A bacterial acetyltransferase capable of regioselective N-acetylation of antibiotics and histones

The Salmonella enterica chromosomally encoded AAC(6')-Iy has been shown to confer broad aminoglycoside resistance in strains in which the structural gene is expressed. The three-dimensional structures reported place the enzyme in the large Gcn5-related N-acetyltransferase (GNAT) superfamily. The structure of the CoA-ribostamycin ternary complex allows us to propose a chemical mechanism for the reaction, and comparison with the Mycobacterium tuberculosis AAC(2')-CoA-ribostamycin complex allows us to define how regioselectivity of acetylation is achieved. The AAC(6')-Iy dimer is most structurally similar to the Saccharomyces cerevisiae Hpa2-encoded histone acetyltransferase. We demonstrate that AAC(6')-Iy catalyzes both acetyl-CoA-dependent self-alpha-N-acetylation and acetylation of eukaryotic histone proteins and the human histone H3 N-terminal peptide. These structural and catalytic similarities lead us to propose that chromosomally encoded bacterial acetyltransferases, including those functionally identified as aminoglycoside acetyltransferases, are the evolutionary progenitors of the eukaryotic histone acetyltransferases.     

Divergent function in the crotonase superfamily: an anhydride intermediate in the reaction catalyzed by 3-hydroxyisobutyryl-CoA hydrolase

3-Hydroxyisobutyryl-CoA hydrolase (HICH), a member of the enoyl-CoA (crotonase) superfamily, catalyzes the hydrolysis of 3-hydroxyisobutyryl-CoA to 3-hydroxyisobutyrate. Like other members of the superfamily, the sequence of HICH contains conserved sequences for an oxyanion hole that stabilizes anionic intermediates. In contrast to most members of the superfamily, the reaction catalyzed by HICH does not proceed via formation of a thioester enolate anion; instead, evidence based on substrate deuterium isotope effects, the reactivity of substrate analogues that cannot form thioester enolate anions, single-turnover experiments in H218O, and the kinetic phenotypes of site-directed mutants provide evidence for a mechanism involving the formation of an anhydride intermediate involving Glu143 in the active site. In the reactions catalyzed by many members of the superfamily, homologues of Glu143 abstract the alpha proton of the thioester substrate to generate the thioester enolate anion intermediate. Presumably, one or more of the anionic tetrahedral intermediates on the HICH reaction coordinate are stabilized by the oxyanion hole. Thus, we conclude that the conserved oxyanion hole in this superfamily can be used to stabilize a variety of anionic intermediates.     

Targeted Histone Peptides: Insights into the Spatial Regulation of the Methyltransferase PRC2 by using a Surrogate of Heterotypic Chromatin

Eukaryotic genomes are dynamically regulated through a host of epigenetic stimuli. The substrate for these epigenetic transactions, chromatin, is a polymer of nucleosome building blocks. In native chromatin, each nucleosome can differ from its neighbors as a result of covalent modifications to both the DNA and the histone packaging proteins. The heterotypic nature of chromatin presents a formidable obstacle to biochemical studies seeking to understand the role of context on epigenetic regulation. A chemical approach to the production of heterotypic chromatin that can be used in such studies is introduced. This method involves the attachment of a user‐defined modified histone peptide to a designated nucleosome within the polymer by using a peptide nucleic acid (PNA) targeting compound. This strategy was applied to dissect the effect of chromatin context on the activity of the histone methyltransferase PRC2. The results show that PRC2 can be stimulated to produce histone H3 methylation from a defined nucleation site.     

