scholarly journals Structural characterization of UDP-galactopyranose mutase from eukaryotic pathogens

2013 ◽  
Author(s):  
◽  
Richa Dhatwalia
Keyword(s):  
Drug Target ◽  
Pathogenic Bacteria ◽  
Leishmania Major ◽  
Biochemical Characterization ◽  
Three Dimensional ◽  
Protozoan Parasites ◽  
Enzymatic Mechanism ◽  
Structural Details

UDP-galactopyranose mutase (UGM) is a unique flavoenzyme that catalyzes the interconversion between UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDP-Galf), without any net transfer of electrons. UGM is a central enzyme involved in the biosynthesis of galactofuranose (Galf). Galf forms a major component of different glycoconjugate structures, lipids and polysaccharides of disease-causing fungi, Aspergillus fumigatus and protozoan parasites such as Trypanosoma cruzi and Leishmania major. Current treatments for diseases caused by these pathogens are limited and use compounds that are either highly toxic or expensive. Thus, new drug development strategies are required for combating these lethal diseases. The unique chemistry of UGMs and its implication in the virulence of pathogenic bacteria, fungi and protozoa and its absence in humans make it a potential drug target. Though bacterial UGMs have been somewhat characterized in detail using structural and biochemical methods, major questions about the catalytic and structural properties of eukaryotic UGMs remain unanswered. Thus, the determination of three-dimensional structures of eukaryotic UGMs might help us in elucidating the enzymatic mechanism of this class of enzymes and potential inhibitor design. The research described in this dissertation address these longstanding questions by providing the first three-dimensional structural details and biochemical characterization of eukaryotic UGMs.

scholarly journals Prevalence of Tonsillitis caused by Streptococcus spp. Among children and the effect of some Lactic acid bacterial (LAB) strain on it

2016 ◽  
Vol 13 (2) ◽  
pp. 218-227
Author(s):  
Baghdad Science Journal
Keyword(s):  
Inhibitory Activity ◽  
Pathogenic Bacteria ◽  
Biochemical Characterization ◽  
Bacterial Isolate ◽  
Inhibition Zone ◽  
Laboratory Culture ◽  
Diffusion Method ◽  
Inhibition Activity ◽  
Str System

In this study 100 samples were collected from infected children with acute and chronic tonsillitis who attended to Al-Yarmook Teaching Hospital (ENT consultation clinic) from 5/12/2013 to 1/3/2014. The result of laboratory culture was positive in 67 samples. Depending on their cultural, morphological and biochemical characterization of bacterial isolate of them were identified as (37.31%) belonged to Streptococcus pyogenes and the diagnosis is confirmed by the use of Remel Rapid STR System, (34.32%) belonged to S.parasanguinis, (11.94%) S.mitis, (11.94%) S.oralis and (4.47%) S.thoraltensis . Results confirmed that cup assay gave highest inhibition zone after 24 hrs compare with well diffusion methods for suspension of L.acidophilus gave highest inhibition zone after 48 hrs for incubation, while ahigh inhibition zone revealed for suspension of L.fermentum after 24 hrs incubation. the study included also the measurement of the inhibition activity for bacteriocins produced by L.acidophilus bacteria against pathogenic bacteria on nutrient agar by well diffusion method in which results revealed stability of the bacteriocins produced towards PH which kept its activity with PH 4-6 for 24 hrs, and the highest stability was with PH 4, however it lost a lot of its activity with acidic PH less than 2 and alkaline PH as 8. The treatment of bacteriocins with salts such as Nacl it revealed little effect in inhibition zone within 1 & 2% concetrations. The salt MgSo4 & Kcl showed reduction in the inhibitory activity in the low concentration, however the higher concentration of salt caused great reduction and 5% concentration led to loss of inhibitory activity for bacteriocins completely.

