Models for nuclease catalysis: mechanisms for general acid catalysis of the rapid intramolecular displacement of methoxide from a phosphate diester

Dalby, Kevin N.; Kirby, Anthony J.; Hollfelder, Florian

doi:10.1039/p29930001269

Cited by 35 publications

(48 citation statements)

References 23 publications

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“…Ϫ All starting materials (2a, 2b, 2c, 2d, 2e, 7) are commercially available and were used without further purification. Compound 2f [26] was synthesized according to the literature procedure.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Chiral Hypervalent Organo-Iodine(III) Compounds

Hirt¹,

Schuster²,

French³

et al. 2001

Eur. J. Org. Chem.

160

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A series of ortho-substituted chiral hypervalent iodine reagents has been synthesized utilizing a zirconium-mediated iodoacylation reaction, which was followed by a stereoselective reduction, methylation, and an oxidation/ligand-exchange sequence. The evaluation of these new compounds as stereoselective electrophilic reagents towards alkenes and ketones is reported. Enantioselectivities as high as 65% have been achieved in the dioxytosylation of styrene and of up to 40% in the oxytosylation of propiophenone. X-ray structure

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Section: Methodsmentioning

confidence: 99%

“…2-Bromophenol was protected as the benzyl ether [26] and subjected to the reaction sequence with acetonitrile and iodine to give iodo ketone 3f in good yield.…”

Section: Scheme 2 Synthesis Of Chiral Hypervalent Iodine Compound 1kmentioning

confidence: 99%

Chiral Hypervalent Organo-Iodine(III) Compounds

Hirt¹,

Schuster²,

French³

et al. 2001

Eur. J. Org. Chem.

160

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“…It has been shown that the ␤ lg for a series of aryl-phosphate diester compounds is even less negative (␤ lg ϭ Ϫ0.2) in the active site of RNase A, suggesting a considerable contribution of electrophilic catalysis in the active site (33). Brønsted analysis using aryl-phosphate diester compounds gave a Brønsted coefficient, ␤, of 0.67 (␣ of 0.33) (32,34). In the study presented here, a Brønsted coefficient was obtained by using a natural RNA phosphodiester as the substrate: for a mechanism of general base catalysis, ␤ is 0.51, or for the kinetically equivalent mechanism, specific base͞general acid catalysis, ␣ is 0.49.…”

Section: Discussionmentioning

confidence: 99%

Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

Shih

Been

2001

Proc. Natl. Acad. Sci. U.S.A.

139

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Ribozymes of hepatitis delta virus have been proposed to use an active-site cytosine as an acid-base catalyst in the self-cleavage reaction. In this study, we have examined the role of cytosine in more detail with the antigenomic ribozyme. Evidence that proton transfer in the rate-determining step involved cytosine 76 (C76) was obtained from examining cleavage activity of the wild-type and imidazole buffer-rescued C76-deleted (C76⌬) ribozymes in D 2O and H2O. In both reactions, a similar kinetic isotope effect and shift in the apparent pKa indicate that the buffer is functionally substituting for the side chain in proton transfer. Proton inventory of the wild-type reaction supported a mechanism of a single proton transfer at the transition state. This proton transfer step was further characterized by exogenous base rescue of a C76⌬ mutant with cytosine and imidazole analogues. For the imidazole analogues that rescued activity, the apparent pKa of the rescue reaction, measured under k cat͞KM conditions, correlated with the pKa of the base. From these data a Brønsted coefficient (␤) of 0.51 was determined for the base-rescued reaction of C76⌬. This value is consistent with that expected for proton transfer in the transition state. Together, these data provide strong support for a mechanism where an RNA side chain participates directly in general acid or general base catalysis of the wild-type ribozyme to facilitate RNA cleavage. G eneral acid-base catalysis † is common in enzymecatalyzed systems where proton transfer occurs in the transition state of the chemical step. General acid-base catalysis can accelerate chemical-catalyzed reactions 10-to 100-fold in solution (1); in enzyme systems, results from mutagenesis data indicate that the rate acceleration can be as high as 10 6 -fold (2-4). With protein enzymes, general acid-base catalysis is commonly achieved by amino acid side chains with pKa values near neutral pH. However, RNA side chains have pKa values significantly higher or lower than neutral pH and, thus, would not generally be well suited for general acid-base catalysis. For an RNA side chain to participate directly in general acid-base catalysis, a significant shift in its pKa would appear to be required. Because most ribozymes require divalent cations for optimal activity, it has been proposed that hydrated divalent metal ions may act as a general acid or base in ribozyme catalysis (5-7). Divalent metal ions also can facilitate proton transfer through direct coordination to the attacking nucleophile (8 -11). Thus, while there is precedent for the role of metal ions in catalyzing proton transfer in ribozymes, there is very little information on the direct involvement of RNA side chains in general acid-base catalysis.Hepatitis delta virus (HDV) ribozymes, like other small ribozymes, catalyze a transesterification reaction of a phosphodiester linkage, generating a 2Ј,3Ј-cyclic phosphate and a 5Ј-hydroxyl. The proposed mechanism involves the adjacent 2Ј-hydroxyl group as an intramolecular nucleophile, a pen...

