Mechanistic and inhibition studies of chorismate-utilizing enzymes

2005 ◽  
Vol 33 (4) ◽  
pp. 763-766 ◽  
Author(s):  
O. Kerbarh ◽  
E.M.M. Bulloch ◽  
R.J. Payne ◽  
T. Sahr ◽  
F. Rébeillé ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Higher Plants ◽  
Three Dimensional ◽  
Antimicrobial Effect ◽  
Three Dimensional Model ◽  
Antimicrobial Drugs ◽  
Apicomplexan Parasites ◽  
Covalent Intermediate ◽  
Inhibition Studies ◽  
First Time

The shikimate biosynthetic pathway is utilized in algae, higher plants, bacteria, fungi and apicomplexan parasites; it involves seven enzymatic steps in which phosphoenolpyruvate and erythrose 4-phosphate are converted into chorismate. In Escherichia coli, five chorismate-utilizing enzymes catalyse the synthesis of aromatic compounds such as L-phenylalanine, L-tyrosine, L-tryptophan, folate, ubiquinone and siderophores such as yersiniabactin and enterobactin. As mammals do not possess such a biosynthetic system, the enzymes involved in the pathway have aroused considerable interest as potential targets for the development of antimicrobial drugs and herbicides. As an initiative to investigate the mechanism of some of these enzymes, we showed that the antimicrobial effect of (6S)-6-fluoroshikimate is the result of irreversible inhibition of 4-amino-4-deoxychorismate synthase by 2-fluorochorismate. Based on this study, a catalytic mechanism for this enzyme was proposed, in which the residue Lys-274 is involved in the formation of a covalent intermediate. In another study, Yersinia enterocolitica Irp9, which is involved in the biosynthesis of the siderophore yersiniabactin, was for the first time biochemically characterized and shown to catalyse the formation of salicylate from chorismate via isochorismate as a reaction intermediate. A three-dimensional model for this enzyme was constructed that will guide the search for potent inhibitors of salicylate formation, and hence of bacterial iron uptake.

Problems Associated with the Use of Skirts on Hovercraft

1967 ◽  
Vol 182 (1) ◽  
pp. 201-218
Author(s):  
W. A. Crago
Keyword(s):  
Three Dimensional ◽  
Model Tests ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Operational Conditions ◽  
The Third ◽  
Rough Water ◽  
Delamination Life ◽  
First Time

The lecture commences with a brief description of early hovercraft work and shows how the advent of flexible extensions to the peripheral jets—or ‘skirts’—constituted a breakthrough without which the hovercraft would never have become a practical proposition with the ability to operate over waves and rough ground. It is shown that the introduction of skirts, whilst providing a solution in one respect, also led to a series of problems and three of these are singled out for further discussion. First it is shown that whilst a relatively high internal skirt pressure is desirable to maintain skirt shape under operational conditions, this pressure can also lead to a high rough water drag. The second problem is that of ‘plough in’ and overturning, which is intimately associated with the use of skins. The hydrodynamic mechanisms of both these undesirable phenomena are for the first time explained in detail and are illustrated by means of data obtained from two- and three-dimensional model tests. The third problem raised by the introduction of skirts is skirt oscillation and wear. The techniques necessary to investigate delamination are described and some of the factors which have been shown to be important in increasing delamination life are outlined.

Functional expression of theSpodoptera exiguachitinase to examine the virtually screened inhibitor candidates

2019 ◽  
Vol 109 (6) ◽  
pp. 741-751
Author(s):  
L. Zhang ◽  
Z. Guan ◽  
Z. Pan ◽  
H. Ge ◽  
D. Zhou ◽  
...  
Keyword(s):  
Spodoptera Exigua ◽  
Three Dimensional ◽  
Recombinant Baculovirus ◽  
Functional Expression ◽  
Beet Armyworm ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Inhibitor Activity ◽  
New Information ◽  
First Time

AbstractChitinase is responsible for insect chitin hydrolyzation, which is a key process in insect molting and pupation. However, little is known about the chitinase ofSpodoptera exigua(SeChi). In this study, based on theSeChi gene (ADI24346) identified in our laboratory, we constructed the recombinant baculovirus P-Chi for the expression of recombinantSeChi (rSeChi) in Hi5 cells. The rSeChi was purified by chelate affinity chromatography, and the purified protein showed activity comparable with that of a commercialSgChi, suggesting that we harvested activeSeChi for the first time. The purified protein was subsequently tested for enzymatic properties and revealed to exhibit its highest activity at pH 8 and 40 C. Using homology modeling and molecular docking techniques, the three-dimensional model ofSeChi was constructed and screened for inhibitors. In two rounds of screening, twenty compounds were selected. With the purified rSeChi, we tested each of the twenty compounds for inhibitor activity against rSeChi, and seven compounds showed obvious activity. This study provided new information for the chitinase of beet armyworm and for chitinase inhibitor development.

