Sample records for phosphoranes
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Liu, Tingting; Zhao, Lijiao; Zhong, Rugang
2013-02-01
DNA phosphotriester adducts are common alkylation products of DNA phosphodiester moiety induced by N-nitrosoureas. The 2-hydroxyethyl phosphotriester was reported to hydrolyze more rapidly than other alkyl phosphotriesters both in neutral and in alkaline conditions, which can cause DNA single strand scission. In this work, DFT calculations have been employed to map out the four lowest activation free-energy profiles for neutral and alkaline hydrolysis of triethyl phosphate (TEP) and diethyl 2-hydroxyethyl phosphate (DEHEP). All the hydrolysis pathways were illuminated to be stepwise involving an acyclic or cyclic phosphorane intermediate for TEP or DEHEP, respectively. The rate-limiting step for all the hydrolysis reactions was found to be the formation of phosphorane intermediate, with the exception of DEHEP hydrolysis in alkaline conditions that the decomposition process turned out to be the rate-limiting step, owing to the extraordinary low formation barrier of cyclic phosphorane intermediate catalyzed by hydroxide. The rate-limiting barriers obtained for the four reactions are all consistent with the available experimental information concerning the corresponding hydrolysis reactions of phosphotriesters. Our calculations performed on the phosphate triesters hydrolysis predict that the lower formation barriers of cyclic phosphorane intermediates compared to its acyclic counter-part should be the dominant factor governing the hydrolysis rate enhancement of DEHEP relative to TEP both in neutral and in alkaline conditions.
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Ganguly, Abir; Thaplyal, Pallavi; Rosta, Edina; Bevilacqua, Philip C; Hammes-Schiffer, Sharon
2014-01-29
The hepatitis delta virus (HDV) ribozyme catalyzes a self-cleavage reaction using a combination of nucleobase and metal ion catalysis. Both divalent and monovalent ions can catalyze this reaction, although the rate is slower with monovalent ions alone. Herein, we use quantum mechanical/molecular mechanical (QM/MM) free energy simulations to investigate the mechanism of this ribozyme and to elucidate the roles of the catalytic metal ion. With Mg(2+) at the catalytic site, the self-cleavage mechanism is observed to be concerted with a phosphorane-like transition state and a free energy barrier of ∼13 kcal/mol, consistent with free energy barrier values extrapolated from experimental studies. With Na(+) at the catalytic site, the mechanism is observed to be sequential, passing through a phosphorane intermediate, with free energy barriers of 2-4 kcal/mol for both steps; moreover, proton transfer from the exocyclic amine of protonated C75 to the nonbridging oxygen of the scissile phosphate occurs to stabilize the phosphorane intermediate in the sequential mechanism. To explain the slower rate observed experimentally with monovalent ions, we hypothesize that the activation of the O2' nucleophile by deprotonation and orientation is less favorable with Na(+) ions than with Mg(2+) ions. To explore this hypothesis, we experimentally measure the pKa of O2' by kinetic and NMR methods and find it to be lower in the presence of divalent ions rather than only monovalent ions. The combined theoretical and experimental results indicate that the catalytic Mg(2+) ion may play three key roles: assisting in the activation of the O2' nucleophile, acidifying the general acid C75, and stabilizing the nonbridging oxygen to prevent proton transfer to it.
