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At least 271 records · Page 15Linked to original sources
PubMed1999

Molecular mechanism of VanHst, an alpha-ketoacid dehydrogenase required for glycopeptide antibiotic resistance from a glycopeptide producing organism.

The vancomycin resistance enzyme VanH is an alpha-ketoacid dehydrogenase that stereospecifically reduces pyruvate to D-lactate, which is required for the synthesis of the depsipeptide D-alanine-D-lactate. This compound then forms an integral part of the bacterial cell wall replacing the vancomycin target dipeptide D-alanine-D-alanine, thus the presence of VanH is essential for glycopeptide resistance. In this work, the VanH homologue from the glycopeptide antibiotic producing organism Streptomyces toyocaensis NRRL 15009, VanHst, has been overexpressed in Escherichia coli and purified, and its substrate specificity and mechanism were probed by steady-state kinetic methods and site-directed mutagenesis. The enzyme is highly efficient at pyruvate reduction with kcat/Km = 1.3 x 10(5) M-1 s-1 and has a more restricted alpha-ketoacid substrate specificity than VanH from vancomycin resistant enterococci (VRE). Conversely, VanHst shows no preference between NADH and NADPH while VanH from VRE prefers NADPH. The kinetic mechanism for VanHst was determined using product and dead-end inhibitors to be ordered BiBi with NADH binding first followed by pyruvate and products leaving in the order D-lactate, NAD+. Site-directed mutagenesis indicated that Arg237 plays a role in pyruvate binding and catalysis and that His298 is a candidate for an active-site proton donor. Glu266, which has been suggested to modulate the pKa of the catalytic His in other D-lactate dehydrogenases, was found to fulfill a similar role in VanHst, lowering a pKa value of kcat/Km nearly 2 units. These results now provide the framework for additional structure and inhibitor design work on the VanH family of antibiotic resistance enzymes.

Anti-Bacterial Agents↗
PubMed2001

Commensurate and incommensurate hydrogen bonds. An exercise in crystal engineering.

Ureas characteristically form one-dimensional hydrogen-bonded alpha-networks with a repeat distance of about 4.60 A. Oxamides form similar alpha-networks with a longer 5.05 A repeat distance. The urea of glycine and the oxamide of glycine were each cocrystallized with a series of four bipyridines, including two urea derivatives and two oxamide derivatives. This series of eight cocrystals was studied by X-ray diffraction in order to see what would happen when molecules that would normally form alpha-networks with incommensurate distances were forced into the same crystal. The two all-urea crystals and the two all-oxamide crystals contained the expected alpha-networks with repeat distances in accordance with normal urea or oxamide values. Four of the crystals were mixed, containing both oxamide and urea molecules. Three consisted of two-dimensional beta-networks with alternating parallel urea and oxamide subnetworks. The repeat distances averaged 4.87 A, a value close to the value expected for oxamides, but shorter than any previously observed examples. In the fourth mixed crystal, the urea alpha-network formed with a normal urea repeat distance, but the oxamide network did not form, the oxamide adopting an unusual molecular conformation that maximizes intramolecular hydrogen bonds instead.

Crystallization↗
PubMed2003

Synthesis and quantitative structure-activity relationships of oxanilates as chemical hybridizing agents for wheat (Triticum aestivum L.).

Chemical hybridizing agents (CHAs) can facilitate two-line breeding in heterosis programs of crops. Twenty-seven oxanilates having different aromatic substitutions were synthesized and screened as CHAs on two genotypes of wheat, PBW 343 and HD 2733, during two Rabi (winter) seasons, 2000-01 and 2001-02. The oxanilates prepared by thermal condensation of anilines with diethyl oxalate or by acylation with ethoxycarbonyl methanoyl chloride were sprayed at 1000 and 1500 ppm at the premeiotic stage of wheat, when the length of the emerging spike of the first node was 7-8 mm. Pollen sterility and spikelet sterility were measured in each treatment. Ethyl oxanilates 5, 6, and 25,containing 4-F, 4-Br, and 4-CF(3) aromatic substituents, respectively, induced greater than 98% spikelet sterility, the desired level, at 1500 ppm. Quantitative structure-activity relationship analysis revealed a direct relationship between F(p) and molecular mass but an inverse relationship between MR, E(S), and R in influencing the bioactivity. Several F(1) hybrids were developed using 5, and at least one showed heterosis.

Agriculture↗
PubMed2003

Fragment screening and assembly: a highly efficient approach to a selective and cell active protein tyrosine phosphatase 1B inhibitor.