A Three-Dimensional Model of Droplet Impinging, Solidification and Suspension on the Substrate

2011 ◽  
Vol 346 ◽  
pp. 222-227
Author(s):  
Sheng Zhu ◽  
Feng Liang Yin ◽  
Jian Liu ◽  
Yuan Yuan Liang
Keyword(s):  
Surface Tension ◽  
Manufacturing Process ◽  
Three Dimensional ◽  
Metal Droplet ◽  
The Body ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
High Impact Velocity ◽  
The Impact ◽  
First Time

A three-dimensional model was built to study a molten metal droplet impact on an edge of the substrate in droplet deposition manufacturing process for the first time. The whole calculation domain, including the substrate, was described using same fluid conservation equations, which is to say that the remolding and solidification of substrate was considered also. Droplet free surface was tracked by volume-of-fluid (VOF) algorithm. The effect of surface tension on the droplet was taken into consideration by means of considering surface tension to be a component of the body force. The simulated results show that the droplet in liquid phase can keep suspending on the substrate at a role of surface tension. A too high impact velocity would make parts of droplet splash away the substrate which is not allowed in manufacturing process. The offset between edge of droplet and side edge of substrate influences dramatically the impact of the droplet.

scholarly journals Three-dimensional model evaluation of the Ozone Depletion Potentials for n-propyl bromide, trichloroethylene and perchloroethylene

2010 ◽  
Vol 10 (7) ◽  
pp. 17889-17910 ◽  
Author(s):  
D. J. Wuebbles ◽  
K. O. Patten ◽  
D. Wang ◽  
D. Youn ◽  
M. Martínez-Avilés ◽  
...  
Keyword(s):  
Ozone Depletion ◽  
Transport Model ◽  
Stratospheric Ozone ◽  
Three Dimensional ◽  
Three Dimensional Model ◽  
Chemistry Transport Model ◽  
Atmospheric Lifetime ◽  
Land Surfaces ◽  
Simplified Modeling ◽  
First Time

Abstract. The existing solvents trichloroethylene (TCE) and perchloroethylene (PCE) and proposed solvent n-propyl bromide (nPB) have atmospheric lifetimes from days to a few months, but contain chlorine or bromine that could affect stratospheric ozone. Several previous studies estimated the Ozone Depletion Potentials (ODPs) for various assumptions for location of nPB emissions, but these studies used simplified modeling treatments. The primary purpose of this study is to reevaluate the ODP for nPB using a current-generation chemistry-transport model of the troposphere and stratosphere. For the first time, ODPs for TCE and PCE are also evaluated. Emissions representing industrial use of each compound are incorporated on land surfaces from 30° N to 60° N. The atmospheric chemical lifetime obtained for nPB is 24.7 days, similar to past literature, but the ODP is 0.0049, lower than in past studies. The derived atmospheric lifetime for TCE is 13.0 days and for PCE is 111 days. The corresponding ODPs are 0.00035 and 0.0060, respectively.

Active-site characterization of Candida boidinii formate dehydrogenase

2001 ◽  
Vol 354 (2) ◽  
pp. 455-463 ◽  
Author(s):  
Nikolaos E. LABROU ◽  
Daniel J. RIGDEN
Keyword(s):  
Nucleotide Sequence ◽  
Molecular Modelling ◽  
Formate Dehydrogenase ◽  
Catalytic Mechanism ◽  
Three Dimensional ◽  
Site Directed Mutagenesis ◽  
Candida Boidinii ◽  
Three Dimensional Model ◽  
Embl Nucleotide Sequence Database ◽  
Anchor Group