Screening for inhibitors of histone deacetylase by incorporating a spraying method to micro-arrayed compound screening

We have developed a method of spraying assay reagents onto a target gel in the Micro-Arrayed Compound Screening ( micro ARCS) format. After application of target gels to compound sheets, subsequent reagents can be applied by spraying onto the target gel. The spraying method conserves on assay reagents by up to 10-fold, eliminates the need for casting additional agarose gels, and increases the throughput of a screen by 3-fold. To demonstrate the efficacy of applying the spraying method to micro ARCS, we screened over 600,000 compounds for inhibitors of histone deacetylase (HDAC). Commercially available HDAC substrate and reaction developer were sprayed directly onto the gel to initiate the reaction and to amplify the signal, respectively. Picks in the primary screen were retested at a density of 384 compounds per sheet in the micro ARCS format. IC(50) values for active compounds were confirmed in a 96-well plate assay. The screen identified several small molecule inhibitors of the enzyme, including members of several classes of known HDAC inhibitors. The combination of the high-density format of micro ARCS, the efficiency of the spraying method, and a timed sequence of adding assay reagents permitted a screening throughput of 200,000 tests an hour. We present the details of the screening format and the analysis of the hits from the screen.     

Quantitation by fast-atom bombardment mass spectrometry: assay of cytidine 3',5'-cyclic monophosphate-responsive protein kinase.

A protein kinase, stimulated by cytidine 3',5'-cyclic monophosphate, is conventionally assayed by monitoring the incorporation of radiolabelled phosphate from adenosine triphosphate into a histone substrate. Here the assay of the protein kinase is carried out by positive-ion fast-atom bombardment mass spectrometric analysis of the enzyme incubation mixture after the reaction has been terminated. The data so obtained show good agreement with data obtained by the conventional radiometric assay: the intrinsic advantage of the mass spectrometric assay is the capacity for multiple component monitoring; the ability of the kinase to bind competing cyclic nucleotides together with integral adenosine triphosphatase (ATPase) and phosphodiesterase activity can also be assessed.     

Gold Nanoparticle Based Fluorescence Resonance Energy Transfer Immunoassay for the Detection of the Histone Deacetylase Activity using a Fluorescent Peptide Probe

A novel platform for detection of histone deacetylase (HDAC) activity has been developed using a gold nanoparticle based fluorescence resonance energy transfer (FRET) immunoassay. This strategy combined the acetylated fluorescent peptide probe with the anti-acetyl antibody functionalized Au NPs to measure the deacetylation activity of histone deacetylase sirtuin2. Enzymatic deacetylation of the acetylated peptide substrate was detected by a gold nanoparticle labeled anti-acetyl peptide antibody with the formation of the immunocomplex resulting in energy transfer between the fluorescent dyes and the nanoparticles. Due to the highly efficient fluorescence quenching of the gold nanoparticles, the proposed method shows a low background and favorable sensitivity. In addition, this approach can be applied to the evaluation of HDAC inhibitor activity. The proposed platform should facilitate the development of new assays for HDAC activity and other histone modifications.     

Characterization of yeast histone H3-specific type B histone acetyltransferases identifies an <Emphasis Type="Italic">ADA2</Emphasis>-independent Gcn5p activity

Background  

The acetylation of the core histone NH₂-terminal tails is catalyzed by histone acetyltransferases. Histone acetyltransferases can be classified into two distinct groups (type A and B) on the basis of cellular localization and substrate specificity. Type B histone acetyltransferases, originally defined as cytoplasmic enzymes that acetylate free histones, have been proposed to play a role in the assembly of chromatin through the acetylation of newly synthesized histones H3 and H4. To date, the only type B histone acetyltransferase activities identified are specific for histone H4.     