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NASA Astrophysics Data System (ADS)
Schneider, Philipp; Tropper, Peter; Kaindl, Reinhard
2013-04-01
In this study we report P-rich olivine and the tric-calcium phosphate (TCP) stanfieldite in partially molten quartzphyllites from the ritual immolation site at the Goldbichl, near Innsbruck in the Tyrol, Austria. During partial melting, foamy patches of dark glassy material formed at the surface of the rocks and also as layers within the rocks. The pyrometamorphic rocks contain mostly the mineral assemblage olivine + orthopyroxene + plagioclase + spinel + glass. During the investigation of slag samples from this prehistoric ritual immolation site, extremely P-rich, apatite-bearing micro-domains were found. In these domains phosphoran olivine was found whose P contents are approaching the maximum P contents in olivine according to the experimental investigations of Boesenberg and Hewins (Geochim Cosmochim Acta 74:1923-1941, 2010). The textures within these domains indicate strongly disequilibrium conditions. The phosphoran olivines formed due to reactions involving apatite and the mineral assemblage of the quartzphyllites, and coexist with plagioclase and a tri-calcium phosphate phase (TCP) showing stanfieldite Ca4(Mg, Fe2+, Mn2+)5(PO4)6 composition. In terms of its chemical composition, olivine shows a wide range in composition with P ranging from 0.3 to 0.54 a.p.f.u, which corresponds to maximal 23 wt.% P2O5. These are the highest P-contents in olivine reported from rocks so far. The incorporation of P correlates with decreasing Si contents according to the charge balancing scheme 2{{P}^{5+ }}+□{{M}_{1,2 }}=2S{{i}^{4+ }}+{{( {Mg,Fe} )}^{2+ }}{{M}_{1,2 }} . Therefore P can only be incorporated in combination with a vacancy on the M1,2 position. Micro-Raman spectroscopy of phosphoran olivines indicates that these olivines can easily be identified with this method due to the strong signals of the SiO4 and PO4 vibrations. The external vibrations of the M1,2 sites at low wave-numbers are more complex than for P-free olivine. This might be due to the effect of P5+ on the M1 2+ and M2 2+ positions and the formation of vacancies on these sites. Since micro-Raman investigations of the TCP phase yielded no conclusive match with a known Raman spectrum of a phosphate mineral so far, therefore it is most likely that the TCP phase is stanfieldite, whose Raman spectrum has not been obtained yet. Schematical Schreinemakers analysis in the system CaO-Al2O3-FeO-SiO2-P2O5-H2O shows that P-rich olivine (fayalite-sarcopside solid solution) can form from mineral reactions involving chlorite, apatite and quartz and show that the occurrence of P-rich Fe-olivines spans a large T-range but is restricted to domains with high aSiO2. The mineral assemblage in the P-rich micro-domains shows that the formation of phosphoran olivine is not only restricted to the interaction between bone material and rocks in slags from ritual immolation sites as suggested by Tropper et al. (Eur J Mineral 16:631-640, 2004) from the immolation site in Oetz but can form locally due to the pyrometamorphic breakdown of a P-rich accessory precursor phase such as apatite.
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Elsässer, Brigitta; Valiev, Marat; Weare, John H
2009-03-25
The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism. Most of this debate centers around the roles of the conserved residues, structures of the transition state or states, the possibility of a stable intermediate, and the charge and structure of this intermediate. In this communication we report calculations of the mechanism of the hydrolysis step in this reaction using a comprehensive QM/MM theoretical approach that includes a high level calculation of the interactions in the QM region, free energy estimates along an NEB optimized reaction path, and the inclusion of the interaction of the protein surroundings and solvent. Contrary to prior calculations we find a stable pentacoordinated dianionic phosphorane intermediate in the reaction path supporting an A(N)+D(N) reaction mechanism. In the transition state in the path from the reactant to the intermediate state (with barrier of 3.96 kcal/mol and intermediate stability of 2.21 kcal/mol) a proton from the attacking water is partially transferred to the His119 residue and the PO bond only partially formed from the remaining nucleophilic OH(-) species (bond order (BO) 0.11). In passing from the intermediate to the product state (barrier 13.22 kcal/mol) the PO bond on the cyclic phosphorane intermediate is nearly broken (BO 0.28) and the transfer of the proton from the Lys41 is almost complete (Lys41-H BO 0.87). In the product state a proton has been transferred from Lys41 to the O2' position of the sugar. The role of Lys41 as the catalytic acid is a result of the relative positioning of the Lys41 and His12 in the catalytic site. This configuration is supported by calculations and docking studies.
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Stereoselective Syntheses of Soman Analog
1993-04-28
only one pseudorotatomer cycle exists. Surprisingly. la-f are hydrolytically stable in the absence of acid ; phosphorane lb, for example, remained...unchanged in CDCl3 for at least 2 weeks even in the presence of water or 0.1 N NaOH at room temperature. However, la-f are extremely labile to aqueous acids ...1 and 2 are hydrolytically stable in neutral and basic conditions, but extremely labile to aqueous acids : they remained unchanged for at least 3 days
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De Vivo, Marco; Dal Peraro, Matteo; Klein, Michael L.
