Solvent Isotope Effects in H<sub>2</sub>O−D<sub>2</sub>O Mixtures (Proton Inventories) on Serine-Protease-Catalyzed Hydrolysis Reactions. Influence of Oxyanion Hole Interactions and Medium Effects

Much interest has focused on the mechanisms of the five naturally occurring self-cleaving ribozymes, which, in spite of catalyzing the same reaction, adopt divergent strategies. These ribozymes, with the exception of the recently described glmS ribozyme, do not absolutely require divalent metal ions for their catalytic chemistries in vitro. A mechanistic investigation of an in vitro-selected, RNA-cleaving DNA enzyme, the bipartite, which catalyzes the same chemistry as the five natural self-cleaving ribozymes, found a mechanism of significant complexity. The DNAzyme showed a bell-shaped pH profile. A dissection of metal usage indicated the involvement of two catalytically relevant magnesium ions for optimal activity. The DNAzyme was able to utilize manganese(II) as well as magnesium; however, with manganese it appeared to function complexed to either one or two of those cations. Titration with hexaamminecobalt(III) chloride inhibited the activity of the bipartite; this suggests that it is a metalloenzyme that utilizes metal hydroxide as a general base for activation of its nucleophile. Overall, the bipartite DNAzyme appeared to be kinetically distinct not only from the self-cleaving ribozymes but also from other in vitro-selected, RNA-cleaving deoxyribozymes, such as the 8-17, 10-23, and 614.

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“…www.chembiochem.org system, of a multiplicity of small isotope effects [28] adding up to give the relatively large cumulative number.…”

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confidence: 99%

The RNA‐Cleaving Bipartite DNAzyme Is a Distinctive Metalloenzyme

et al. 2006

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“…8,9 Chang et al reported that medium effect is also important in that regard. 10 This study in particular investigates the plausibility of explicit solvent molecules other than water molecules proximal to the transition states in acting as the oxyanion-hole environment.…”

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confidence: 99%

SER-HIS-ASP catalytic triad in model non-aqueous solvent environment: A computational study

Lau¹,

Cheng²

2006

Bioorganic & Medicinal Chemistry Letters

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“…The question of which of these steps is rate limiting does not influence the isotope-effect arguments. Kresge immediately pointed out (5) the ambiguity of this interpretation, and later expanded on the point with the inclusion of experimental measurements on an enzymecatalyzed reaction and on host-guest complexation (6,7). A linear dependence such as we observed (eq.…”

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confidence: 81%

The role of the medium in solvent isotope effects on serine protease action

Tian¹,

Tan²,

Schowen³

et al. 1999

Can. J. Chem.

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The hydrolysis of N-carbobenzyloxyaminoacyl-O-p-nitrophenyl esters derived from L-leucine, Lphenylalanine, and L-tryptophan, with catalysis by bovine pancreatic α-chymotrypsin at pH 7.00 at 25.00°C in water containing acetonitrile from 15.0% to 60% (v/v), exhibits values of k cat /K m that decrease as the 34th to 36th power of the activity of water and values of k cat that are essentially constant. Solvent isotope effects k cat (H 2 O)/ k cat (D 2 O) range from 2.1 to 3.0 with proton inventories (dependences of k cat (n) on n, the atom fraction of deuterium in the water component of the solvent) that are linear, regardless of the amount of acetonitrile in the medium. The isotope effect on k cat thus appears to arise from a single transition-state site and to be little affected by the medium. Contributions from the medium to solvent isotope effects on enzymic reactions clearly exist but appear not to be detectable in the deacylation reactions of acyl chymotrypsins.Résumé : Pour les réactions d'hydrolyse des esters N-carbobenzyloxyaminoacyl-O-p-nitrophénylés dérivés de la Lleucine, de la L-phénylalanine et du L-tryptophane catalysées par l'α-chymotrypsine pancréatique bovine, à un pH de 7,0, à 25,00°C, dans de l'eau contenant de l'acétonitrile à des concentrations allant de 15,0 à 60% (v/v), les valeurs de k cat sont pratiquement constantes alors que celles de k cat /K m diminuent en fonction de l'activité de l'eau portée à des puissances allant de 34 à 36. Les effets isotopiques de solvant, k cat (H 2 O)/k cat (D 2 O) vont de 2,1 à 3,0 avec des inventaires de proton (dépendances de k cat (n) sur n, la fraction atomique de deutérium dans la composante aqueuse du solvant) qui sont linéaires, quelle que soit la quantité d'acétonitrile dans le milieu. Il semble donc que les effets isotopiques sur k cat découlent d'un seul site de l'état de transition et qu'ils ne sont pas très affectés par le milieu. Il est évident qu'il existe des contributions du milieu sur les effets isotopiques du solvant sur des réactions enzymatiques; ils ne semblent toutefois pas décelables dans les réactions de désacylations des acyl chymotrypsines.Mots clés : effets isotopiques du solvant, inventaires de proton, effets de solvant, catalyse enzymatique, α-chymotrypsine.[Traduit par la Rédaction] Tian et al. 786 1The entire isotope effect was therefore taken to arise from the single protonic site bridging between water and histidine. Although structure 1 portrays the transition state for forma-Can.

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Solvent Isotope Effects in H₂O−D₂O Mixtures (Proton Inventories) on Serine-Protease-Catalyzed Hydrolysis Reactions. Influence of Oxyanion Hole Interactions and Medium Effects

Cited by 24 publications

References 24 publications

The RNA‐Cleaving Bipartite DNAzyme Is a Distinctive Metalloenzyme

The RNA‐Cleaving Bipartite DNAzyme Is a Distinctive Metalloenzyme

SER-HIS-ASP catalytic triad in model non-aqueous solvent environment: A computational study

The role of the medium in solvent isotope effects on serine protease action

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Solvent Isotope Effects in H2O−D2O Mixtures (Proton Inventories) on Serine-Protease-Catalyzed Hydrolysis Reactions. Influence of Oxyanion Hole Interactions and Medium Effects

Cited by 24 publications

References 24 publications

The RNA‐Cleaving Bipartite DNAzyme Is a Distinctive Metalloenzyme

The RNA‐Cleaving Bipartite DNAzyme Is a Distinctive Metalloenzyme

SER-HIS-ASP catalytic triad in model non-aqueous solvent environment: A computational study

The role of the medium in solvent isotope effects on serine protease action

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Product

Resources

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Solvent Isotope Effects in H₂O−D₂O Mixtures (Proton Inventories) on Serine-Protease-Catalyzed Hydrolysis Reactions. Influence of Oxyanion Hole Interactions and Medium Effects