Role of Sulfhydryl Groups in Activating Enzymes. Properties of Escherichia coli Lysine-Transfer Ribonucleic Acid Synthetase*

Effects of Arsenic on Trichloroethene-Dechlorination Activities of Dehalococcoides mccartyi 195

Arsenic and trichloroethene (TCE) are among the most prevalent groundwater contaminants in the United States. Co-contamination of these two compounds has been detected at 63% of current TCE-contaminated National Priorities List sites. When in situ TCE reductive dechlorination is stimulated by the addition of fermentable substrates to generate a reducing environment, the presence of arsenic can be problematic because of the potential for increased mobilization and toxicity caused by the reduction of arsenate [As(V)] to arsenite [As(III)]. This study assesses the effects of arsenic exposure on the TCE-dechlorinating activities of Dehalococcoides mccartyi strain 195. Our results indicate that 9.1 μM As(III) caused a 50% decrease in D. mccartyi cell growth. While As(V) concentrations up to 200 μM did not initially impact TCE dechlorination, inhibition was observed in cultures amended with 200 μM As(V) and 100 μM As(V) in 12 and 17 days, respectively, corresponding with the accumulation of As(III). Transcriptomic and metabolomic analyses were performed to evaluate cellular responses to both As(V) and As(III) stress. Amendment of amino acids enhanced arsenic tolerance of D. mccartyi. Results from this study improve our understanding of potential inhibitions of D. mccartyi metabolism caused by arsenic and can inform the design of bioremediation strategies at co-contaminated sites.

Photoelectron spectroscopy and density functional theory studies of (FeS)mH- (m = 2-4) cluster anions: effects of the single hydrogen

Single hydrogen containing iron hydrosulfide cluster anions (FeS)_mH^- (m = 2-4) are studied by photoelectron spectroscopy (PES) at 3.492 eV (355 nm) and 4.661 eV (266 nm) photon energies, and by Density Functional Theory (DFT) calculations. The structural properties, relative energies of different spin states and isomers, and the first calculated vertical detachment energies (VDEs) of different spin states for these (FeS)_mH^- (m = 2-4) cluster anions are investigated at various reasonable theory levels. Two types of structural isomers are found for these (FeS)_mH^- (m = 2-4) clusters: (1) the single hydrogen atom bonds to a sulfur site (SH-type); and (2) the single hydrogen atom bonds to an iron site (FeH-type). Experimental and theoretical results suggest such available different SH- and FeH-type structural isomers should be considered when evaluating the properties and behavior of these single hydrogen containing iron sulfide clusters in real chemical and biological systems. Compared to their related, respective pure iron sulfur (FeS)_m^- clusters, the first VDE trend of the diverse type (FeS)_mH_0,1^- (m = 1-4) clusters can be understood through (1) the different electron distribution properties of their highest singly occupied molecular orbital employing natural bond orbital analysis (NBO/HSOMO), and (2) the partial charge distribution on the NBO/HSOMO localized sites of each cluster anion. Generally, the properties of the NBO/HSOMOs play the principal role with regard to the physical and chemical properties of all the anions. The change of cluster VDE from low to high is associated with the change in nature of their NBO/HSOMO from a dipole bound and valence electron mixed character, to a valence p orbital on S, to a valence d orbital on Fe, and to a valence p orbital on Fe or an Fe-Fe delocalized valence bonding orbital. For clusters having the same properties for NBO/HSOMOs, the partial charge distributions at the NBO/HSOMO localized sites additionally affect their VDEs: a more negative or less positive localized charge distribution is correlated with a lower first VDE. The single hydrogen in these (FeS)_mH^- (m = 2-4) cluster anions is suggested to affect their first VDEs through the different structure types (SH- or FeH-), the nature of the NBO/HSOMOs at the local site, and the value of partial charge number at the local site of the NBO/HSOMO.

