The nature of phosphate residue binding in the phosphorylated form of succinyl-CoA-synthetase from pigeon breast muscle

The hydrolytic stability of phosphorylated pigeon breast muscle succinyl-CoA synthetase within a wide pH range was studied. It was found that within complex I the phosphate-protein bond is hydrolyzed at alkaline values of pH (11.0 and 13.0); at acidic pH values this bond is hydrolyzed by 50%. Within complex II the phosphate-protein bond is hydrolyzed at acidic pH values and is stable at alkaline pH values. The reaction of the phosphorylated enzyme with hydroxylamine and diisopropylfluorophosphate results in protein dephosphorylation by 50%. Ion-exchange chromatography of the radioactive phosphorylated enzyme II alkaline hydrolyzate (3 n NaOH, 3 hours, 100 degrees C) revealed that the radioactivity was distributed between 1-N-, 3-N-phosphohistidine and 1.3-N-diphosphohistidine fractions. The experimental results suggest that in the phosphorylated enzyme I phosphate is bound to the protein to form an acyl phosphate and phosphoester bonds, while in the phosphorylated enzyme II phosphate binding to the protein occurs with the formation of phosphoamide bonds.     

DNA-duplexes with phosphoamide bond: interaction with restriction endonucleases EcoRII and SsoII

We studied the interaction of EcoRII and SsoII restriction endonucleases with synthetic DNA duplexes, containing 3'N----5'P and 3'P----5'N phosphoamide internucleotide bonds in one of the cleavage points. Enzymatic hydrolysis of the modified strand of the duplexes is blocked in all cases. The presence of phosphoamide bonds was found to reduce the rate of cleavage of the natural strand by EcoRII and to have no influence in case of SsoII. Properties of the EcoRII endonuclease complex with its substrate, containing non-cleavable 3'N----5'P internucleotide bonds in each cleavage point, were examined. In the presence of Mg2+ ions the equilibrium association constant of the enzyme-substrate complex is 3-fold reduced, and the dissociation rate constant of the complex is increased by 1.5 times.     

Oligonucleotides and Nucleotide-Peptides. LIV. The Synthesis and Hydrolytic Properties of Adenylyl-(5′→N∊)-lysylpeptides — Model Compounds of the AMP-RNA Ligase Covalent Complex

Abstract

RNA ligase active center model compounds-adenylyl-(5′N_?)-lysylpeptides were synthesized. The stability of these compounds in aqueous solutions was studied and it was shown, that the carboxyl group of lysine and glutamic acid or hydroxyl group of threonine have no effect upon the hydrolytic mechanism of the adenylyl-(5′N_?)-lysylpeptides. This led to conclusion, that the hydrolysis of the AMP-RNA ligase complex is dependant upon other amino acid functional groups, which may be located next to the phosphoamide center, as a result of tertiary protein structure.     

Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments. V. Study of single-strand cleavages.

Concatemer DNA duplexes which contain at the EcoRII restriction endonuclease cleavage sites (formula; see text) phosphodiester, phosphoamide or pyrophosphate internucleotide bonds have been synthesized. It has been shown that this enzyme did not cleave the substrate at phosphoamide bond. EcoRII endonuclease catalyzes single-strand cleavages both in dA- and dT-containing strands of the recognition site if the cleavage of the other strand has been blocked by modification of scissile bond or if the other strand has been cleaved. This enzyme interacts with both strands of the DNA recognition site, each of them being cleaved independently on the cleavage of another one. Nucleotide sequences flanking the EcoRII site on both sides are necessary for effective cleavage of the substrate.     

Stereochemistry of nucleic acids and polynucleotides. VI. Minimum energy conformations of dimethyl phosphate

As part of a study on the conformation of polynucleotides and nucleic acids the preferred conformations of the model conpound dimethyl phosphate are worked out using potential energy functions. In calculating the total potential energy associated with the conformation, nonbonded, torsional, and electrostatic terms have been considered. The variation of the total conformational energy is represented as a function of two torsion angles ? and ψ which are the rotations about the two phosphoester bonds. The most stable conformations are found to be the gauche–gauche conformations about these bonds. The conformations observed for phosphodiesters in the solid state and in the proposed structures of polynucleotides and nucleic acids cluster around the minimum. Also, regions of minimum energy correspond well with the typical allowed regions of a representative dinucleotide.     