Using an NMR-based fragment screening and X-ray crystal structure-based assembly, starting with millimolar ligands for both the catalytic site and the second phosphotyrosine binding site, we have identified a small-molecule inhibitor of protein tyrosine phosphatase 1B with low micromolar inhibition constant, high selectivity (30-fold) over the highly homologous T-cell protein tyrosine phosphatase, and good cellular activity in COS-7 cells.

Animals↗
PubMed2001

Structural versatility of oxalamide-based compounds: a computational study on the isomerization of the oxalamide group and the structural preferences of the polyoxalamides.

The conformational properties of the oxalamide group and crystal structure of several polyoxalamides have been investigated by computational methods. First, a detailed quantum mechanical study of the conformational preferences of N,N'-dimethyloxalamide is reported. Results, which were obtained at the MP2/6-31G(d) level, provide not only the minimum energy conformations but also a description of the energetics and structural changes associated to the isomerization process of the oxalamide group. These quantum mechanical results together with those obtained from additional calculations have been used to develop a set of force-field parameters for the oxalamide group. Molecular mechanics calculations have been performed to test the parameters and to provide new information in terms of energy contributions about the isomerization of the oxalamide group. On the other hand, the new set of parameters has been used to investigate the structural preferences of polyoxalamides (-[NH-CO-CO-NH-(CH(2))(n)]-) by PCSP calculations. Results indicated that polyoxalamides with an even number of methylene groups adopt a structure with one hydrogen bonding direction, whereas polymers with an odd number of methylene groups prefer a structure with two hydrogen bonding directions. The latter crystal structure is completely different from that observed in conventional polyamides and has been investigated in detail through Monte Carlo simulations.

Crystallization↗
PubMedDate not supplied

[Monomers for oligonucleotide synthesis with linkers carrying reactive residues: I. Synthesis of deoxynucleoside derivatives with methoxyoxalamide groups in heterocyclic bases].

A number of monomers for the standard phosphoamidite oligodeoxynucleotide synthesis that carry reactive methoxyoxalamide groups attached to the thymidine, 2'-deoxycytidine, and 2'-deoxyadenosine heterocyclic bases were prepared. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 3; see also http://www.maik.ru.

Amides↗
PubMedDate not supplied

[Monomers for oligonucleotide synthesis with linkers carrying reactive residues: II. Synthesis of phosphoamidites based of uridine and cytosine and containing a linker with methoxyoxalamide groups in position 2'].

A convenient preparative synthesis of 2'-amino-2'-deoxyuridine was developed. Starting from 2'-amino-2'-deoxyuridine and 2'-amino-2'-deoxycytidine, monomers for the phosphoamidite oligonucleotide synthesis were obtained that carry a linker with methoxyoxalamide groups in position 2'. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 3; see also http://www.maik.ru.

Amides↗
PubMed1998

Effects of lodoxamide, disodium cromoglycate and fluorometholone on tear leukotriene levels in vernal keratoconjunctivitis.

PURPOSE: We compared tear leukotriene B4 (LTB4) and leukotriene C4 (LTC4) levels of vernal keratoconjunctivitis (VKC) patients with those of age-matched controls and evaluated the effects of disodium cromoglycate (DCG) 2%, lodoxamide 0.1% and fluorometholone 0.1% on the tear LTB4 and LTC4 levels of the VKC patients. METHODS: Thirty VKC patients were divided into three groups and their tear LTB4 and LTC4 levels measured with an enzyme-linked immunoassay technique before and after treatment with either lodoxamide 0.1%, DCG 2% or fluorometholone 0.1%. The results were compared with the tear LTB4 and LTC4 levels of 10 healthy control subjects. During this trial period, clinical scores for signs and symptoms of VKC were also evaluated. RESULTS: In the VKC patients median tear LTB4 and LTC4 levels were 349.0 pg/ml (range 213.3-707.7 pg/ml) and 225.2 pg/ml (range 196.1-241.1 pg/ml) respectively--significantly higher than the control group (p = 0.0065 for LTB4 and p = 0.0003 for LTC4). After treatment, LTB4 levels decreased significantly in all treatment groups when compared with baseline (for the lodoxamide group, p = 0.01; for the DCG group, p = 0.008; for the fluorometholone group, p = 0.045). LTC4 levels were also significantly reduced after treatment in all three treatment groups (for the lodoxamide group, p = 0.0209; for the DCG group, p = 0.0284; for the fluorometholone group, p = 0.0109). CONCLUSIONS: Tear LTB4 and LTC4 levels are significantly higher in VKC patients than controls, which points to a possible role of lipoxygenase pathway products in the pathophysiology of ocular allergic disorders. Lodoxamide 0.1%, DCG 2% and fluorometholone 0.1% were all effective in reducing LTB4 and LTC4 levels in VKC.