Alteration of methotrexate binding to human serum albumin induced by oxidative stress. Spectroscopic comparative study

Changes of oxidative modified albumin conformation by comparison of non-modified (HSA) and modified (oHSA) human serum albumin absorption spectra, Red Edge Excitation Shift (REES) effect and fluorescence synchronous spectra were investigated. Studies of absorption spectra indicated that changes in the value of absorbance associated with spectral changes in the region from 200 to 250nm involve structural alterations related to variations in peptide backbone conformation. Analysis of the REES effect allowed for the observation of changes caused by oxidation in the region of the hydrophobic pocket containing the tryptophanyl residue. Synchronous fluorescence spectroscopy confirmed changes of the position of the tryptophanyl and tyrosil residues fluorescent band. Effect of oxidative stress on binding of methotrexate (MTX) was investigated by spectrofluorescence, UV-VIS and (1)HNMR spectroscopy. MTX caused the fluorescence quenching of non-modified (HSA) and modified (oHSA) human serum albumin molecule. The values of binding constants, Hill's coefficients and a number of binding sites in the protein molecule in the high affinity binding site were calculated for the binary MTX-HSA and MTX-oHSA systems. For these systems, qualitative analysis in the low affinity binding sites was performed with the use of the (1)HNMR technique.

Spectroscopic analysis of the impact of oxidative stress on the structure of human serum albumin (HSA) in terms of its binding properties

Oxygen metabolism has an important role in the pathogenesis of rheumatoid arthritis (RA). Reactive oxygen species (ROS) are produced in the course of cellular oxidative phosphorylation and by activated phagocytic cells during oxidative bursts, exceed the physiological buffering capacity and result in oxidative stress. ROS result in oxidation of serum albumin, which causes a number of structural changes in the spatial structure, may influence the binding and cause significant drug interactions, particularly in polytherapy. During the oxidation modification of amino acid residues, particularly cysteine and methionine may occur. The aim of the study was to investigate the influence of oxidative stress on human serum albumin (HSA) structure and evaluate of possible alterations in the binding of the drug to oxidized human serum albumin (oHSA). HSA was oxidized by a chloramine-T (CT). CT reacts rapidly with sulfhydryl groups and at pH 7.4 the reaction was monitored by spectroscopic techniques. Modification of free thiol group in the Cys residue in HSA was quantitatively determined by the use of Ellman's reagent. Changes of albumin conformation were examined by comparison of modified (oHSA) and nonmodified human serum albumin (HSA) absorption spectra, emission spectra, red-edge shift (REES) and synchronous spectroscopy. Studies of absorption spectra indicated that changes in the value of absorbance associated with spectral changes in the region of 200-250 nm involve structural alterations in peptide backbone conformation. Synchronous fluorescence spectroscopy technique confirmed changes of position of tryptophanyl and tyrosyl residues fluorescent band caused by CT. Moreover analysis of REES effect allowed to observe structural changes caused by CT in the region of the hydrophobic pocket containing the tryptophanyl residue. Effect of oxidative stress on binding of anti-rheumatic drugs, sulfasalazine (SSZ) and sulindac (SLD) in the high and low affinity binding sites was investigated by spectrofluorescence, ITC and (1)H NMR spectroscopy, respectively. SSZ and SLD change the affinity of each other to the binding site in non- and modified human serum albumin. The presence of SLD causes the increase of association constant (Ka) of SSZ-oHSA system and the strength of binding and the stability of the complexes has been observed while in the presence of SSZ a displacement of SLD from the SLD-HSA has been recorded. The analysis of (1)H NMR spectral parameters i.e. changes of chemical shifts of the drug indicate that the presence of SSZ and SLD have a mutual influence on changes in the affinity of human serum albumin binding site and this competition takes place not only due to the additional drug but also to the oxidation of HSA.

Adenylation enzyme characterization using gamma -(18)O(4)-ATP pyrophosphate exchange

We present here a rapid, highly sensitive nonradioactive assay for adenylation enzyme selectivity determination and characterization. This method measures the isotopic back exchange of unlabeled pyrophosphate into gamma-(18)O(4)-labeled ATP via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS), electrospray ionization liquid chromatography MS, or electrospray ionization liquid chromatography-tandem MS and is demonstrated for both nonribosomal (TycA, ValA) and ribosomal synthetases (TrpRS, LysRS) of known specificity. This low-volume (6 microl) method detects as little as 0.01% (600 fmol) exchange, comparable in sensitivity to previously reported radioactive assays and readily adaptable to kinetics measurements and high throughput analysis of a wide spectrum of synthetases. Finally, a previously uncharacterized A-T didomain from anthramycin biosynthesis in the thermophile S. refuinius was demonstrated to selectively activate 4-methyl-3-hydroxyanthranilic acid at 47 degrees C, providing biochemical evidence for a new aromatic beta-amino acid activating adenylation domain and the first functional analysis of the anthramycin biosynthetic gene cluster.