A fluorescence-based supramolecular tandem assay for monitoring lysine methyltransferase activity in homogeneous solution

The demand for practical and convenient enzyme assays for histone lysine methyltransferases (HKMTs) emerges along with the rapid development of this young class of enzymes. A supramolecular reporter pair composed of p-sulfonatocalix[4]arene (CX4) and the fluorescent dye lucigenin (LCG) has been used to monitor enzymatic trimethylation of lysine residues in peptide substrates. The assay affords a switch-ON fluorescence response and operates in a continuous, real-time, and label-free fashion. The underlying working principle relies on the higher affinity of the macrocycle towards the trimethylated product of the enzymatic reaction as compared to the substrate, which allows the assay to be carried out in the product-selective mode. The final product incorporates a trimethylammonium moiety, a known high-affinity binding motif for CX4. Two substrates corresponding to the H3 N-terminal tail, namely, S2 (RTKQTARKSTGGKAP) and S6 (QTARKSTGGS), were selected as model compounds for methylation with the Neurospora crassa Dim-5 enzyme and investigated by the newly developed supramolecular tandem HKMTs assay. Only the longer substrate S2 underwent methylation in solution. The potential of the assay for inhibitor screening was demonstrated by means of inhibition studies with 1,10-phenanthroline to afford an inhibition constant of (70±20)?μM.     

Azalysine analogues as probes for protein lysine deacetylation and demethylation

Reversible lysine acetylation and methylation regulate the function of a wide variety of proteins, including histones. Here, we have synthesized azalysine-containing peptides in acetylated and unacetylated forms as chemical probes of the histone deacetylases (HDAC8, Sir2Tm, and SIRT1) and the histone demethylase, LSD1. We have shown that the acetyl-azalysine modification is a fairly efficient substrate for the sirtuins, but a weaker substrate for HDAC8, a classical HDAC. In addition to deacetylation by sirtuins, the acetyl-azalysine analogue generates a novel ADP-ribose adduct that was characterized by mass spectrometry, Western blot analysis, and nuclear magnetic resonance spectroscopy. This peptide-ADP-ribose adduct is proposed to correspond to a derailed reaction intermediate, providing unique evidence for the direct 2'-hydroxyl attack on the O-alkylimidate intermediate that is formed in the course of sirtuin catalyzed deacetylation. An unacetylated azalysine-containing H3 peptide proved to be a potent inhibitor of the LSD1 demethylase, forming an FAD adduct characteristic of previously reported related structures, providing a new chemical probe for mechanistic analysis.     

Determination of enzyme/substrate specificity constants using a multiple substrate ESI-MS assay

The traditional method used to investigate the reaction specificity of an enzyme with different substrates is to perform individual kinetic measurements. In this case, a series of varied concentrations are required to study each substrate and a non-regression analysis program is used several times to obtain all the specificity constants for comparison. To avoid the large amount of experimental materials, long analysis time, and redundant data processing procedures involved in the traditional method, we have developed a novel strategy for rapid determination of enzyme substrate specificity using one reaction system containing multiple competing substrates. In this multiplex assay method, the electrospray ionization mass spectrometry (ESI-MS) technique was used for simultaneous quantification of multiple products and a steady-state kinetics model was established for efficient specificity constant calculation. The system investigated was the bacterial sulfotransferase NodH (NodST), which is a host specific nod gene product that catalyzes the sulfate group transfer from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to natural Nod factors or synthetic chitooligosaccharides. Herein, the reaction specificity of NodST for four chitooligosaccharide acceptor substrates of different chain length (chitobiose, chitotriose, chitotetraose, and chitopentaose) was determined by both individual kinetic measurements and the new multiplex ESI-MS assay. The results obtained from the two methods were compared and found to be consistent. The multiplex ESI-MS assay is an accurate and valid method for substrate specificity evaluation, in which multiple substrates can be evaluated in one assay.     