Adolescent↗
PubMed2001

Relationships between inhibition constants, inhibitor concentrations for 50% inhibition and types of inhibition: new ways of analysing data.

The concentration of an inhibitor that decreases the rate of an enzyme-catalysed reaction by 50%, symbolized i(0.5), is often used in pharmacological studies to characterize inhibitors. It can be estimated from the common inhibition plots used in biochemistry by means of the fact that the extrapolated inhibitor concentration at which the rate becomes infinite is equal to -i(0.5). This method is, in principle, more accurate than comparing the rates at various different inhibitor concentrations, and inferring the value of i(0.5) by interpolation. Its reciprocal, 1/i(0.5), is linearly dependent on v(0)/V, the uninhibited rate divided by the limiting rate, and the extrapolated value of v(0)/V at which 1/i(0.5) is zero allows the type of inhibition to be characterized: this value is 1 if the inhibition is strictly competitive; greater than 1 if the inhibition is mixed with a predominantly competitive component; infinite (i.e. 1/i(0.5) does not vary with v(0)/V) if the inhibition is pure non-competitive (i.e. mixed with competitive and uncompetitive components equal); negative if the inhibition is mixed with a predominantly uncompetitive component; and zero if it is strictly uncompetitive. The type of analysis proposed has been tested experimentally by examining inhibition of lactate dehydrogenase by oxalate (an uncompetitive inhibitor with respect to pyruvate) and oxamate (a competitive inhibitor with respect to pyruvate), and of cytosolic malate dehydrogenase by hydroxymalonate (a mixed inhibitor with respect to oxaloacetate). In all cases there is excellent agreement between theory and experiment.

Animals↗
PubMed1975

Dogfish M4 lactate dehydrogenase: reversible inactivation by pyridoxal 5'-phosphate and complete protection in complexes that mimic the active ternary complex.

Dogfish M4 lactate dehydrogenase, like the corresponding pig enzyme, is inactivated by pyridoxal 5'-phosphate through modification of a single essential lysine residue. The activity is completely protected in the complexes E-NAD+-oxalate, E-NADH-oxamate and E-(NAD+-pyruvate adduct), but only partially protected in E-NAD+, E-NADH, E-NAD+-oxamate and E-NADH-oxalate.

Animals↗
PubMed1978

Affinity chromatography of bacterial lactate dehydrogenases.

The affinity system used was the immobilized oxamate derivative previously used to purify mammalian lactate dehydrogenases. The bacterial dehydrogenases specific for the L-stereoisomer of lactate behaved in the same way as the mammalian enzymes, binding strongly in the presence of NADH. The D-lactate-specific enzymes, however, did not show any biospecific affinity for this gel. The L-specific enzymes could be purified to homogeneity in one affinity-chromatographic step. The D-specific enzymes could be efficiently separated from the L-specific ones and could then be further purified on an immobilized NAD derivative. The mechanism of activation of the lactate dehydrogenase from Streptococcus faecalis by fructose 1,6-bisphosphate was investigated by using the immobilized oxamate gel.

Bacteria↗
PubMed1978

Isolation of human lactate dehydrogenase isoenzyme X by affinity chromatography.

Human isoenzyme LDH-X (lactate dehydrogenase isoenzyme X) was isolated from seminal fluid of frozen semen samples by affinity chromatography by using oxamate-Sepharose and AMP-Sepharose. In the presence of 1.6 mM-NAD+, isoenzyme LDH-X does not bind to AMP-Sepharose, whereas the other lactate dehydrogenase isoenzymes do. This is the crucial point in the isolation of isoenzyme LDH-X from the other isoenzymes. The purified human isoenzyme LDH-X had a specific activity of 146 units/mg of protein.

Adenosine Monophosphate↗
PubMed1982

Slow structural changes shown by the 3-nitrotyrosine-237 residue in pig heart [Tyr(3NO2)237] lactate dehydrogenase.

1. The pKa of the phenolic hydroxy group of the Tyr(3NO2)-237 residue in pig heart [Tyr(3NO2)237]lactate dehydrogenase is 7.2 in the apoenzyme, 7.4 in the enzyme-NADH complex and 7.8 in the enzyme-NADH-oxamate complex. The alkaline shift from apoenzyme to ternary complex is ascribed to the approach of the Glu-107 residue during the movement of the polypeptide loop residues 98-110. 2. The affinities of the nitrated enzyme for NADH and for oxamate (in the presence of NADH) are slightly less than those of the native enzyme. The turnover number for the nitrated enzyme in the pyruvate-to-lactate direction is about 0.75 of the value for the native enzyme. 3. Temperature-jump relaxation experiments of the enzyme saturated with NADH but fractionally saturated with oxamate are interpreted to show that the pKa of the nitrotyrosine residue responds to a protein rearrangement after oxamate binds to the binary enzyme-NADH complex. 4. Transient-kinetic experiments show the environment of the Tyr(3NO2)-237 residue in the enzyme-NADH-pyruvate complex of the steady state to be similar to that in the enzyme-NADH-oxamate inhibitor complex.