Glyoxylate as a Backbone Linkage for a Prebiotic Ancestor of RNA

The origin of the first RNA polymers is central to most current theories for the origin of life. Difficulties associated with the prebiotic formation of RNA have lead to the general consensus that a simpler polymer preceded RNA. However, polymers proposed as possible ancestors to RNA are not much easier to synthesize than RNA itself. One particular problem with the prebiotic synthesis of RNA is the formation of phosphoester bonds in the absence of chemical activation. Here we demonstrate that glyoxylate (the ionized form of glyoxylic acid), a plausible prebiotic molecule, represents a possible ancestor of the phosphate group in modern RNA. Although in low yields (∼ 1%), acetals are formed from glyoxylate and nucleosides under neutral conditions, provided that metal ions are present (e.g., Mg²⁺), and provided that water is removed by evaporation at moderate temperatures (e.g., 65 ^∘C), i.e. under “drying conditions”. Such acetals are termed ga-dinucleotides and possess a linkage that is analogous to the backbone in RNA in both structure and electrostatic charge. Additionally, an energy-minimized model of a gaRNA duplex predicts a helical structure similar to that of A-form RNA. We propose that glyoxylate-acetal linkages would have had certain advantages over phosphate linkages for early self-replicating polymers, but that the distinct functional properties of phosphoester and phosphodiester bonds would have eventually lead to the replacement of glyoxylate by phosphate.     

The trigonal-bipyramidal NO4 ligand set in biologically relevant vanadium compounds and their inorganic models

In the present focused review, vanadate-dependent haloperoxidases and vanadate-inhibited enzymes which catalyze the hydrolysis of phosphoester bonds are addressed. In these systems, vanadate [H_xVO₄]^(3−x)− is covalently coordinated to the imidazolyl moiety of an active site histidine, with a geometrical arrangement close to a trigonal bipyramid. The resulting ligand set, NO₄, and ligand arrangement provide peroxidase activity to the haloperoxidases and, to a certain extent, also to vanadate-inhibited phosphatases. The haloperoxidases are responsible for the oxidative halogenation of a variety of organic substrates. They are also active in other oxidation reactions relying on peroxide as the oxidant, such as the oxidative cyclizations of terpenes and, specifically, the oxygenation of (prochiral) sulfides to (chiral) sulfoxides. These functions can be modeled by vanadium complexes. Attracted interest is paid to {V(NO₄)} complexes that are functional and structural models of the peroxidases. In the vanadate-inhibited phosphatases – structural analogs of the transition state in phosphoester hydrolysis by the native enzymes – the position of the axial histidine can also be taken by cysteinate or serinate, a fact which has implications for the insulin-mimetic potential of vanadate.     

Intermediate products of the RNA-ligase reaction]

The first and the third steps of the RNA-ligase reaction were studied. It was shown that the first step of the reaction consists in a formation of an enzyme-adenylate complex. The optimal conditions for this formation were established. Effects of acids, alkali, hydroxylamine and snake venom phosphodiesterase on the complex suggest that the linkage between the protein and adenylic acid may be of a phosphoester or phosphoamide type. Using synthetic adenylic acid pyrophosphates and mononucleotides (oligonucleotides) the RNA-ligase reaction was shown to involve intermediate pyrophosphates. It was found that the simplest pyrophosphates capable to bind to oligonucleotides in the absence of ATP are adenylic acid pyrophosphates, both of ribo- and deoxyribomononucleotides. The RNA-ligase reaction may be used for elongation of oligonucleotides by one definite mononucleotide or for incorporation of the label into the 3'-end of the polynucleotide chain.     

A comparative study on phosphotransferase activity of acid phosphatases from Raoultella planticola and Enterobacter aerogenes on nucleosides,sugars, and related compounds

Natural and modified nucleoside-5′-monophosphates and their precursors are valuable compounds widely used in biochemical studies. Bacterial nonspecific acid phosphatases (NSAPs) are a group of enzymes involved in the hydrolysis of phosphoester bonds, and some of them exhibit phosphotransferase activity. NSAP containing Enterobacter aerogenes and Raoultella planticola whole cells were evaluated in the phosphorylation of a wide range of nucleosides and nucleoside precursors using pyrophosphate as phosphate donor. To increase the productivity of the process, we developed two genetically modified strains of Escherichia coli which overexpressed NSAPs of E. aerogenes and R. planticola. These new recombinant microorganisms (E. coli BL21 pET22b-phoEa and E. coli BL21 pET22b-phoRp) showed higher activity than the corresponding wild-type strains. Reductions in the reaction times from 21 h to 60 min, from 4 h to 15 min, and from 24 h to 40 min in cases of dihydroxyacetone, inosine, and fludarabine, respectively, were obtained.     

