Structure and function of the energy-converting system of mitochondria

The main energy source for all endergonic processes occurring in living organisms is the phosphate bond energy of nucleoside triphosphates, especially adenosine triphosphate (ATP). In aerobic organisms, as for instance in mammals, more than 90% of ATP is formed during the process called oxidative phosphorylation. In this process, similar to that of muscle contraction and nerve excitation, nature works with vectorial processes taking place at a membrane separating distinct spaces from each other. The present article deals with the operation of a set of water-insoluble membrane proteins and enzymes vectorially transporting electrons, protons and other ions, which finally leads to the formation of ATP. This machinery transforming substrate oxidation energy into chemical energy in the form of the phosphoric anhydride bond of ATP operates with a very high efficiency. The structure and function of the machinery of mitochondrial oxidative phosphorylation are described. It consists of the electron transfer chain, the ATP-synthetase, the adenine nucleotide translocase and the phosphate carrier. The electron transfer chain can be resolved into multiprotein complexes—at three of them energy conversion takes place—and into the electron carriers ubiquinone and cytochrome c. The substrate oxidation energy is converted into the chemical energy of ATP with an electrochemical proton gradient as intermediary form. The energetic aspects of the processes are analyzed by linear irreversible thermodynamics. Great success has been gained during the past few years on the structural characterization of the participating proteins. The function of the various systems is partially elucidated on the molecular level; this concerns especially the mechanism of proton and adenine nucleotide translocation, as well as ATP formation.     

Synthesis of 5'-methylthio coformycins: specific inhibitors for malarial adenosine deaminase

Transition state theory suggests that enzymatic rate acceleration (kcat/knon) is related to the stabilization of the transition state for a given reaction. Chemically stable analogues of a transition state complex are predicted to convert catalytic energy into binding energy. Because transition state stabilization is a function of catalytic efficiency, differences in substrate specificity can be exploited in the design of tight-binding transition state analogue inhibitors. Coformycin and 2'-deoxycoformycin are natural product transition state analogue inhibitors of adenosine deaminases (ADAs). These compounds mimic the tetrahedral geometry of the ADA transition state and bind with picomolar dissociation constants to enzymes from bovine, human, and protozoan sources. The purine salvage pathway in malaria parasites is unique in that Plasmodium falciparum ADA (PfADA) catalyzes the deamination of both adenosine and 5'-methylthioadenosine. In contrast, neither human adenosine deaminase (HsADA) nor the bovine enzyme (BtADA) can deaminate 5'-methylthioadenosine. 5'-Methylthiocoformycin and 5'-methylthio-2'-deoxycoformycin were synthesized to be specific transition state mimics of the P. falciparum enzyme. These analogues inhibited PfADA with dissociation constants of 430 and 790 pM, respectively. Remarkably, they gave no detectable inhibition of the human and bovine enzymes. Adenosine deamination is involved in the essential pathway of purine salvage in P. falciparum, and prior studies have shown that inhibition of purine salvage results in parasite death. Inhibitors of HsADA are known to be toxic to humans, and the availability of parasite-specific ADA inhibitors may prevent this side-effect. The potent and P. falciparum-specific inhibitors described here have potential for development as antimalarials without inhibition of host ADA.     

光亲和标记磷脂酸类似物的合成

合成了光敏基团位于sn-1脂肪酰基上的光亲和标记磷脂酸(PA)类似物,选用了有较高C-H插入效率的全氟苯基叠氮化合物作为光敏基团.用酶化学方法在PA类似物中引入了同位素标记³³P.初步实验表明,合成的PA类似物与天然PA一样对cAMP-磷酸二酯酶有激活作用,提示合成的PA类似物可进一步用于该酶的光亲和标记.     

基于阳离子型共轭聚合物与酶底物探针的磷酸酯酶检测新方法

建立了一种基于阳离子型共轭聚合物与酶底物探针的磷酸酯酶检测新方法. 阳离子型共轭聚合物通过静电吸引与荧光素修饰的带负电荷的三磷酸腺苷结合, 并发生荧光能量共振转移; 当加入磷酸酯酶时, 它可以催化底物三磷酸腺苷上的磷酸酯基团逐渐水解, 得到不带电荷的腺苷, 从而使阳离子型共轭聚合物得以释放, 能量转移效率下降. 实验结果表明, 能量转移效率下降的程度与酶的浓度相关. 该方法操作简单, 响应速度快, 灵敏度高, 易于扩展至其它能催化底物电荷密度变化的酶的检测, 而且还有望应用于对酶具有抑制作用的药物分子的筛选.     