Animals↗
PubMed1991

Pyruvate carboxylase catalysis of phosphate transfer between carbamoyl phosphate and ADP.

In a reaction that is analogous to the phosphorylation of ADP from carboxyphosphate, pyruvate carboxylase catalyses the formation of ATP from carbamoyl phosphate and ADP at a rate that is about 0.3% of the pyruvate-carboxylation reaction and about 3% of the full reverse reaction. Acetyl-CoA stimulates the phosphorylation of ADP from carbamoyl phosphate but is not an essential requirement of the reaction. Mg2+ also stimulates the reaction, and in the range of Mg2+ concentrations considered the effect of V is much larger in the absence of acetyl-CoA than in its presence. Acetyl-CoA and Mg2+ may be acting in a co-operative way to stimulate the phosphorylation of ADP in a similar way to their effects on the pyruvate-carboxylation reaction. The phosphorylation of ADP by carbamoyl phosphate is also stimulated by the presence of biotin in the part of the active site where this reaction occurs, but again it is not absolutely required for the reaction to proceed. The pH profiles of the phosphorylation of ADP by carbamoyl phosphate indicate that there are at least two ionizable residues involved in the reaction, one of which probably has a role in the release of carbamate from the active site.

Acetyl Coenzyme A↗
PubMed1998

Antimicrobial effect of tetramethyldithiooxamide and its application as a biocide.

Tetramethyldithiooxamide (TMDTOA) is a stable and effective inhibitor of metal corrosion. The antimicrobial effects of TMDTOA and its metal compounds were investigated with regard to their use as biocides for water treatment. Growth of a variety of strains of bacteria and yeasts was completely inhibited at 400 mumol l-1 TMDTOA or its metal complexes. At 100 mg l-1 there was a 99.99% reduction in the number of viable micro-organisms; this activity persisted for 1-3 months. TMDTOA can be produced cheaply at 98% purity by a novel method, representing an alternative cost-effective water treatment agent combining corrosion-inhibiting and biocide characteristics.

Colony Count, Microbial↗
PubMed2002

X-ray structure of pyruvate formate-lyase in complex with pyruvate and CoA. How the enzyme uses the Cys-418 thiyl radical for pyruvate cleavage.

The glycyl radical enzyme pyruvate formate-lyase (PFL) synthesizes acetyl-CoA and formate from pyruvate and CoA. With the crystal structure of the non-radical form of PFL in complex with its two substrates, we have trapped the moment prior to pyruvate cleavage. The structure reveals how the active site aligns the scissile bond of pyruvate for radical attack, prevents non-radical side reactions of the pyruvate, and confines radical migration. The structure shows CoA in a syn conformation awaiting pyruvate cleavage. By changing to an anti conformation, without affecting the adenine binding mode of CoA, the thiol of CoA could pick up the acetyl group resulting from pyruvate cleavage.

Acetyltransferases↗
PubMed1998

Effect of lodoxamide on tear leukotriene levels in giant papillary conjunctivitis associated with ocular prosthesis.

Leukotrienes have been shown to play a role in the pathogenesis of ocular inflammatory and allergic reactions like vernal keratoconjunctivitis and contact lens-associated giant papillary conjunctivitis. This study was designed to determine leukotriene B4 (LTB4) and leukotriene C4 (LTC4) levels in the tears of patients with ocular prosthesis-associated giant papillary conjunctivitis (OP-GPC) and to evaluate the effects of lodoxamide 0.1% on tear LTB4 and LTC4 levels of OP-GPC patients. Tear LTB4 and LTC4 levels were determined by an ELISA technique in the tears of ten OP-GPC patients before and after treatment with lodoxamide 0.1% for one month. The results were compared with that of ten healthy control subjects. The mean tear LTB4 and LTC4 levels of the OP-GPC patients were significantly higher than those of the control group. After treatment with lodoxamide 0.1%, tear LTB4 and LTC4 levels of the OP-GPC patients decreased significantly. This is the first report of elevated LTB4 and LTC4 levels in tears of OP-GPC patients and it points to the possible role of leukotrienes in the immunopathogenesis of OP-GPC. The results also indicate that lodoxamide 0.1%, a mast cell membrane stabilizer, is effective in significantly reducing tear LTB4 and LTC4 levels in OP-GPC patients.

Adolescent↗