NAD+-dependent formate dehydrogenase (FDH) from Candida boidinii was cloned and expressed to a high level in Escherichia coli (20% of soluble E. coli protein). Molecular modelling studies were used to create a three-dimensional model of C. boidinii FDH, based on a known structure of the Pseudomonas sp. 101 enzyme. This model was used for investigating the catalytic mechanism by site-directed mutagenesis. Eleven forms of C. boidinii FDH were characterized by steady-state kinetic analysis: the wild type as well as 10 mutants involving single (Phe-69–Ala, Asn-119–His, Ile-175–Ala, Gln-197–Leu, Arg-258–Ala, Gln-287–Glu and His-311–Gln) and double amino acid substitutions (Asn-119–His/His-311–Gln, Gln-287–Glu/His-311–Gln and Gln-287–Glu/Pro-288–Thr). The kinetic results of the mutant enzymes provide the first experimental support that hydrophobic patches, formed by Phe-69 and Ile-175, destabilize substrates and stabilize products. Also, the key role of Arg-258 in stabilization of the negative charge on the migrating hydride was established. Asn-119, besides being an anchor group for formate, also may comprise one of the hinge regions around which the two domains shift on binding of NAD+. The more unexpected results, obtained for the His-311–Gln and Gln-287–Glu/His-311–Gln mutants, combined with molecular modelling, suggest that steric as well as electrostatic properties of His-311 are important for enzyme function. An important structural role has also been attributed to cis-Pro-288. This residue may provide the key residues Gln-287 and His-311 with the proper orientation for productive binding of formate. The FDH nucleotide sequence has been submitted to the EMBL Nucleotide Sequence Database under the accession no. AJ011046.

scholarly journals Characterization of neutralization sites on the circulating variant of swine vesicular disease virus (SVDV): a new site is shared by SVDV and the related coxsackie B5 virus

2002 ◽  
Vol 83 (1) ◽  
pp. 35-44 ◽  
Author(s):  
Belén Borrego ◽  
Elena Carra ◽  
Juan Antonio García-Ranea ◽  
Emiliana Brocchi
Keyword(s):  
Disease Virus ◽  
Three Dimensional ◽  
Three Dimensional Model ◽  
Antigenic Variant ◽  
Detection Systems ◽  
Genetic Groups ◽  
Swine Vesicular Disease Virus ◽  
Unique Markers ◽  
First Time ◽  
Vesicular Disease

Using a panel of new monoclonal antibodies (mAbs), five neutralizing, conformation-dependent sites have been identified on the antigenic variant of swine vesicular disease virus (SVDV) circulating currently. In studies on the antigenic conservation of these sites, the four antigenic/genetic groups of SVDV described showed distinguishable patterns, confirming this classification. By sequencing mAb-resistant mutants, the five sites have been mapped precisely and localized on a three-dimensional model of the SVDV capsid. All were found to be orientated, to a different extent, towards the external surface of the capsid. Three of the five sites, located in VP1, VP2 and VP3, correspond to epitopes identified previously in historic isolates as sites 1, 2a and 3b, respectively. Another site, site IV, which maps to position 258 of VP1, corresponds to an epitope reported recently and is described in this study to be specific for isolates of the most recent antigenic group of SVDV. A fifth site is described for the first time and corresponds to the unique neutralizing site that is common to both SVDV and coxsackie B5 virus; it maps to positions 95 and 98 of VP1, but may also include positions nearby that belong to site 1 on the BC-loop of VP1, suggesting the classification of site Ia. These results may have useful diagnostic and epidemiological applications, since mAbs to the new conserved site Ia provide universal reagents for SVDV detection systems, while the specificity of mAbs to site IV make them unique markers for the most recent strains of SVDV.

scholarly journals Phytoplankton and Bacterial Responses to Monsoon-Driven Water Masses Mixing in the Kuroshio Off the East Coast of Taiwan

2021 ◽  
Vol 8 ◽  
Author(s):  
Chao-Chen Lai ◽  
Chau-Ron Wu ◽  
Chia-Ying Chuang ◽  
Jen-Hua Tai ◽  
Kuo-Yuan Lee ◽  
...  
Keyword(s):  
East Coast ◽  
Three Dimensional ◽  
Euphotic Zone ◽  
Kuroshio Current ◽  
Southwest Monsoon ◽  
Three Dimensional Model ◽  
Southern Taiwan ◽  
First Time ◽  
The Kuroshio ◽  
Mixing Water