The Aryne Phosphate Reaction**

Condensed phosphates are a critically important class of molecules in biochemistry. Non-natural analogues are important for various applications, such as single-molecule real-time DNA sequencing. Often, such analogues contain more than three phosphate units in their oligophosphate chain. Consequently, investigations into phosphate reactivity enabling new ways of phosphate functionalization and oligophosphorylation are essential. Here, we scrutinize the potential of phosphates to act as arynophiles, paving the way for follow-up oligophosphorylation reactions. The aryne phosphate reaction is a powerful tool to—depending on the perspective—(oligo)phosphorylate arenes or arylate (oligo-cyclo)phosphates. Based on Kobayashi-type o-silylaryltriflates, the aryne phosphate reaction enables rapid entry into a broad spectrum of arylated products, like monophosphates, diphosphates, phosphodiesters and polyphosphates. The synthetic potential of these new transformations is demonstrated by efficient syntheses of nucleotide analogues and an unprecedented one-flask octaphosphorylation.     

Europium tetracycline as a luminescent probe for nucleoside phosphates and its application to the determination of kinase activity

The determination of enzyme activities and the screening of enzyme regulators is a major task in clinical chemistry and drug development. A broad variety of enzymatic reactions is associated with the consumption of adenosine triphosphate (ATP), including, in particular, phosphorylation reactions catalyzed by kinases, formation of adenosine cyclic monophosphate (cAMP) by adenylate cyclases, and ATP decomposition by ATPase. We have studied the effect of a series of adenosine (ATP, ADP, AMP, cAMP) and guanosine (GTP, GDP) phosphoric esters, and of pyrophosphate (PP) on the fluorescence emission of the europium tetracycline (EuTC) complex. We found that these compounds have strongly different quenching effects on the luminescence emission of EuTC. The triphosphates ATP and GTP behave as strong quenchers in reducing the fluorescence intensity of EuTC to 25 % of its initial value by formation of a ternary 1:1:1 complex. All other phosphate esters showed a weak quenching effect only. The applicability of this fluorescent probe to the determination of the activity of phosphorylation enzymes is demonstrated by means of creatine kinase as a model for non-membrane-bound kinases. In contrast to other methods, this approach does not require the use of radioactively labeled ATP substrates, additional enzymes, or of rather complex immunoassays.     

焦测序技术及其在遗传分析中的应用

焦测序技术是一种新的实时DNA测序技术。它在DNA聚合酶、三磷酸腺苷硫酸化酶、荧光素酶和三磷酸腺苷双磷酸酶4种酶的协同作用下,使引物延伸聚合脱氧核糖核酸(dNTP)释放焦磷酸盐(PP i)、PP i转换三磷酸腺苷(ATP)、ATP产生荧光信号与dNTP和ATP的降解等化学反应偶联起来,检测结果准确可靠。本文综述了焦测序技术的基本原理、操作步骤和它在单核苷酸多态性(SNP)研究、微生物的分型鉴定和基因甲基化检测等遗传分析中的应用,并对焦测序技术的发展作了展望。     

Application of phosphonate and thiophosphate analogues of nucleotides to studies of some enzyme reactions

The enzymatic cleavage of a scissile P O bond can be blocked by recourse to phosphonate analogues of biological phosphate esters. α-Fluorophosphonates have an enhanced electronegativity at the bridging carbon, which, in many cases, makes them superior to simple methylene phosphonates for the study of enzyme reactions. Thus, the β,γ-difluoro-methylene analogue of ATP is a good substrate for the interferon-induced (2→5)A_n synthetase, which converts it into a (2→5)A₄ species having a 5′-β,γ-difluoromethylenetriphosphate. This binds strongly to RNase L but does not activate it. The unsymmetrical Ap₄Aases from Artemia and Lupin are strongly inhibited by P^1,P⁴-dithiophosphate analogues of diadenosyl-5′,5‴-P¹,P⁴-tetraphosphate although nonregiospecific cleavage of certain P²,P³-methylene analogues can be observed. Some of these analogues are remarkably effective inhibitors of platelet aggregation and are effective inhibitors in vivo of arterial blood-clotting in rabbits. Separation of all diastereoisomers of P¹,P⁴-dithiophosphate analogues of Ap₄A is achieved cleanly using reverse-phase hplc chromatography and this provides direct access to β,γ-CHF-bridged analogues of ATP with resolved stereochemistry at the CHF center. Lastly, growing cells of Dictyostelium discoideum not only tolerate a range of substituted methylene bisphosphonates in their growth medium but actually incorporate them into nucleotide analogues of ATP and Ap₄A.     