2009-01-01
Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA·DNA hybrids. This enzyme is implicated in replication initiation and DNA topology restoration and represents a very promising target for anti-HIV drug design. Structural information has been provided by high-resolution crystal structures of the complex RNase H/RNA·DNA from Bacillus halodurans (Bh), which reveals that two metal ions are required for formation of a catalytic active complex. Here, we use classical force field-based and quantum mechanics/molecular mechanics calculations for modeling the nucleotidyl transfer reaction in RNase H, clarifying the role of the metal ions and the nature of the nucleophile (water versus hydroxide ion). During the catalysis, the two metal ions act cooperatively, facilitating nucleophile formation and stabilizing both transition state and leaving group. Importantly, the two Mg2+ metals also support the formation of a meta-stable phosphorane intermediate along the reaction, which resembles the phosphorane intermediate structure obtained only in the debated β-phosphoglucomutase crystal. The nucleophile formation (i.e., water deprotonation) can be achieved in situ, after migration of one proton from the water to the scissile phosphate in the transition state. This proton transfer is actually mediated by solvation water molecules. Due to the highly conserved nature of the enzymatic bimetal motif, these results might also be relevant for structurally similar enzymes belonging to the NT superfamily. PMID:18662000
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Atomistic Details of the Associative Phosphodiester Cleavage in Human Ribonuclease H
DOE Office of Scientific and Technical Information (OSTI.GOV)
Elsasser, Brigitta M.; Fels, Gregor
2010-07-30
During translation of the genetic information of DNA into proteins, mRNA is synthesized by RNA polymerase and after the transcription process degraded by RNase H. The endoribonuclease RNase H is a member of the nucleotidyl-transferase (NT) superfamily and is known to hydrolyze the phosphodiester bonds of RNA which is hybridized to DNA. Retroviral RNase H is part of the viral reverse transcriptase enzyme that is indispensable for the proliferation of retroviruses, such as HIV. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. In our study we investigated the molecular mechanism of RNA cleavage by humanmore » RNase H using a comprehensive high level DFT/B3LYP QM/MM theoretical method for the calculation of the stationary points and nudged elastic band (NEB) and free energy calculations to identify the transition state structures, the rate limiting step and the reaction barrier. Our calculations reveal that the catalytic mechanism proceeds in two steps and that the nature of the nucleophile is a water molecule. In the first step, the water attack on the scissile phosphorous is followed by a proton transfer from the water to the O2P oxygen and a trigonal bipyramidal pentacoordinated phosphorane is formed. Subsequently, in the second step the proton is shuttled to the O30 oxygen to generate the product state. During the reaction mechanism two Mg2+ ions support the formation of a stable associated in-line SN2-type phosphorane intermediate. Our calculated energy barrier of 19.3 kcal mol*1 is in excellent agreement with experimental findings (20.5 kcal mol*1). These results may contribute to the clarification and understanding of the RNase H reaction mechanism and of further enzymes from the RNase family.« less
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EVIDENCE FOR TWO-STAGE MELTING IN THE BRAHIN PALLASITE PARENT BODY
NASA Astrophysics Data System (ADS)
Sonzogni, Y.; Devouard, B.; Provost, A.; Devidal, J.