X-ray topographic determination of the granular structure in a graphite mosaic crystal: a three-dimensional reconstruction

2000 ◽  
Vol 33 (4) ◽  
pp. 1023-1030 ◽  
Author(s):  
M. Ohler ◽  
M. Sanchez del Rio ◽  
A. Tuffanelli ◽  
M. Gambaccini ◽  
A. Taibi ◽  
...  
Keyword(s):  
Structural Parameters ◽  
Pyrolytic Graphite ◽  
Three Dimensional ◽  
X Ray ◽  
Dimensional Reconstruction ◽  
Mosaic Crystals ◽  
Spatial Locations ◽  
Crystalline Domains

Section topographs recorded at different spatial locations and at different rocking angles of a highly oriented pyrolytic graphite (HOPG) crystal allow three-dimensional maps of the local angular-dependent scattering power to be obtained. This is performed with a direct reconstruction from the intensity distribution on such topographs. The maps allow the extraction of information on local structural parameters such as size, form and internal mosaic spread of crystalline domains. This data analysis leads to a new method for the characterization of mosaic crystals. Perspectives and limits of applicability of this method are discussed.

Local bond order parameters for accurate determination of crystal structures in two and three dimensions

2018 ◽  
Vol 20 (42) ◽  
pp. 27059-27068 ◽  
Author(s):  
Hossein Eslami ◽  
Parvin Sedaghat ◽  
Florian Müller-Plathe
Keyword(s):  
Crystal Structures ◽  
Bond Order ◽  
Accurate Determination ◽  
Three Dimensional ◽  
Order Parameters ◽  
Three Dimensions ◽  
Local Order ◽  
Crystalline Structures

Local order parameters for the characterization of liquid and different two- and three-dimensional crystalline structures are presented.

Cloning and Characterization of a Novel N-acetylglucosaminidase (AtlD) from Enterococcus faecalis

2018 ◽  
Vol 28 (1) ◽  
pp. 14-27 ◽  
Author(s):  
Carlos Eduardo Serrano-Maldonado ◽  
Israel García-Cano ◽  
Augusto González-Canto ◽  
Eliel Ruiz-May ◽  
Jose Miguel Elizalde-Contreras ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Food Industry ◽  
Pathogenic Bacteria ◽  
Heterologous Protein ◽  
Biochemical Characterization ◽  
Ph Values ◽  
Food Borne ◽  
Sds Page ◽  
Exclusion Chromatography

The <i>atlD</i> gene from<i></i> an <i>Enterococcus faecalis</i> strain isolated from a Mexican artisanal cheese was cloned, sequenced and expressed in <i>Escherichia coli</i> in order to perform a biochemical characterization<i>.</i> A partial amino acid sequence of the heterologous protein was obtained by LC-MS/MS, and it corresponded to a novel peptidoglycan hydrolase designated AtlD. Its molecular mass was 62–75 kDa, as determined by SDS-PAGE, zymography, Western blot, and exclusion chromatography. Electrofocusing rendered an isoelectric point (pI) of 4.8. It exhibited N-acetylglucosaminidase activity, with an optimal pH and temperature between 6–7 and 50°C, respectively. It retained 85% activity with NaCl at 1,000 mM, but it was susceptible to divalent ions, particularly Zn<sup>2+</sup>. It showed antibacterial activity against <i>Listeria monocytogenes</i>,<i> Staphylococcus aureus</i>, and enterococcal<i></i> strains of clinical origin. Due to the fact that it showed activity versus pathogenic bacteria, and because of its capabilities under ionic strength, temperature, and pH values present in food matrices, it could be applied as an additive in the food industry. This study will aid in the design of new antibacterial agents of natural origin to combat food-borne diseases, and it could be used as an industrial or hospital hygiene agent as well.

Liquid chromatography mass spectrometry based characterization of epitope configurations

2020 ◽  
Vol 12 (45) ◽  
pp. 5476-5484
Author(s):  
Maren Christin Stillesby Levernæs ◽  
Arelí Urtubia Moe ◽  
Sigurd Leinæs Bøe ◽  
Elisabeth Paus ◽  
Léon Reubsaet ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Liquid Chromatography Mass Spectrometry ◽  
Three Dimensional Structure ◽  
Chromatography Mass Spectrometry ◽  
Pre Treatment

Here we evaluate a quick and easy tool for determination of epitope configuration using immunocapture and liquid chromatography mass spectrometry (LC-MS) subsequent to pre-treatment of the target protein to disrupt its three-dimensional structure.

scholarly journals Genetic and Biochemical Characterization of a Novel Monoterpene ɛ-Lactone Hydrolase from Rhodococcus erythropolis DCL14