Application of molecular absorption properties of horseradish peroxidase for self-indicating enzymatic interactions and analytical methods

In this paper an in depth study is presented of the use of the horseradish peroxidase (HRP) enzyme as a self-indicating biorecognition reagent in UV-vis molecular absorption spectrometry. The HRP/H2O2 reaction mechanism in the absence of an external substrate has been clarified, and the interaction between HRP and glucose oxidase (GOx) has been studied. It has been demonstrated that GOx can act as a substrate of HRP; in both cases the kinetic constants have been obtained and mathematical models have been developed. Second, the HRP/H2O2 reaction is used to follow a H2O2-producing enzymatic reaction, the glucose reaction with GOx being used as a model. As an application of this, two methodologies have been proposed for glucose determination: with or without previous incubation of glucose with GOx. In both cases mathematical models relating HRP absorbance changes to glucose concentration have been developed and tested; both methods have been optimized, analytically characterized, and tested for glucose determination in samples. The methodology described could be applied to other heme-proteins and to other H2O2-producing enzymatic reactions. The models permit the reaction constants to be calculated. From the analytical chemistry point of view the models allow the prediction of the method sensitivity for other analytes involved in this type of reaction if the kinetic constants are known and can be used in the design of optical sensors.     

BZ类双催化及非催化化学振荡反应

本文报道以香草醛(以OA表示)为底物的双催化振荡反应以及以2,7-二羟基萘二酚(以DN表示)为有机底物的非催化振荡反应,对二类不同体系的振荡反应机理作了初步的探索。实验部分1.试剂和仪器实验中的反应物均采用分析纯,所有溶液均在去离子水中制备,测定时主要采用PXS-215型离子活度计,XWT-台式自动平衡记录仪。2.实验方法使用超级恒温槽,控制在所需温度下进行反应,以溴离子选择性电极测量并记录反应过程中电位随时间的变化来反映[Br~-]的变化,以Hg|Hg_2SO_4|K_2SO_4为参比电极,振荡现象也可以用HP8451紫外可见分光光度计测定特定波长的吸光率变化进行观察。     

Voltammetric determination of alkaline phosphatase and horseradish peroxidase activity using 3-indoxyl phosphate as substrate Application to enzyme immunoassay

The use of 3-indoxyl phosphate (3-IP) as an electrochemical substrate for ELISAs with voltammetric detection was investigated. Indirect measurements of alkaline phosphatase (AP) and horseradish peroxidase (HRP) activity in solution were carried out. Picomolar levels of both enzymes can be detected, which enables the design of electrochemical immunoassays using this substrate. The enzymatic turnover of the substrate gives indigo blue, insoluble in aqueous solutions. This product is easily converted into its soluble parent compound, indigo carmine (IC), by addition of fuming sulphuric acid to the reaction media. IC shows a reversible voltammetric peak at the formal potential of −0.15 V (versus Ag pseudo-reference electrode) when a screen-printed carbon electrode (SPCE) is used. The peak current of this process constitutes the analytical signal. Using this approach an ELISA assay to quantify pneumolysin (PLY, a toxin related to respiratory infections) was carried out using AP or HRP as enzymatic label. Calibration plots obtained are reported. 3-IP is demonstrated to be the first suitable substrate for the two most common enzyme labels used in immunoassays.     

化学镀镍诱发过程的研究 I:金属催化活性的鉴别和反应机理

Electroless plating is known to be an autocatalytic process. For the reaction to start, the substrate metall should be either catalytic or activated by a suitable catalyst. For example, steel and nickel can be plated directly, but in the case of copper or brass, catalytic metal inducing is need. In this paper, the catalytic activity of different metals and their inducing effects were in vestigated by measuring stationary potentials nd stationary potential-time curves. Experimental results showed: (1) The stationary potential of metal provides a simple parameter to estimate the catalytic activity of metals in electroless nickeling. When 1-hydroxyethylidenediphosphonic acid (HEDP) aelectroless nickeling bath containing NaH2PO2 as reducing agent is used, electrolessnickeling may proceed spontaneously, if the stationary potential of metal is more nagative than -0.60V, no matter whether nickel (autocatalytic active) or other metals(non-autocatalytic active) is used as substrate. (2)When an autocatalytic meta is in contact with the substrate metal in the bath, a sudden decrease of stationary potential is observed. The whole inducing process could be finished within 0.5-2 sec. (3) The stationary potential of electroless nickeling coating in HEDP bath at 80`C is-0.72V, consequently nickel coating itself is a catalytic active metal. Once an electroless nickeling coating is deposited on a substrate metal, electroless nickeling reaction can then proceed continuously. (4) The sufficient conditions of electroless nickeling in HEDP bath containing NaH2PO2 are that the stationary potential of substrate metal must be more nagative than -0.60V and that the temperature of electroless nickeling bath should be higher than 50`C. (5) Inducing mechanism of electroless nickeling can be explained with chemical cell consisting of substrate metal and catalytic metal. Electrons from catalytic metal would suddenly decrease the stationary potential of substrate metal, H+ and Ni2+ complex ion would be reduced on the substrate me     

Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations

We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents promiscuous activity as a diesterase. The analysis of our simulations, carried out by means of molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, shows that the reaction takes place through a D(N)A(N) or dissociative mechanism, the same mechanism employed by AP in the hydrolysis of monoesters. The promiscuous activity observed in this superfamily can be then explained on the basis of a conserved reaction mechanism. According to our simulations the specialization in the hydrolysis of phosphomonoesters or phosphodiesters, developed in different members of the superfamily, is a consequence of the interactions established between the protein and the oxygen atoms of the phosphate group and, in particular, with the oxygen atom that bears the additional alkyl group when the substrate is a diester. A water molecule, belonging to the coordination shell of the Mg(2+) ion, and residue Lys328 seem to play decisive roles stabilizing a phosphomonoester substrate, but the latter contributes to increase the energy barrier for the hydrolysis of phosphodiesters. Then, mutations affecting the nature or positioning of Lys328 lead to an increased diesterase activity in AP. Finally, the capacity of this enzymatic family to catalyze the reaction of phosphoesters having different leaving groups, or substrate promiscuity, is explained by the ability of the enzyme to stabilize different charge distributions in the leaving group using different interactions involving either one of the zinc centers or residues placed on the outer side of the catalytic site.     

Dual Nickel(II)/Mechanoredox Catalysis: Mechanical-Force-Driven Aryl-Amination Reactions Using Ball Milling and Piezoelectric Materials

The combination of a nickel(II) catalyst and a mechanoredox catalyst under ball-milling conditions promotes mechanical-force-driven C−N cross-coupling reactions. In this nickel(II)/mechanoredox cocatalyst system, the modulation of the oxidation state of the nickel center, induced by piezoelectricity, is used to facilitate a highly efficient aryl-amination reaction, which is characterized by a broad substrate scope, an inexpensive combination of catalysts (NiBr₂ and BaTiO₃), short reaction times, and an almost negligible quantity of solvents. Moreover, this reaction can be readily up-scaled to the multi-gram scale, and all synthetic operations can be carried out under atmospheric conditions without the need for complicated reaction setups. Furthermore, this force-induced system is suitable for excitation-energy-accepting molecules and poorly soluble polyaromatic substrates that are incompatible with solution-based nickel(II)/photoredox cocatalysts.     

Capillary electrophoresis with laser-induced fluorescence detection as a tool for enzyme characterization and inhibitor screening.

An effective, rapid and economical CE/LIF (capillary electrophoresis/laser-induced fluorescence) method was developed and applied to the characterization of signal peptidase (SPase) enzyme, which is a target for the screening of new drug candidates. In this method, CE separates the product from the substrate and LIF selectively detects the fluorescence-labeled product and substrate. By measuring the increase of the product as a function of time, one can monitor the progression of the enzyme reaction. The progression curves were also used for screening inhibitors for this enzyme. The effects of various reaction conditions were also studied and discussed. In addition, this CE/LIF method was applied to the determination of the enzyme activity, the quality control of the substrate and/or enzymes, and the cross-reactivity of inhibitors to the enzyme. It can be concluded that this method is suitable for high throughput screening (HTS) assays because it can deliver fast, sensitive, quantitative, and reliable results.     