2009-12-01
We identified two types of melt inclusions in olivine crystals from the Brahin main-group pallasite, similar to those described in [1, 2]. Both types are abundant and coexist within a same olivine grain. The first type are isolated, 1-10 µm large, elongated to tubular, and oriented along the [001] axis of the olivine host (as determined by EBSD). These inclusions are phosphate-rich, typically made of stanfieldite, a bubble, often phosphoran olivine (21-32 wt% P2O5), plus occasional minute phases including metal-sulfide blebs and daubreelite. These isolated inclusions look primary, but microprobe mapping of P revealed the scars of former fractures joining these inclusions. The second type are 2-dimensional arrays of abundant chromite inclusions (<100 µm) and metal-sulfide assemblages (<50 µm). Typical metal-sulfide inclusions contain metal (kamacite and/or taenite ) + troilite + phosphoran olivine (6-24 wt% P2O5) + occasional minute grains of withlockite, shreibersite, daubreelite, and silica. These 2D arrays show the same morphological features that characterize secondary inclusions and healed fractures in olivine xenocrysts and other terrestrial minerals. Discussion: The phosphoran olivines are known in pallasites [3] but to our knowledge it is the first description of this mineral in inclusions. We identify this phase as olivine based on its steochiometry, (Mg,Fe,Ca)4-x(Si1-xPx)2O8, and its structure (as evidenced by EBSD). The value of 32 wt% P2O5 is the highest of all P-rich olivines reported so far [3, 4, 5, 6]. Such high P contents suggest an extended solid solution between olivine and chopinite [7]. Melt inclusions in Brahin seem to record two distinct HT events. According to phase diagrams, a single silicate melt enriched in P might be sufficient to form these phosphate-rich inclusions at T < 1200°C. On the contrary, at least two immiscible melts are required to form the secondary inclusions: a silicate-chromite melt and a metal-sulfide one. The abundance of chromite requires temperatures > ca. 1800°C in order to accommodate Cr in the silicate melt. It seems likely that these secondary inclusions result from a shock that took place while the stony-iron assembly of the Brahin pallasite was already formed. On the other hand, the lack of metal-sulfide associated with the phosphate-rich inclusions may imply that the iron part of the Brahin pallasite was not present when these inclusions were formed. References: [1] Buseck P.R. 1977. Geochimica and Cosmochimica Acta 41:711-740. [2] Koviazin S.V. and Podgornykh N.M. 2006. 37th Lunar and Planetary Science Conference pp. 1235-1236. [3] Buseck P.R. and Clark J. 1984. Mineralogical Magazine 48:229-235. [4] Agrell S.O. et al. 1998. Mineralogical Magazine 62:265-269. [5] Tropper P. et al. 2004. European Journal of Mineralogy 16:631-640. [6] Boesenberg J.S. et al. 2004. 35th Lunar and Planetary Science Conference pp. 1366-1367. [7] Grew E.S. et al. 2007. European Journal of Mineralogy 19:229-245.
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Phosphorus-containing nucleophiles in reactions with polyfluorinated organic compounds
NASA Astrophysics Data System (ADS)
Furin, Georgii G.
1993-03-01
The review presents a compilation of new expelimental data on the reactions of phosphorus-containing nucleophiles [triphenylphosphine, trialkylphosphines, trialkyl phosphites, phosphorus tris(diethylamide), etc.] with perfluorinated olefins and aromatic and heterocyclic compounds, leading to substances both with and without a phosphorus atom. It is shown that the interaction of phosphorus tris(diethylamide) and trialkylphosphines with organic polyfluoro-compounds and perfluoroolefins leads to the formation of phosphoranes, the decomposition of which is accompanied by the generation of aryl and alkenyl anions. The reactions of these anions with C-electrophiles and compounds containing mobile halogen atoms are examined. In addition, the pathways in the Arbuzov reaction involving a series of unsaturated perfluorinated compounds are analysed. Possible applications of these reactions in organic synthesis are demonstrated. The bibliography includes 120 references.
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Medeiros, Michelle; Wanderlind, Eduardo H; Mora, José R; Moreira, Raphaell; Kirby, Anthony J; Nome, Faruk
2013-10-07
Hydroxylamine reacts as an oxygen nucleophile, most likely via its ammonia oxide tautomer, towards both phosphate di- and triesters of 2-hydroxypyridine. But the reactions are very different. The product of the two-step reaction with the triester TPP is trapped by the NH2OH present in solution to generate diimide, identified from its expected disproportionation and trapping products. The reaction with H3N(+)-O(-) shows general base catalysis, which calculations show is involved in the breakdown of the phosphorane addition-intermediate of a two-step reaction. The reactivity of the diester anion DPP(-) is controlled by its more basic pyridyl N. Hydroxylamine reacts preferentially with the substrate zwitterion DPP(±) to displace first one then a second 2-pyridone, in concerted S(N)2(P) reactions, forming O-phosphorylated products which are readily hydrolysed to inorganic phosphate. The suggested mechanisms are tested and supported by extensive theoretical calculations.