A comparative study of the O-3 reactivity of isomeric N-dimethylmaleoyl-protected d-glucosamine and d-allosamine acceptors

Four isomeric N-dimethylmaleoyl 4,6-O-benzylidene-protected d-hexosamine acceptors (2, 3, 4, and 5) with all possible configurations at C-1 and C-3 (e.g., derived from d-glucosamine and d-allosamine) were prepared, and the assessment of their O-3 relative reactivity through competition experiments using the known per-O-acetylated d-galactopyranosyl trichloroacetimidate donor (15) was then carried out. The reactivities are in the order 4 ? 2 > 5 > 3. The analysis of the NMR spectra of 2–5 at different temperature and modeling experiments carried out on analogs of 2–5 (DFT) and on the acceptors themselves (MM) are coincident, and have helped to establish the stability of the different hydrogen bonds, and of the conformers which carry them. The whole results suggest that the electronic effects (hydrogen bonds) are required to explain the observed trend, in spite of the axial conformation of the most reactive hydroxyl group. The steric effects appear only when hydrogen bonds are weak.     

The role of hydrophobic /hydrophilic balance in the activity of structurally flexible vs. rigid cytolytic polypeptides and analogs developed on their basis

ABSTRACT

Introduction: Being important representatives of various proteomes, membrane-active cationic peptides (CPs) are attractive objects as lead compounds in the design of new antibacterial, anticancer, antifungal, and antiviral molecules. Numerous CPs are found in insect and snake venoms, where many of them reveal cytolytic properties. Due to advances in omics technologies, the number of such peptides is growing dramatically.

Areas covered: To understand structure–function relationships for CPs in a living cell, detailed analysis of their hydrophobic/hydrophilic properties is indispensable. We consider two structural classes of membrane-active CPs: latarcins (Ltc) from spider and cardiotoxins (CTXs) from snake venoms. While the former are void off disulfide bonds and conformationally flexible, the latter are structurally rigid and cross-linked with disulfide bonds. In order to elucidate structure–activity relationships behind their antibacterial, anticancer, and hemolytic effects, the properties of these polypeptides are considered on a side-by-side basis.

Expert commentary: An ever-increasing number of venom-derived membrane-active polypeptides require new methods for identification of their functional propensities and sequence-based design of novel pharmacological substances. We address these issues considering a number of the designed peptides, based either on Ltc or CTX sequences. Experimental and computer modeling techniques required for these purposes are delineated.     

The use of <Superscript>1</Superscript>H–<Superscript>31</Superscript>P GHMBC and covariance NMR to unambiguously determine phosphate ester linkages in complex polysaccharide mixtures

Poly- and oligo-saccharides are commonly employed as antigens in many vaccines. These antigens contain phosphoester structural elements that are crucial to the antigenicity, and hence the effectiveness of the vaccine. Nuclear Magnetic Resonance (NMR) is a powerful tool for the site-specific identification of phosphoesters in saccharides. We describe here two advances in the characterization of phosphoesters in saccharides: (1) the use of ¹H–³¹P GHMBC to determine the site-specific identity of phosphoester moieties in heterogeneous mixtures and (2) the use of Unsymmetrical/Generalized Indirect Covariance (U/GIC) to calculate a carbon-phosphorus 2D spectrum. The sensitivity of the ¹H–³¹P GHMBC is far greater than the “standard” ¹H–³¹P GHSQC and allows long-range ^3–5J_HP couplings to be readily detected. This is the first example to be reported of using U/GIC to calculate a carbon-phosphorus spectrum. The U/GIC processing affords, in many cases, a fivefold to tenfold or greater increase in signal-to-noise ratios in the calculated spectrum. When coupled with the high sensitivity of ¹H–³¹P HMBC, U/GIC processing allows the complete and unambiguous assignments of phosphoester moieties present in heterogeneous samples at levels of ~5% (or less) of the total sample, expanding the breadth of samples that NMR can be used to analyze. This new analytical technique is generally applicable to any NMR-observable phosphoester.     