Magnesium isotope effects in enzymatic phosphorylation

Recent discovery of magnesium isotope effect in the rate of enzymatic synthesis of adenosine triphosphate (ATP) offers a new insight into the mechanochemistry of enzymes as the molecular machines. The activity of phosphorylating enzymes (ATP-synthase, phosphocreatine, and phosphoglycerate kinases) in which Mg(2+) ion has a magnetic isotopic nucleus 25Mg was found to be 2-3 times higher than that of enzymes in which Mg(2+) ion has spinless, nonmagnetic isotopic nuclei 24Mg or 26Mg. This isotope effect demonstrates unambiguously that the ATP synthesis is a spin-dependent ion-radical process. The reaction schemes, suggested to explain the effect, imply a reversible electron transfer from the terminal phosphate anion of ADP to Mg(2+) ion as a first step, generating ion-radical pair with singlet and triplet spin states. The yields of ATP along the singlet and triplet channels are controlled by hyperfine coupling of unpaired electron in 25Mg+ ion with magnetic nucleus 25Mg. There is no difference in the ATP yield for enzymes with 24Mg and 26Mg; it gives evidence that in this reaction magnetic isotope effect (MIE) operates rather than classical, mass-dependent one. Similar effects have been also found for the pyruvate kinase. Magnetic field dependence of enzymatic phosphorylation is in agreement with suggested ion-radical mechanism.     

Emissive Synthetic Cofactors: Enzymatic Interconversions of tzA Analogues of ATP,NAD+, NADH,NADP+, and NADPH

A series of enzymatic transformations, which generate visibly emissive isofunctional cofactors based on an isothiazolo[4,3‐d]pyrimidine analogue of adenosine ( ^tz A ), was developed. Nicotinamide adenylyl transferase condenses nicotinamide mononucleotide and ^tz ATP to yield N^tzAD⁺ , which can be enzymatically phosphorylated by NAD⁺ kinase and ATP or ^tz ATP to the corresponding N^tzADP⁺ . The latter can be engaged in NADP‐specific coupled enzymatic transformations involving conversion to N^tzADPH by glucose‐6‐phosphate dehydrogenase and reoxidation to N^tzADP⁺ by glutathione reductase. The N^tzADP⁺ / N^tzADPH cycle can be monitored in real time by fluorescence spectroscopy.     

Matrix-assisted laser desorption/ionization mass spectrometry with re-engineered 2,5-dihydroxybenzoic acid derivative

Dihydroxybenzoic acid was modified to three analogues (M2, M4 and M6). The analogues exhibited specific properties that resulted in enhancement of analyte signal intensity with or without addition of iodine compared to the underivatized parent. Addition of iodine to M2, an ester of dihydroxybenzoic acid that had a terminal double bond in the alkyl chain, resulted in peak intensities comparable to the parent, indicating that iodine interaction across the double bond resulted in enhancement although the exact mechanism is not fully understood. No enhancement on addition of iodine was observed for M4, which had a long alkyl chain that contained no double bonds. The alkyl chain allowed micelle formation in solution, which in turn allowed more uniform analyte-to-matrix mixing. The final analogue combined the long alkyl chain of M4 with the double bond of M2 and exhibited either similar peak intensities to that of dihydroxybenzoic acid or better. Micelle formation in solution was examined using spectroscopy and in the solid by reflective microscopy. The standard deviation from spot to spot was considerably lower relative to dihydroxybenzoic acid (RSD 3.4%vs. 14.2%). Unlike dihydroxybenzoic acid, the novel matrix M6 was able to yield characteristic peaks for analytes such as ubiquitin.     

Multidentate Europium Chelates as Luminoionophores for Anion Recognition: Impact of Ligand Design on Sensitivity and Selectivity,and Applicability to Enzymatic Assays

The design of photoluminescent molecular probes for the selective recognition of anions is a major challenge for the development of optical chemical sensors. The reversible binding of anions to lanthanide centers is one promising option for the realization of anion sensors, because it leads in some cases to a strong luminescence increase by the replacement of quenching water molecules. Yet, it is an open problem to gain control of the sensitivity and selectivity of the luminescence response. Primarily, the selective detection of (poly)phosphate species such as nucleotides has emerged as a demanding task, because they are involved in many biological processes and enzymatic reactions. We designed a series of pyridyl‐based multidentate europium complexes (seven‐, six‐, and five‐dentate) including sensitizing chromophores and studied their luminescence intensity and lifetime responses to different (poly)phosphates (adenosine triphosphate (ATP), adenosine diphosphate (ADP), adenosine monophosphate (AMP), cyclic adenosine monophosphate (cAMP), pyrophosphate, and phosphate anions), and carboxyanions (citrate, malate, oxalacetate, succinate, α‐ketoglutarate, pyruvate, oxalate, carbonate). The results reveal that the number of free coordination sites has a significant impact on the sensitivity and selectivity of the response. Because of its reversibility, the lanthanide probes can be applied to monitor the activity of ATP‐consuming enzymes such ATPases and apyrases, which is demonstrated by means of the five‐dentate complex.     