Lysyl-tRNA synthetase

Lysyl-tRNA synthetase catalyses the formation of lysyl-transfer RNA, Lys-tRNA(Lys), which then is ready to insert lysine into proteins. Lysine is important for proteins since it is one of only two proteinogenic amino acids carrying an alkaline functional group. Seven genes of lysyl-tRNA synthetases have been localized in five organisms, and the nucleotide and the amino acid sequences have been established. The lysyl-tRNA synthetase molecules are of average chain lengths among the aminoacyl-tRNA synthetases, which range from about 300 to 1100 amino acids. Lysyl-tRNA synthetases act as dimers; in eukaryotes they can be localized in multienzyme complexes and can contain carbohydrates or lipids. Lysine tRNA is recognized by lysyl-tRNA synthetase via standard identity elements, namely anticodon region and acceptor stem. The aminoacylation follows the standard two-step mechanism. However the accuracy of selecting lysine against the other amino acids is less than average. The first threedimensional structure of a lysyl-tRNA synthetase worked out very recently, using the enzyme from the Escherichia coli lysU gene which binds one molecule of lysine, is similar to those of other class II synthetases. However, none of the reaction steps catalyzed by the enzyme is clarified to atomic resolution. Thus surprising findings might be possible. Lysyl-tRNA synthetase and its precursors as well as its substrates and products are targets and starting points of many regulation circuits, e.g. in multienzyme complex formation and function, dinucleoside polyphosphate synthesis, heat shock regulation, activation or deactivation by phosphorylation/dephosphorylation, inhibition by amino acid analogs, and generation of antibodies against lysyl-tRNA synthetase. None of these pathways is clarified completely.

A cysteine in the C-terminal region of alanyl-tRNA synthetase is important for aminoacylation activity

Alanyl-tRNA synthetase (AlaRS) from Escherichia coli is a multimeric enzyme that catalyzes the esterification of alanine to tRNA(Ala) in the ATP-dependent aminoacylation reaction. The functional binding of all three substrates follows Michaelis-Menten kinetics. The role of cysteines in this enzyme has been evaluated via modification of these residues with p-(hydroxymercuri)phenylsulfonic acid, monobromobimane, and 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB). The former two reagents induce nearly complete inactivation of AlaRS aminoacylation activity and the release of all tightly bound zinc. In the case of mild DTNB treatment, only two of the six cysteines in AlaRS are modified, with release of all zinc and partial loss of aminoacylation activity. These experiments indicate the importance of one or more cysteines, other than those thought to be coordinated with zinc, in the aminoacylation reaction. Substitution of each of the cysteine residues outside the zinc-binding motif with serine does not disrupt zinc binding. However, the cysteine most removed in primary sequence from the active site (Cys665) is identified as important in the aminoacylation step. Mutation of Cys665 to serine induces a 120-fold decrease in the catalytic efficiency of this enzyme, primarily through a kcat effect, and introduces sigmoidal kinetics (nH = 1.8) with respect to the RNA substrate. The results demonstrate that a simple manipulation in the C-terminal region can introduce positive cooperativity in this otherwise noncooperative enzyme.

The inhibitory effect of Alcide, an antimicrobial drug, on protein synthesis in Escherichia coli

Alcide, a broad-spectrum antimicrobial drug, has been shown to kill a wide range of common pathogenic bacteria as well as fungi, in vitro. This agent consists of Part A and Part B which contain sodium chlorite and lactic acid as the active ingredients, respectively. The mixing of these two parts immediately prior to use results in the formation of chlorine dioxide (ClO2), a potent germicidal compound. Exposure of exponentially growing E. coli cells to Alcide resulted in a rapid inhibition of growth as well as loss of viability. Alcide inhibited DNA, RNA, and protein synthesis; however, RNA and protein synthesis were affected at much lower concentrations. The accumulation of the amino acid analog amino-isobutyric acid into growing cultures of E. coli was only partially impaired by Alcide. Cell-free protein synthesis using an RNA directed system was inhibited by Alcide and this effect was lessened in the presence of mercaptoethanol. Higher concentrations of Alcide (1 mM) oxidized 25% of the methionine to methionine sulfoxide. Aminoacylation of E. coli bulk tRNA was decreased in vitro and the aminoacylation of tRNAfMet was particularly sensitive to Alcide.