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Hydrolysis of tRNA(sup Phe) on Suspensions of Amino Acids
NASA Technical Reports Server (NTRS)
Gao, Kui; Orgel, Leslie E.
2001-01-01
RNA is adsorbed strongly on suspensions of many moderately soluble organic solids. In some cases, the hydrolysis of tRNA(sup Phe) is greatly accelerated by adsorption, and the major sites of hydrolysis are changed from those that are important in homogeneous solution. Here we show that the hydrolysis is greatly accelerated by suspensions of aspartic acid and beta-glutamic acid but not by suspensions of alpha-glutamic acid, asparagine, or glutamine. The non-enzymatic hydrolysis of RNA has been studied extensively, especially because of its relevance to the mechanisms of action of ribozymes and to biotechnology and therapy. Many ribonucleases, ribozymes, and non-biological catalysts function via acid-base catalysis of an intramolecular transesterification mechanism in which the 2'-OH group attacks the adjacent phosphate group. The pentacoordinated phosphorane intermediate may collapse back to starting material, or yield isomerized or cleaved products.
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DeYonker, Nathan J; Webster, Charles Edwin
2015-07-14
Tyrosyl-DNA phosphodiesterase I (Tdp1) is a DNA repair enzyme conserved across eukaryotes that catalyzes the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3'-phosphate of DNA. Atomic level details of the mechanism of Tdp1 are proposed and analyzed using a fully quantum mechanical, geometrically constrained model. The structural basis for the computational model is the vanadate-inhibited crystal structure of human Tdp1 (hTdp1, Protein Data Bank entry 1RFF ). Density functional theory computations are used to acquire thermodynamic and kinetic data along the catalytic pathway, including the phosphoryl transfer and subsequent hydrolysis. Located transition states and intermediates along the reaction coordinate suggest an associative phosphoryl transfer mechanism with five-coordinate phosphorane intermediates. Similar to both theoretical and experimental results for phospholipase D, the proposed mechanism for hTdp1 also includes the thermodynamically favorable possibility of a four-coordinate phosphohistidine "dead-end" product.
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A DNAzyme requiring two different metal ions at two distinct sites
Zhou, Wenhu; Zhang, Yupei; Huang, Po-Jung Jimmy; Ding, Jinsong; Liu, Juewen
2016-01-01
Most previously reported RNA-cleaving DNAzymes require only a single divalent metal ion for catalysis. We recently reported a general trivalent lanthanide-dependent DNAzyme named Ce13d. This work shows that Ce13d requires both Na+ and a trivalent lanthanide (e.g. Ce3+), simultaneously. This discovery is facilitated by the sequence similarity between Ce13d and a recently reported Na+-specific DNAzyme, NaA43. The Ce13d cleavage rate linearly depends on the concentration of both metal ions. Sensitized Tb3+ luminescence and DMS footprinting experiments indicate that the guanines in the enzyme loop are important for Na+-binding. The Na+ dissociation constants of Ce13d measured from the cleavage activity assay, Tb3+ luminescence and DMS footprinting are 24.6, 16.3 and 47 mM, respectively. Mutation studies indicate that the role of Ce3+ might be replaced by G23 in NaA43. Ce3+ functions by stabilizing the transition state phosphorane, thus promoting cleavage. G23 competes favorably with low concentration Ce3+ (below 1 μM). The G23-to-hypoxanthine mutation suggests the N1 position of the guanine as a hydrogen bond donor. Together, Ce13d has two distinct metal binding sites, each fulfilling a different role. DNAzymes can be quite sophisticated in utilizing metal ions for catalysis and molecular recognition, similar to protein metalloenzymes. PMID:26657636
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Bimetallic catalysis involving dipalladium(I) and diruthenium(I) complexes.