Reverse proteolysis promoted by in situ generated peptide ester fragments

In this contribution we describe a general synthesis concept for the in situ preparation of protease specific reactants using methyl thioesters as universal precursors. The precursor esters are readily available by standard synthesis procedures and can be used directly as reactants for protease-mediated peptide coupling reactions. Alternatively, they can serve as initial building blocks for the in situ preparation of various types of substrate mimetics. The synthesis of the latter is achieved by a one-pot spontaneous transthioesterification reaction of the parent thioester (Y-(Xaa)(n)-SMe-->Y-(Xaa)(n)-SR; R: CH(2)CH(2)COOH, CH(2)C(6)H(5), C(6)H(4)NHC(:NH)NH(2)), which proceeds efficiently in both a sequential manner and parallel to the subsequent enzymatic reaction. The resulting substrate mimetics act as efficient acyl donor components and show the typical behavior of substrate mimicry enabling irreversible reactions with originally nonspecific acyl moieties. Neither a workup of the substrate mimetic intermediate nor changes of the reaction conditions during the whole synthesis process are required. Model peptide syntheses using trypsin, alpha-chymotrypsin, and V8 protease as the biocatalysts proved the function of the approach and illustrated its synthetic value for protease-mediated reactions and the compatibility of the approach with state-of-the-art solid-phase peptide ester synthesis methods.     

Preparation of CoNi high surface area porous foams by substrate controlled electrodeposition

We demonstrate that nanofabrication of 3D dendritic CoNi alloy foams with an open porous structure can be achieved by electrodeposition onto a single-crystalline Cu(111) substrate at ambient conditions. The very low wettability of this substrate caused by its low surface energy allows tailoring the CoNi deposit morphology. This is concluded from a comparison of polycrystalline Cu substrates with single-crystalline ones of different orientations. The advantages of the present CoNi alloy foams are low internal stresses and good mechanical stability on the substrate. In a second step, by comparing the catalytic properties of the achieved foam with those of CoNi layers obtained on polycrystalline Cu substrates, it is shown that the morphology of the CoNi layers has a decisive influence on the kinetics of the surface redox reaction. The higher reaction rate makes the open foam suitable as catalyst for oxygen evolution in electrolysers. The reversibility of the redox process provides great potential for the achieved porous layers to be used as positive material in alkaline batteries.     

A new method to evaluate the unfolding activity of chaperone unit ClpA based on Fe-S cluster disruption

ATP-dependent proteases unfold their substrates and then refold (via chaperone activity) or degrade (via protease activity) them. The proteases choose between these two activities by selecting their substrates; however, little is known about their substrate selection mechanism. The present study attempts to clarify this mechanism by investigating the role of the Escherichia coli (E. coli) ATP-dependent protease ClpAP. To address this, a reaction system that can measure both chaperone and protease activities simultaneously must be constructed. However, the chaperone activities cannot be evaluated in the presence of protease units. Green fluorescent protein (GFP) is usually used as a model substrate of ClpAP; the fluorescence decrease reflects the degradation of substrates. However, it is difficult to evaluate the chaperone activity of ClpAP using this system, because it cannot distinguish between intact and refolded substrates. Therefore, it is necessary to evaluate the exact unfolding activity while avoiding restoration of substrate spectroscopic characteristics due to chaperone activity. In this study, E. coli Ferredoxin (Fd) was used as a new model substrate for ClpAP to evaluate its unfolding activity. Intact and refolded substrates may be distinguished by the existence of an Fd Fe-S cluster. To verify this hypothesis, the absorption spectrum of Fd complexed with ClpA, the chaperone unit of ClpAP, was measured. A decrease in two peaks derived from the Fe-S cluster was observed, indicating that the Fe-S cluster of Fd was disrupted by the ClpA chaperone. This reaction system should prove useful to evaluate the exact unfolding activity of ATP-dependent proteases.