Biogeochemical responses to mixing were examined in two cruise surveys along a transect across the Kuroshio Current (KC) in May and July 2020. Two stations located at the South China Sea (SCS)–KC mixing and the KC waters were chosen for the diel study. In the euphotic zone (~100 m depth), the average values of nitrate (0.97–1.62 μM), chlorophyll-a (Chl-a, 0.36–0.40 mg/m3), and primary production (PP; 3.46 ± 1.37 mgC/m3/day) of the mixing water station (MWS) of the two cruises were several folds higher than those of the KC station (KCS; nitrate, 0.03–0.10 μM; Chl-a, 0.14–0.24 mg/m3; and PP, 0.91 ± 0.47 mgC/m3/day). In the July cruise, the maximal bacterial production (BP) at the MWS (3.31 mgC/m3/day) was 82% higher in comparison with that of the KCS (1.82 mgC/m3/day); and the readings of Chl-a showed no trend with BP in the oligotrophic KCS, but a positive relationship was found among these measurements at the mesotrophic MWS. This implies that the trophic status of the system might affect phytoplankton–bacteria interactions. The backward-trajectory analyses conducted by an observation-validated three-dimensional model identified that the prevailing southwest monsoon drove a northeastward “intrusion” of the SCS waters in July 2020, resulted in mixing between SCS and Kuroshio (KC) waters off the east coast of southern Taiwan. For the first time, this study demonstrates that the high biological biomass and activities that occur in the KC are induced by the northward intrusion of the SCS waters.

scholarly journals Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Sona Valuchova ◽  
Pavlina Mikulkova ◽  
Jana Pecinkova ◽  
Jana Klimova ◽  
Michal Krumnikl ◽  
...  
Keyword(s):  
Higher Plants ◽  
Three Dimensional ◽  
Cell Lineage ◽  
Light Sheet ◽  
Three Dimensional Model ◽  
Light Sheet Microscopy ◽  
Meiotic Chromosomes ◽  
Short Period ◽  
Germline Differentiation ◽  
Subcellular Resolution

In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.

scholarly journals A Cat's Eye view of the Eskimo from Saturn

2011 ◽  
Vol 7 (S283) ◽  
pp. 366-367 ◽  
Author(s):  
Maria-Teresa García-Díaz ◽  
Jose-Alberto López ◽  
Wofgang Steffen ◽  
Michael G. Richer ◽  
Hortensia Riesgo
Keyword(s):  
Three Dimensional ◽  
Line Of Sight ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Data Set ◽  
Spatially Resolved ◽  
Complex Morphology ◽  
Spectroscopic Information ◽  
Expansion Pattern ◽  
First Time

AbstractThe 3-D and kinematic structure of the Eskimo nebula, NGC 2392, has been notoriously difficult to interpret given its complex morphology, multiple kinematic components and its nearly pole-on orientation along the line of sight. Here we present the most comprehensive high resolution spectroscopic mapping of the Eskimo planetary nebula to date. The data consist of 21 spatially resolved, long-slit echelle spectra tightly spaced over the Eskimo and along its bipolar jets. This data set allowed us to construct a velocity-resolved [NII] channel map of the nebula with a resolution of 10 km/s that disentagles the differente kinematic components of the nebula and reveals clearly for the first time the kinematic expansion pattern for each of the components. The spectroscopic information is combined with a HST image to construct the first detailed three dimensional model of the Eskimo with the code SHAPE. With this model we demostrate that the Eskimo is nearly a twin to the Saturn nebula, but rotated 90° to the line sight. Furthermore, we show that the main characteristics of our model apply to the general properties of the group of elliptical planetary nebulae with ansae, once the orientation is considered.

scholarly journals Imaging plant germline differentiation within Arabidopsis flower by light sheet microscopy

2019 ◽  
Author(s):  
Sona Valuchova ◽  
Pavlina Mikulkova ◽  
Jana Pecinkova ◽  
Jana Klimova ◽  
Michal Krumnikl ◽  
...  
Keyword(s):  
Higher Plants ◽  
Three Dimensional ◽  
Cell Lineage ◽  
Light Sheet ◽  
Three Dimensional Model ◽  
Light Sheet Microscopy ◽  
Meiotic Chromosomes ◽  
Short Period ◽  
Germline Differentiation ◽  
Subcellular Resolution

AbstractIn higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.

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