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“…In 3.25 [55] (Scheme 2.28) a highly efficient nucleophilic reaction ðEM > 10 10 Þ supports the general acid catalyzed displacement of methoxide as methanol. Two model systems illustrate the potential of such effects.…”

Section: Scheme 226mentioning

confidence: 86%

General Acid–Base Catalysis in Model Systems

Kirby

2006

Hydrogen‐Transfer Reactions

Self Cite

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IntroductionProton transfer is the most common reaction in living systems, in which reactions have to be strictly controlled, and most are catalyzed by enzymes. The great majority of enzyme catalyzed reactions are ionic, involving heterolytic bond making and breaking, and thus the creation or neutralization of charge. Under conditions of constant pH this requires the transfer of protons (Eq. (2.1)). ð2:1ÞGeneral acid and general base catalysis are terms commonly used to describe two different characteristics of reactions, the (observable) form of the rate law or a (hypothetical) reaction mechanism proposed to account for it. It is important to be aware of (and for authors to make clear) which is meant in a particular case.General acid-base catalysis provides mechanisms for bringing about the necessary proton transfers without involving hydrogen or hydroxide ions, which are present in water at concentrations of only about 10 À7 M under physiological conditions. At pHs near neutrality relatively weak acids and bases can compete with lyonium or lyate species because they can be present in much higher concentrations. 2.1.1 KineticsThe basics of general acid and general base catalysis are described clearly and in detail in Chapter 8 of Maskill [1]. Acid-base catalysis is termed specific if the rate of the reaction concerned depends only on the acidity (pH, etc.) of the medium. This is the case if the reaction involves the conjugate acid or base of the reactant preformed in a rapid equilibrium process -normal behavior if the reactant is weakly basic or acidic. The conjugate acid or base is then, by definition, a strong 975 acid or base, and the reverse proton transfer to solvent is thus rapid, probably diffusion-controlled -and certainly faster than a competing forward reaction involving the making or breaking of covalent bonds. This forward reaction of the conjugate acid or base of the reactant is therefore rate determining, and the rate expression -for example for the hydrolysis of an unreactive ester (Scheme 2.1)contains only a single term in (lyonium) acid concentration:General acid-base catalysis is defined experimentally by the appearance in the rate law of acids and/or bases other than lyonium or lyate ions. For example, the hydrolysis of enol ethers 1.2 (Scheme 2.2) is general acid-catalyzed. In strong acid the rate expression will be the same as in Scheme 2.1, but near neutral pH the rate is found to depend also on the concentration of the buffer ðHA þ A À Þ used to maintain the pH. Measurements at different buffer ratios show that the catalytic species is the acid HA. (If more than one acid is present there will be an additional term k HAi ½HA i ½1:2 for each.)If in these experiments the measurements at different buffer ratios showed that the catalytic species was the conjugate base A À the reaction would be kinetically general base catalyzed. In which case HA and A À would probably subsequently be referred to as BH þ and B. Thus the enolisation of ketones is general base catalysed (Scheme 2.3). Àd½1:3=dt ¼ k...

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Models for nuclease catalysis: mechanisms for general acid catalysis of the rapid intramolecular displacement of methoxide from a phosphate diester

Cited by 35 publications

References 23 publications

Chiral Hypervalent Organo-Iodine(III) Compounds

Chiral Hypervalent Organo-Iodine(III) Compounds

Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

General Acid–Base Catalysis in Model Systems

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