Release of Enzymatically Active Deubiquitinating Enzymes upon Reversible Capture by Disulfide Ubiquitin Reagents

Deubiquitinating enzymes (DUBs) catalyze the cleavage of ubiquitin from target proteins. Ubiquitin is post‐translationally attached to proteins and serves as an important regulatory signal for key cellular processes. In this study, novel activity‐based probes to study DUBs were synthesized that comprise a ubiquitin moiety and a novel disulfide warhead at the C‐terminus. These reagents can bind DUBs covalently by forming a disulfide bridge between the active‐site cysteine residue and the ubiquitin‐based probe. As disulfide bridges can be broken by the addition of a reducing agent, these novel ubiquitin reagents can be used to capture and subsequently release catalytically active DUBs, whereas existing capturing agents bind irreversibly. These novel reagents allow for the study of these enzymes in their active state under various conditions.     

Emissive Synthetic Cofactors: Enzymatic Interconversions of tzA Analogues of ATP,NAD+, NADH,NADP+, and NADPH

A series of enzymatic transformations, which generate visibly emissive isofunctional cofactors based on an isothiazolo[4,3‐d]pyrimidine analogue of adenosine ( ^tz A ), was developed. Nicotinamide adenylyl transferase condenses nicotinamide mononucleotide and ^tz ATP to yield N^tzAD⁺ , which can be enzymatically phosphorylated by NAD⁺ kinase and ATP or ^tz ATP to the corresponding N^tzADP⁺ . The latter can be engaged in NADP‐specific coupled enzymatic transformations involving conversion to N^tzADPH by glucose‐6‐phosphate dehydrogenase and reoxidation to N^tzADP⁺ by glutathione reductase. The N^tzADP⁺ / N^tzADPH cycle can be monitored in real time by fluorescence spectroscopy.     

Isosteres of Natural Phosphates. Methylene and Hydroxyrnethylene Analogues of Tyrosine O-Phosphate

Abstract

The ability of phosphonic acid analogues isosteric with natural phosphate esters to Serve as inhibitors of enzymatic phosphate hydrolysis has been documented in a wide variety of systems.¹ The use of such an analogue in place of the natural phosphate ester provides a functionality which the enzyme may not be able to distinguish from the natural ester, but which is incapable of being hydrolyzed. In some instances the use of hydroxymethylene analogues has resulted in a greater degree of recognition, and resultant inhibition of hydrolytic activity, than the simple methylene analogues.² On this basis, the methylene and hydroxymethylene analogues of tyrosine O-phosphate appear to be reasonable candidates to Serve as inhibitors for phosphoprotein phosphatases and alkaline phosphatase, and as probes for biological mechanisms.     

A simple, high sensitivity mutation screening using Ampligase mediated T7 endonuclease I and Surveyor nuclease with microfluidic capillary electrophoresis

Mutation and polymorphism detection is of increasing importance for a variety of medical applications, including identification of cancer biomarkers and genotyping for inherited genetic disorders. Among various mutation-screening technologies, enzyme mismatch cleavage (EMC) represents a great potential as an ideal scanning method for its simplicity and high efficiency, where the heteroduplex DNAs are recognized and cleaved into DNA fragments by mismatch-recognizing nucleases. Thereby, the enzymatic cleavage activities of the resolving nucleases play a critical role for the EMC sensitivity. In this study, we utilized the unique features of microfluidic capillary electrophoresis and de novo gene synthesis to explore the enzymatic properties of T7 endonuclease I and Surveyor nuclease for EMC. Homoduplex and HE DNAs with specific mismatches at desired positions were synthesized using PCR (polymerase chain reaction) gene synthesis. The effects of nonspecific cleavage, preference of mismatches, exonuclease activity, incubation time, and DNA loading capability were systematically examined. In addition, the utilization of a thermostable DNA ligase for real-time ligase mediation was investigated. Analysis of the experimental results has led to new insights into the enzymatic cleavage activities of T7 endonuclease I and Surveyor nuclease, and aided in optimizing EMC conditions, which enhance the sensitivity and efficiency in screening of unknown DNA variations.     