About a Formamide-Based Origin of Informational Polymers: Syntheses of Nucleobases and Favourable Thermodynamic Niches for Early Polymers

Formamide NH₂CHO chemistry provides a unitary frame into which several pieces of the origin-of-life puzzle may be adjusted. Synthetic processes were uncovered which, starting from formamide and prebiotically easily available common catalysts, yield all the necessary nucleic bases precursors, including acyclonucleosides. Formamide allows phosphorylations and trans-phosphorylations, favours the micellar aggregation of surfactants and, most importantly, determines conditions in which the formation of nucleic polymers is thermodynamically favoured. In the detected conditions, the phosphoester bonds are more stable in the polymeric than in the monomeric form, thus allowing formation and survival of informational nucleic polymers. Presented at: National Workshop on Astrobiology: Search for Life in the Solar System, Capri, Italy, 26 to 28 October, 2005.     

Conserved sequence pattern in a wide variety of phosphoesterases.

A unique sequence pattern, designated the GD/GNH signature, was shown to be conserved in a wide variety of phosphoesterases. The enzymes containing this signature cleave phosphoester bonds in such different substrates as (1) phosphoserine and phosphothreonine in polypeptides; (2) bis(5'-nucleosidyl)-tetraphosphates; (3) nucleoside 5' phosphates; (4) 2',3'-cyclic nucleotide phosphates; (5) polynucleotides; (6) 2'-5' phosphodiesters in RNA (intron) lariats; (7) sphingomyelin; and (7) various phosphomonoesters. Two conserved acidic amino acid residues and a conserved histidine residue may be directly involved in phosphoester bond cleavage.     

Occurrence of a cyclic AMP-dependent protein kinase on the outer surface of rat epididymal spermatozoa.

Endogenous protein kinase activity was detected on the outer surface of rat cauda epididymal spermatozoa. The kinase activity of the intact sperm cells catalyses the transfer of the terminal phosphate of exogenous [γ³²-P] ATP to the alkali labile phosphoester bonds of exogenous calf thymus histones. There was little uptake of [γ³²-P] ATP and phosphorylation of endogenous proteins by intact spermatozoa. The amount of histones phosphorylated by the peripherial kinase is directly proportional to the sperm numbers and the reaction is linear for approx. 5 min. Cyclic AMP (2.5 μM) activates the kinase (approx. 120%) and also causes the release of the enzyme from spermatozoa into the medium. Approx. 80% of the peripherial kinase activity is released after 30 seconds of incubation of spermatozoa.     

In vivo phosphorylation of neurofilament proteins in the central nervous system of immature rat and rabbit

Neurofilament proteins from brain and spinal cord of immature rat (20–35 days of age) and rabbit (15–17 days of age) were prepared by an axonal flotation technique. Examination of rat filament preparations by electron microscopy revealed a preponderance of 10 nm diameter filaments that were usually loosely aggregated although some bundles of more tightly packed filaments were present as well. The neurofilament triplet proteins of the rat and rabbit central nervous system were found to be phosphorylated 24 hr after the intracerebral injection of [³²P]orthophosphate when examined by sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by fluorography. Examination of each eluted neurofilament protein from both species showed that [³²P]phosphate was retained after reelectrophoresis and fluorography. Evidence is presented that the [³²P] phosphate is covalently linked to the purified neurofilament proteins by phosphoester bonds.     

Evidence for the presence of chromatin-bound deoxyribonucleic acid phosphatase-exonuclease in Yoshida sarcoma ascites cells

An enzyme which cleaves the phosphoester bond of 3′-phosphoryl termini of DNA was isolated and purified from the chromatin of Yoshida sarcoma cells. The DNA phosphatase is specific for only 3′-phosphorylated DNA with a lesser activity for its single stranded form. Phosphoester bonds of various nucleotides, 3′-phosphorylated RNA and 5′-phosphorylated DNA were not hydrolysed by the enzyme. The DNA phosphatase required 10 mM MgCl₂, and was inactivated by 70 % with 1 mM ?-chloromercuribenzoate and completely by heat treatment at 70° for 5 min. Furthermore, an exonuclease activity could not be separated from the purified DNA phosphatase.     

Synthesis of Novel DNA Analoues Containing Aminomethylphosphonate Internucleoside Linkages

Abstract

Modified oligodeoxyribounucleotides with asminomethylphonate bonds between nucleoside residues were prepared and investigated for their hybridization properties toward DNA and RNA.     

有机磷农药降解酶及其基因工程研究进展

有机磷农药是国内外使用最广泛的农药之一,为农业丰收做出了很大贡献。但是,有机磷农药具有抑制人体乙酰胆碱酯酶的功能,对人存在着程度不同的毒性。有机磷农药降解酶可降解有机磷农药分子,破坏有机磷农药的磷酯键而使其脱毒。综述了有机磷农药降解酶及其特性,以及相关基因的分离克隆和基因工程研究进展。