Arginyl-tRNA synthetase from Escherichia coli K12. Purification, properties, and sequence of substrate addition

Arginyl-tRNA synthetase from Escherichia coli K12 has been purified more than 1000-fold with a recovery of 17%. The enzyme consists of a single polypeptide chain of about 60 000 molecular weight and has only one cysteine residue which is essential for enzymatic activity. Transfer ribonucleic acid completely protects the enzyme against inactivation by p-hydroxymercuriben zoate. The enzyme catalyzes the esterification of 5000 nmol of arginine to transfer ribonucleic acid in 1 min/mg of protein at 37 degrees C and pH 7.4. One mole of ATP is consumed for each mole of arginyl-tRNA formed. The sequence of substrate binding has been investigated by using initial velocity experiments and dead-end and product inhibition studies. The kinetic patterns are consistent with a random addition of substrates with all steps in rapid equilibrium except for the interconversion of the cental quaternary complexes. The dissociation constants of the different enzyme-substrate complexes and of the complexes with the dead-end inhibitors homoarginine and 8-azido-ATP have been calculated on this basis. Binding of ATP to the enzyme is influenced by tRNA and vice versa.

Histidyl-transfer-ribonucleic-acid synthetase from Salmonella typhimurium. Studies of the sulfhydryl groups

The reactivity of the sulfhydryl groups of histidyl-t RNA synthetase from Salmonella typhimurium and the effect of substrates on the reactivity has been studied using p-hydroxymercuribenzoate and 5, 5'-dithiobis (2-nitrobenzoic acid) as reagents. It has been found that 5, 5'-dithiobis (2-nitrobenzoic acid) titrates only two sulfhydryl groups per molcule of enzyme and the reaction is essenaitlly monophasic, while p-hydroxymercuribenzoate titrates four sulhydryl groups. As observed kinetically the reaction with p-hydroxymercuribenzoate is strongly biphasic, each phase corresponding to about two sulfhydryl groups per enzyme molecule. With both reagents no detectable difference in sulfhydryl group reactivity was observed when ATP, histidine and tRNA specific for histidine were added individually or in combination to the enzyme. The enzyme activity slowly changes after two or four sulhydryl groups are blocked by 5, 5'-dithiobis (2-nitrobenzoic acid) or p-hydroxymercuribenzoate respectively. A new, stable level of activity is reached that is characterized by a different Km value for the aminoacylation reaction. The results indicate that the sulfhydryl groups reacting with the two reagents used here are neither directly involved in the binding of the substrates nor in the catalytic process. The ultimate change in enzyme activity after reaction of the sulfhydryl groups suggests a transition to an alternative enzyme structure.

Studies on the conformational changes of mitochondrial malate dehydrogenase in urea-phosphate solutions

Pig-heart mitochondrial malate dehydrogenase is gradually inactivated in 4 M urea. During the inactivation, sulfhydryl groups on the protein are exposed in a first-order reaction. The reaction is followed spectrophotometricaily using the sulfhydryl reagent, 5,5′-dithiobis(2-nitrobenzoate) (DTNB). Titration with DTNB in the presence of urea exposes 10 to 12 sulfhydryl groups per molecule of mitochondrial malate dehydrogenase. The enzyme is also inactivated when diluted in water but no sulfhydryl groups are unmasked. The loss of activity and the appearance of sulfhydryl groups in urea solutions do not take place at the same rate.The conformational changes of malate dehydrogenase that occur in urea solutions are partially prevented by inorganic phosphate ions, and less so by the substrates NADH, NAD+, oxalacetate (OAA), and L-malate. The protection against loss of enzyme activity by inorganic phosphate ions is pH-dependent. Both inorganic phosphate and NADH considerably reduce the first-order rate constant for sulfhydryl appearance in 4 M urea. Protection of the enzyme against sulfhydryl appearance in urea solutions by pre-incubation with the substrates indicates that about two sulfhydryl groups per molecule of mitochondrial malate dehydrogenase are involved in substrate binding. Thus, the substrates must keep the active site of the enzyme intact. They either bind to the sulfhydryl groups or prevent the protein molecule from completely unfolding.