Das, Raj K; Saha, Biswajit; Rahaman, S M Wahidur; Bera, Jitendra K
2010-12-27
Dipalladium(I) and diruthenium(I) compounds bridged by two [{(5,7-dimethyl-1,8-naphthyridin-2-yl)amino}carbonyl]ferrocene (L) ligands have been synthesized. The X-ray structures of [Pd(2)L(2)][BF(4)](2) (1) and [Ru(2)L(2)(CO)(4)][BF(4)](2) (2) reveal dinuclear structures with short metal-metal distances. In both of these structures, naphthyridine bridges the dimetal unit, and the site trans to the metal-metal bond is occupied by weakly coordinating oxygen from the amido fragment. The catalytic utilities of these bimetallic compounds are evaluated. Compound 1 is an excellent catalyst for phosphine-free, Suzuki cross-coupling reactions of aryl bromides with arylboronic acids and provides high yields in short reaction times. Compound 1 is also found to be catalytically active for aryl chlorides, although the corresponding yields are lower. A bimetallic mechanism is proposed, which involves the oxidative addition of aryl bromide across the Pd-Pd bond and the bimetallic reductive elimination of the product. Compound 1 is also an efficient catalyst for the Heck cross-coupling of aryl bromides with styrenes. The mechanism for aldehyde olefination with ethyl diazoacetate (EDA) and PPh(3), catalyzed by 2, has been fully elucidated. It is demonstrated that 2 catalyzes the formation of phosphorane utilizing EDA and PPh(3), which subsequently reacts with aldehyde to produce a new olefin and phosphine oxide. The efficacy of bimetallic complexes in catalytic organic transformations is illustrated in this work.
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Katz, Michael J.; Moon, Su-Young; Mondloch, Joseph E.; ...
2015-02-24
The hydrolysis of nerve agents is of primary concern due to the severe toxicity of these agents. Using a MOF-based catalyst (UiO-66), we have previously demonstrated that the hydrolysis can occur with relatively fast half-lives of 50 minutes. However, these rates are still prohibitively slow to be efficiently utilized for some practical applications (e.g., decontamination wipes used to clean exposed clothing/skin/vehicles). We thus turned our attention to derivatives of UiO-66 in order to probe the importance of functional groups on the hydrolysis rate. Three UiO-66 derivatives were explored; UiO-66-NO 2 and UiO-66-(OH) 2 showed little to no change in hydrolysismore » rate. However, UiO-66-NH 2 showed a 20 fold increase in hydrolysis rate over the parent UiO-66 MOF. Half-lives of 1 minute were observed with this MOF. In order to probe the role of the amino moiety, we turned our attention to UiO-67, UiO-67-NMe 2 and UiO-67-NH 2. In these MOFs, the amino moiety is in close proximity to the zirconium node. We observed that UiO-67-NH 2 is a faster catalyst than UiO-67 and UiO-67-NMe 2. We conclude that the role of the amino moiety is to act as a proton-transfer agent during the catalytic cycle and not to hydrogen bond or to form a phosphorane intermediate.« less
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Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.
Harris, Michael E; Piccirilli, Joseph A; York, Darrin M
2015-11-01
The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.
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Nwe, Kido; Richard, John P; Morrow, Janet R
2007-11-28
The macrocycles 1,4,7-tris(carbamoylmethyl)-1,4,7,10-tetrazacyclododecane (1), 1,4,7-tris[(N-ethyl)carbamoylmethyl]-1,4,7,10-tetraazacyclododecane (2), 1,4,7-tris[(N,N-diethyl)carbamoylmethyl]-1,4,7,10-tetraazacyclododecane (3) and their Eu(III) complexes are prepared. Studies using direct Eu(III) excitation luminescence spectroscopy show that all three Eu(III) complexes exhibit only one predominant isomer with two bound waters under neutral to mildly basic conditions (Eu(X)(H(2)O)(2) for X = 1-3). There are no detectable ligand ionizations over the pH range 5.0-8.0 for Eu(3), 5.0-8.5 for Eu(2) or 5.0-9.5 for Eu(1). The three Eu(III) complexes show a linear dependence of second-order rate constants for the cleavage of 4-nitrophenyl-2-hydroxyethylphosphate (HpPNP) on pH in the range 6.5-8.0 for Eu(3), 7.0-8.5 for Eu(2) and 7.0-9.0 for Eu(1). This pH-rate profile is consistent with the Eu(III) complex-substrate complex being converted to the active form by loss of a proton and with Eu(III) water pK(a) values that are higher than 8.0 for Eu(3), 8.5 for Eu(2) and 9.0 for Eu(1). Inhibition studies show that Eu() binds strongly to the dianionic ligand methylphosphate (K(d) = 0.28 mM), and more weakly to diethylphosphate (K(d) = 7.5 mM), consistent with a catalytic role of the Eu(III) complexes in stabilizing the developing negative charge on the phosphorane transition state.