Spectrofluorimetric Study on the Weak Interaction between ATP and Na-4-Tosyl-L-arginine Methyl Ester Hydrochloride

In this paper, some new results on the selective weak interaction between Na-4-tosyl-L-arginine methyl ester hydrochloride （TAME） and adenosine-5＇-triphosphate （ATP） have been reported. Fluorescence spectrophotometry and Fourier transform infrared （FT-IR） spectroscopy were used to investigate this kind of weak interaction. In fluorescence experiments, obvious fluorescence quenching phenomena were observed when TAME was added, which indicated the weak interactions between TAME and ATP. It has been identified by fluorescence titration experiments that TAME exhibited high selectivity to ATP over ADP and AMP. FT-IR spectral results showed that an ATP-TAME adduct was formed. The experimental results indicated that the interaction sites were the guanidinium group of TAME main-chain and the γ-phosphate group of ATP, and the interaction took place through hydrogen bonding and electrostatic force. In addition, the effects of metal ions on the weak interaction between ATP and TAME, or between ATP and analogues of L-arginine were studied.     

Binding of single nucleotides to H+-ATP synthases observed by fluorescence resonance energy transfer

F(0)F(1)-ATP synthases couple proton translocation with the synthesis of ATP from ADP and phosphate. The enzyme has three catalytic nucleotide binding sites, one on each beta-subunit; three non-catalytic binding sites are located mainly on each alpha-subunit. In order to observe substrate binding to the enzyme, the H(+)-ATP synthase from Escherichia coli was labelled selectively with the fluorescence donor tetramethylrhodamine (TMR) at position T106C of the gamma-subunit. The labelled enzymes were incorporated into liposomes and catalysed proton-driven ATP synthesis. The substrate ATP-Alexa Fluor 647 was used as the fluorescence acceptor to perform intermolecular fluorescence resonance energy transfer (FRET). Single molecules are detected with a confocal set-up. When one ATP-Alexa Fluor 647 binds to the enzyme, FRET can be observed. Five stable states with different intermolecular FRET efficiencies were distinguished for enzyme-bound ATP-Alexa Fluor 647 indicating binding to different binding sites. Consecutive hydrolysis of excess ATP resulted in stepwise changes of the FRET efficiency. Thereby, gamma-subunit movement during catalysis was directly monitored with respect to the binding site with bound ATP-Alexa Fluor 647.     

A Multiple Enzyme Method for Maasurement of K,Na ATPase

Abstract

A multiple enzyme method for spectrophotometrical measurement of K, Na ATPase activity is described. The method includes three enzymatic steps: Hydrolyses of ATP by ATPase, conversion of inosine to hypoxanthine and ribose -1- phosphate by purine nucleoside phosphorylase and finally xanthine oxidase mediated oxidation of hypoxanthine to xanthine with consequent formation of formazan from a tetrazolium salt. The phospholytic cleavage of inosine in the medium is dependent of an ATPase- phosphate complex.     

8-(p-CF3-cinnamyl)-modified purine nucleosides as promising fluorescent probes

Natural nucleotides are not useful as fluorescent probes because of their low quantum yields. Therefore, a common methodology for the detection of RNA and DNA is the application of extrinsic fluorescent dyes coupled to bases in oligonucleotides. To overcome the many limitations from which fluorescent nucleotide-dye conjugates suffer, we have developed novel purine nucleosides with intrinsic fluorescence to be incorporated into oligonucleotide probes. For this purpose we synthesized adenosine and guanosine fluorescent analogues 7-25, conjugated at the C8 position with aryl/heteroaryl moieties either directly, or via alkenyl/alkynyl linkers. Directly conjugated analogues 7-14, exhibited high quantum yields, φ >0.1, and short λ(em) (<385 nm). Alkynyl conjugated analogues 22-25, exhibited low quantum yields, φ <0.075, and λ(em)<385 nm. The alkenyl conjugated analogues 15-21, exhibited λ(em) 408-459 nm. While analogues 15,16, and 20 bearing an EDG on the aryl moiety, exhibited φ <0.02, analogues 17, and 21 with EWG on the aryl moiety, exhibited extremely high quantum yields, φ ≈ 0.8, suggesting better intramolecular charge transfer. We determined the conformation of selected adenosine analogues. Directly conjugated analogue 8 and alkynyl conjugated analogue 22, adapted the syn conformation, whereas alkenyl conjugated analogue 15 adapted the anti conformation. Based on the long emission wavelengths, high quantum yields, anti conformation and base-paring compatibility, we suggest analogues 17 and 21 for further development as fluorescent probes for the sensitive detection of genetic material.