2001 ◽  
Vol 67 (2) ◽  
pp. 733-741 ◽  
Author(s):  
Cécile J. B van der Vlugt-Bergmans ◽  
Mariët J. van der Werf
Keyword(s):  
Ring Opening ◽  
Biochemical Characterization ◽  
Rhodococcus Erythropolis ◽  
Open Reading Frames ◽  
Apparent Homogeneity ◽  
Terminal Amino ◽  
Acyl Coenzyme A ◽  
Reading Frames

ABSTRACT A monoterpene ɛ-lactone hydrolase (MLH) from Rhodococcus erythropolis DCL14, catalyzing the ring opening of lactones which are formed during degradation of several monocyclic monoterpenes, including carvone and menthol, was purified to apparent homogeneity. It is a monomeric enzyme of 31 kDa that is active with (4R)-4-isopropenyl-7-methyl-2-oxo-oxepanone and (6R)-6-isopropenyl-3-methyl-2-oxo-oxepanone, lactones derived from (4R)-dihydrocarvone, and 7-isopropyl-4-methyl-2-oxo-oxepanone, the lactone derived from menthone. Both enantiomers of 4-, 5-, 6-, and 7-methyl-2-oxo-oxepanone were converted at equal rates, suggesting that the enzyme is not stereoselective. Maximal enzyme activity was measured at pH 9.5 and 30°C. Determination of the N-terminal amino acid sequence of purified MLH enabled cloning of the corresponding gene by a combination of PCR and colony screening. The gene, designated mlhB(monoterpene lactone hydrolysis), showed up to 43% similarity to members of the GDXG family of lipolytic enzymes. Sequencing of the adjacent regions revealed two other open reading frames, one encoding a protein with similarity to the short-chain dehydrogenase reductase family and the second encoding a protein with similarity to acyl coenzyme A dehydrogenases. Both enzymes are possibly also involved in the monoterpene degradation pathways of this microorganism.

Biochemical characterization of serine acetyltransferase and cysteine desulfhydrase from Leishmania major

2010 ◽  
Vol 173 (2) ◽  
pp. 170-174 ◽  
Author(s):  
Daniela Marciano ◽  
Marianela Santana ◽  
Brian Suárez Mantilla ◽  
Ariel Mariano Silber ◽  
Cristina Marino-Buslje ◽  
...  
Keyword(s):  
Leishmania Major ◽  
Biochemical Characterization ◽  
Serine Acetyltransferase ◽  
Cysteine Desulfhydrase

scholarly journals High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hina Andaleeb ◽  
Najeeb Ullah ◽  
Sven Falke ◽  
Markus Perbandt ◽  
Hévila Brognaro ◽  
...  
Keyword(s):  
Alternative Fuels ◽  
Biochemical Characterization ◽  
Three Dimensional ◽  
Detailed Comparison ◽  
Structural Features ◽  
Dimensional Structure ◽  
Nectria Haematococca ◽  
Chemical Reagents ◽  
Beechwood Xylan

Abstract Enzymatic degradation of vegetal biomass offers versatile procedures to improve the production of alternative fuels and other biomass-based products. Here we present the three-dimensional structure of a xylanase from Nectria haematococca (NhGH11) at 1.0 Å resolution and its functional properties. The atomic resolution structure provides details and insights about the complex hydrogen bonding network of the active site region and allowed a detailed comparison with homologous structures. Complementary biochemical studies showed that the xylanase can catalyze the hydrolysis of complex xylan into simple xylose aldopentose subunits of different lengths. NhGH11 can catalyze the efficient breakdown of beechwood xylan, xylan polysaccharide, and wheat arabinoxylan with turnover numbers of 1730.6 ± 318.1 min−1, 1648.2 ± 249.3 min−1 and 2410.8 ± 517.5 min−1 respectively. NhGH11 showed maximum catalytic activity at pH 6.0 and 45 °C. The mesophilic character of NhGH11 can be explained by distinct structural features in comparison to thermophilic GH11 enzymes, including the number of hydrogen bonds, side chain interactions and number of buried water molecules. The enzymatic activity of NhGH11 is not very sensitive to metal ions and chemical reagents that are typically present in associated industrial production processes. The data we present highlights the potential of NhGH11 to be applied in industrial biomass degradation processes.

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