theoretical approach we have used to investigate this problem, but it is designed for the nonspecialist. The results show that in alcohol dehydrogenase, dynamic protein motion is in fact strongly coupled to chemical reaction in such a way as to promote catalysis. This result is in concert with both experimental data and interpretations for this and other enzyme systems studied in the laboratories of the two other investigators who have published reviews in this issue.     

On the discriminability of hROIs, human visually selected regions-of-interest

Many studies have tried to answer an important question: is it possible to predict human visually selected regions-of-interest (hROIs)? hROIs are defined as the loci of eye fixations and they can be analyzed by their spatial distribution over the visual stimulus and their temporal ordering. We used a simplified set of geometrical spatial kernels and linear filter models as bottom-up conspicuity operators that produce algorithmically selected regions-of-interest, aROIs. As a direct approach we measured the ability of these aROIs to predict human scanpaths. The level of prediction is measured by two similarity indices: S _p for spatial similarity and S _s for temporal ordering similarity. At the same time we assessed the discriminability of the hROI loci, in terms of conspicuity, with respect to non-selected (not of interest) regions of an image. We prove that this discrimination is possible and further correlates with the positional similarity index S _p . Other human scanpath experimental conditions are presented in parsing diagrams and discussed. A general top–down/bottom–up scanpath model is finally formulated.     

Disruption of microtubular network attenuates histamine-induced dilation in rat mesenteric vessels

Cytoplasmic microtubules are important in many cellular homeostatic processes in the cell. They regulate cell shape and movement as well as serving as a network by which vesicles and membrane-bound organelles can travel. Lately, there have been many studies demonstrating that microtubules are involved in regulation of intracellular signaling and, therefore, affect vascular reactivity. In this study, we tested the hypothesis that microtubule disruption attenuates agonist-induced endothelium-dependent vasodilation. Isolated mesenteric arterial bed from normotensive rats was preconstricted with phenylephrine, and dose-response curves for histamine, acetylcholine (ACh), sodium nitroprusside (SNP), and pinacidil were performed before and after incubation with nocodazole or colchicine. Treatment of the vascular beds with nocodazole or colchicine significantly attenuated histamine relaxation but did not change the ACh-, SNP-, or pinacidil-induced vasorelaxation. Nocodazole did not cause an additional attenuation of the histamine-mediated dilation in mesenteric vessels in the presence of N-nitro-L-arginine methyl ester, high extracellular K⁺, or K⁺ channel blockers. These data suggest that disruption of microtubules affects an essential endothelial component of histamine-mediated vasodilation in the mesenteric arterial bed. The mechanism(s) involved in this effect might be related to an impairment of endothelial NO synthesis, which might not be as important for the ACh as for the histamine vasodilator response in rat mesenteric vessels. These results demonstrate the importance of the microtubular system for endothelium-dependent NO-mediated smooth muscle relaxation. nocodazole; nitric oxide; mesenteric arterial bed     

Monoclonal antibody AP33 defines a broadly neutralizing epitope on the hepatitis C virus E2 envelope glycoprotein

Hepatitis C virus (HCV) remains a significant threat to the general health of the world's population, and there is a pressing need for the development of new treatments and preventative vaccines. Here, we describe the generation of retrovirus-based pseudoparticles (HCVpp) incorporating a panel of full-length E1E2 clones representative of the major genotypes 1 through 6, and their application to assess the reactivity and neutralizing capability of antisera and monoclonal antibodies raised against portions of the HCV E2 envelope protein. Rabbit antisera raised against either the first hypervariable region or ectodomain of E2 showed limited and strain specific neutralization. By contrast, the monoclonal antibody (MAb) AP33 demonstrated potent neutralization of infectivity against HCVpp carrying E1E2 representative of all genotypes tested. The concentration of AP33 required to achieve 50% inhibition of infection by HCVpp of diverse genotypes ranged from 0.6 to 32 mug/ml. The epitope recognized by MAb AP33 is linear and highly conserved across different genotypes of HCV. Thus, identification of a broadly neutralizing antibody that recognizes a linear epitope is likely to be of significant benefit to future vaccine and therapeutic antibody development.     

Nitrosyl heme production compared in endotoxemic and hemorrhagic shock

We compared nitric oxide production and nitrosyl hemoglobin steady state concentrations during the early phases of endotoxemic and hemorrhagic shock of equivalent severity. Sprague-Dawley rats were randomly assigned to (1) sham-operated control, (2) hemorrhage, and (3) intravenous endotoxin. Electron paramagnetic resonance spectroscopy was used to measure NO in the vasculature (binding to hemoglobin) and in the liver (binding to cytochrome P450). Despite similar changes in cardiorespiratory variables and identical microvascular pO(2), nitrosyl hemoglobin concentrations were significantly higher in endotoxemic rats than in rats in hemorrhagic shock, suggesting increased rates of NO production. A substantial venous minus arterial concentration gradient was observed for nitrosyl hemoglobin. This increased in line with the plasma total nitrite + nitrate concentration. Nitrosyl hemoglobin formation is likely to occur predominantly in the venous pool, suggesting that removal of NO from hemoglobin in the presence of oxygen may be faster than previously thought. In the liver, an increase in intracellular heme-NO complexes was detected in endotoxemic rats compared with rats in hemorrhagic shock; this was associated with increased reduction of the mitochondrial respiratory chain and is suggestive of NO inhibition of mitochondrial respiration.     

Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of <Emphasis Type="Italic">Bifidobacterium longum</Emphasis> NCC2705

Background  

Analysis of the first reported complete genome sequence ofBifidobacterium longumNCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness toStreptomyces coelicolorandMycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes.     

New short route to unsaturated fluoroketonucleosides: case of 5-fluoro-1-(6-O-acetyl-3,4-di-deoxy-3-fluoro-beta-D-glycero-hex-3-eno-pyranos-2-ulosyl) uracil

The proposed short synthesis involves two key steps: Oxidation of the isopropylidene derivative of the 3-fluoronucleoside possessing a free hydroxyl group in 2-position and acetylation of deprotected 3-fluoro-2-ketonucleoside which, after a beta-elimination reaction, gives the desired unsaturated ketonucleoside 5.     

Bordetella pertussis, the causative agent of whooping cough, evolved from a distinct, human-associated lineage of B. bronchiseptica

Bordetella pertussis, B. bronchiseptica, B. parapertussis(hu), and B. parapertussis(ov) are closely related respiratory pathogens that infect mammalian species. B. pertussis and B. parapertussis(hu) are exclusively human pathogens and cause whooping cough, or pertussis, a disease that has resurged despite vaccination. Although it most often infects animals, infrequently B. bronchiseptica is isolated from humans, and these infections are thought to be zoonotic. B. pertussis and B. parapertussis(hu) are assumed to have evolved from a B. bronchiseptica-like ancestor independently. To determine the phylogenetic relationships among these species, housekeeping and virulence genes were sequenced, comparative genomic hybridizations were performed using DNA microarrays, and the distribution of insertion sequence elements was determined, using a collection of 132 strains. This multifaceted approach distinguished four complexes, representing B. pertussis, B. parapertussis(hu), and two distinct B. bronchiseptica subpopulations, designated complexes I and IV. Of the two B. bronchiseptica complexes, complex IV was more closely related to B. pertussis. Of interest, while only 32% of the complex I strains were isolated from humans, 80% of the complex IV strains were human isolates. Comparative genomic hybridization analysis identified the absence of the pertussis toxin locus and dermonecrotic toxin gene, as well as a polymorphic lipopolysaccharide biosynthesis locus, as associated with adaptation of complex IV strains to the human host. Lipopolysaccharide structural diversity among these strains was confirmed by gel electrophoresis. Thus, complex IV strains may comprise a human-associated lineage of B. bronchiseptica from which B. pertussis evolved. These findings will facilitate the study of pathogen host-adaptation. Our results shed light on the origins of the disease pertussis and suggest that the association of B. pertussis with humans may be more ancient than previously assumed.     

Crystal structure of the beta-chain of human hepatocyte growth factor-like/macrophage stimulating protein

Hepatocyte growth factor like/macrophage stimulating protein (HGFl/MSP) and hepatocyte growth factor/scatter factor (HGF/SF) define a distinct family of vertebrate-specific growth factors structurally related to the blood proteinase precursor plasminogen and with important roles in development and cancer. Although the two proteins share a similar domain structure and mechanism of activation, there are differences between HGFl/MSP and HGF/SF in terms of the contribution of individual domains to receptor binding. Here we present a crystal structure of the 30 kDa beta-chain of human HGFl/MSP, a serine proteinase homology domain containing the high-affinity binding site for the RON receptor. The structure describes at 1.85 Angstrom resolution the region of the domain corresponding to the receptor binding site recently defined in the HGF/SF beta-chain, namely the central cleft harboring the three residues corresponding to the catalytic ones of active proteinases (numbers in brackets define the sequence position according to the standard chymotrypsinogen numbering system) [Gln522 (c57), Gln568 (c102) and Tyr661 (c195)] and an adjacent loop flanking the S1 specificity pocket and containing residues Asn682 (c217) and Arg683 (c218) previously shown to be essential for binding of HGFl/MSP to the RON receptor. The study confirms the concept that the serine proteinase homology domains of HGFl/MSP and HGF/SF bind their receptors in an 'enzyme-substrate' mode, reflecting the common evolutionary origin of the plasminogen-related growth factors and the proteinases of the clotting and fibrinolytic pathways. However, analysis of the intermolecular interactions in the crystal lattice of beta-chain HGFl/MSP fails to show the same contacts seen in the HGF/SF structures and does not support a conserved mode of dimerization of the serine proteinase homology domains of HGFl/MSP and HGF/SF responsible for receptor activation.