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Gu, Hong; Zhang, Shuming; Wong, Kin-Yiu; Radak, Brian K.; Dissanayake, Thakshila; Kellerman, Daniel L.; Dai, Qing; Miyagi, Masaru; Anderson, Vernon E.; York, Darrin M.; Piccirilli, Joseph A.; Harris, Michael E.
2013-01-01
Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can provide insight into biological catalysis. Catalysis of RNA 2′-O-transphosphorylation by ribonuclease A is proposed to involve electrostatic stabilization and acid/base catalysis, although the structure of the rate-limiting transition state is uncertain. Here, we describe coordinated kinetic isotope effect (KIE) analyses, molecular dynamics simulations, and quantum mechanical calculations to model the transition state and mechanism of RNase A. Comparison of the 18O KIEs on the 2′O nucleophile, 5′O leaving group, and nonbridging phosphoryl oxygens for RNase A to values observed for hydronium- or hydroxide-catalyzed reactions indicate a late anionic transition state. Molecular dynamics simulations using an anionic phosphorane transition state mimic suggest that H-bonding by protonated His12 and Lys41 stabilizes the transition state by neutralizing the negative charge on the nonbridging phosphoryl oxygens. Quantum mechanical calculations consistent with the experimental KIEs indicate that expulsion of the 5′O remains an integral feature of the rate-limiting step both on and off the enzyme. Electrostatic interactions with positively charged amino acid site chains (His12/Lys41), together with proton transfer from His119, render departure of the 5′O less advanced compared with the solution reaction and stabilize charge buildup in the transition state. The ability to obtain a chemically detailed description of 2′-O-transphosphorylation transition states provides an opportunity to advance our understanding of biological catalysis significantly by determining how the catalytic modes and active site environments of phosphoryl transferases influence transition state structure. PMID:23878223
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Cavalier, Michael C.; Kim, Song-Gun; Neau, David
2012-03-22
The molecular basis of fructose-2,6-bisphosphatase (F-2,6-P{sub 2}ase) of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB) was investigated using the crystal structures of the human inducible form (PFKFB3) in a phospho-enzyme intermediate state (PFKFB3-P {center_dot} F-6-P), in a transition state-analogous complex (PFKFB3 {center_dot} AlF{sub 4}), and in a complex with pyrophosphate (PFKFB3 {center_dot} PP{sub i}) at resolutions of 2.45, 2.2, and 2.3 {angstrom}, respectively. Trapping the PFKFB3-P {center_dot} F-6-P intermediate was achieved by flash cooling the crystal during the reaction, and the PFKFB3 {center_dot} AlF{sub 4} and PFKFB3 {center_dot} PP{sub i} complexes were obtained by soaking. The PFKFB3 {center_dot} AlF{sub 4} and PFKFB3 {center_dot} PP{sub i}more » complexes resulted in removing F-6-P from the catalytic pocket. With these structures, the structures of the Michaelis complex and the transition state were extrapolated. For both the PFKFB3-P formation and break down, the phosphoryl donor and the acceptor are located within {approx}5.1 {angstrom}, and the pivotal point 2-P is on the same line, suggesting an 'in-line' transfer with a direct inversion of phosphate configuration. The geometry suggests that NE2 of His253 undergoes a nucleophilic attack to form a covalent N-P bond, breaking the 2O-P bond in the substrate. The resulting high reactivity of the leaving group, 2O of F-6-P, is neutralized by a proton donated by Glu322. Negative charges on the equatorial oxygen of the transient bipyramidal phosphorane formed during the transfer are stabilized by Arg252, His387, and Asn259. The C-terminal domain (residues 440-446) was rearranged in PFKFB3 {center_dot} PP{sub i}, implying that this domain plays a critical role in binding of substrate to and release of product from the F-2,6-P{sub 2}ase catalytic pocket. These findings provide a new insight into the understanding of the phosphoryl transfer reaction.« less