Catalytic proficiency

The kinetic constants for the carboxypeptidase A catalyzed hydrolysis at pH 9 and 25° were /ccal=61 s Km=0.29 mM. In other words, the enzyme afforded a rate enhancement of 11 orders of magnitude (kcJkchem= 4.7xlO11), and a catalytic proficiency of 15 orders of magnitude ((kL.JKm)/... 

In physics, the time rate of change of motional velocity resulting from changes in a body s speed and/or direction. In biochemistry, acceleration refers to an increased rate of a chemical reaction in the presence of an enzyme or other catalyst. See Catalytic Rate Enhancement Catalytic Proficiency Efficiency Function... 

The ratio of the rate of an enzyme- (or ribozyme-) catalyzed reaction to the rate of the reaction in the absence of catalysis. This ratio equals kcJknon, where Acat is the turnover number and Anon is the noncatalyzed rate constant. See Catalytic Proficiency... 

A quantitative measure of an enzyme s ability to lower the activation barrier for the reaction of a substrate in solution. Catalytic proficiency (a unitless parameter) equals the enzyme-catalyzed reaction rate constant (expressed as Acat/Xm) divided by the rate constant (Anon) for the noncatalyzed reference reaction. 

CATALYTIC RATE ENHANCEMENT CATALYTIC PROFICIENCY EFFICIENCY FUNCTION Acceptor,... 

MULTIENZYME POLYPEPTIDE AUTONOMOUS CATALYTIC DOMAIN CATALYTIC ENHANCEMENT CATALYTIC PROFICIENCY CATALYTIC EFFICIENCY REFERENCE REACTION Catalytic rate acceleration,... 

ELECTRODE KINETICS OXIDATION REFERENCE REACTION CATALYTIC PROFICIENCY REGIOSELECTIVITY... 

Miller, B.G. Wolfenden, R. (2002) Catalytic proficiency the unusual case of OMP decarboxylase. Annu. Rev. Biochem. 71, 847-885. 

Enzyme-catalyzed reactions involve specific, rapid combination of substrate and enzyme to form a complex that is rapidly converted to products through transition states that are controlled by the enzyme s environment. Since enzymes are homogeneous chemical catalysts, we expect them to operate by routes that parallel some of the same processes in reactions that do not involve enzymes. The relative magnitude of enzymic and nonenzymic catalytic parameters has been called catalytic proficiency by Wolfenden6,17 24 and this has been a subject of intense current interest.7,25 32 Wolfenden noted that while nonenzymic reactions have diverse rates, enzyme-catalyzed processes are highly evolved to be comparable in rate, no matter how slow their nonenzymic counterparts. 

The range of catalytic proficiencies for enzymes suggests that there are features of catalysis in enzymes that involve factors other than stabilization of transition states. One important distinction is that the enzyme active site contains catalytic groups that are able to access reactive intermediates, while intermediates formed in solution have lifetimes that are less than the time needed for a reagent to diffuse to the site of the reaction.33 In the enzyme, groups are initially associated with the bound substrate in a specific array and continue to be available through the course of the reaction. Diffusional introduction of catalytic groups is overcome by pre-association of the catalysts and reactant prior to the formation of any reactive intermediate. This accesses modes of catalysis that are not possible if the catalyst and intermediate must become associated after the intermediate has formed. 

Recent investigations of the enzyme chorismate mutase show how modelling can contribute to fundamental debates in enzymology, such as analysing the importance of transition state stabilization in catalysis, and alternative proposals to explain enzyme catalytic proficiency. 

Murray JB, Seyhan AA, Walter NG, Burke JM, Scott WG. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 1998 5 587-595. Nakano S, Cerrone AL, Bevilacqua PC. Mechanistic characterization of the HDV genomic ribozyme classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. Biochemistry 2001 40 12022-12038. 

Radzicka and Wolfenden [24] elegantly show that both are correct and that they yield different and valuable information about the effects of the enzyme. The relevant equations have been gathered into Chart 4.1. The quantity [(kcat/KM)/kuncj, given the name catalytic proficiency, measures the equilibrium constant for binding of the transition state for the uncatalyzed reaction to the unoccupied active site of the enzyme (see Eq. (iv) in Chart 4.1), and thus the total stabilization of that transition state by the enzyme. The quantity [kcat/kunc] is called the rate enhancement and measures (Eq. (v) of Chart 4.1) the equilibrium constant for expulsion of the reactant-state substrate molecule from the active site and its replacement in the active site by the transition state for the uncatalyzed reaction. The quantity there-... 

The two quantities, catalytic proficiency (which has the dimensions in the example above) and rate enhancement (which is dimensionless in the example above), give a valid account of two aspects of enzyme catalysis. The catalytic proficiency, as the equilibrium constant for transition-state binding to the free enzyme, measures quantitatively the affinity of the free enzyme for the transition state. The free-energy equivalent of the catalytic proficiency gives the total transition-state stabilization by the enzyme. The rate enhancement, as the equilibrium constant for the expulsion of a substrate molecule from the active site of the enzyme and its replacement by a transition-state molecule, quantitatively describes the relative affinity of the enzyme for the transition state compared to the reactant-state substrate. 

Furthermore, a useful way of assessing the magnitude of promiscuous activities is the rate acceleration iKsa/Kncm) or catalytic proficiency ( cat/- M/ uncat)- These parameters are indicative because they take into account the inherent reactivity of the substrate. In many cases, promiscuous activities occur, or are measured, with highly reactive substrates. Such activities are in a way expected. However, there are many cases in which promiscuous activities take place with substrates that are less activated than the native one. Examples include, the amidase activity of esterases such as lipases (Table 1, entry 7), the phosphodiesterase activities of P. diminuta PTE and alkaline phosphatase (Table 1, entries 10 and 8), and the PTE activities or various lactonases (Table 1, entries 11-13 and the notable fact that some of these lactonases do not hydrolyze the more activated aryl esters). In such cases, the chemical challenge posed by a less activated substrate is reflected in the more favorable comparisons of rate accelerations, or catalytic proficiencies, for the native versus the promiscuous substrates. 

Lad C, Williams H, Wolfenden, R. The rate of hydrolysis of phosphomonoester dianions and the exceptional catalytic proficiencies of protein and inositol phosphatases. Proc Natl Acad Sci U S A 2003 100 5607-5610. 

For ODCase, non-covalent mechanisms have often been proposed, as reflected in three of the mechanisms shown in Fig. 2. This is the crux of the attention showered on ODCase how can this enzyme achieve its rate acceleration without the use of cofactors, metals, or acid-base catalysis From Wolfenden s measurements of the uncatalyzed reaction of 1-methylorotic acid in water, he calculated the rate enhancement (kcat/kun) in the enzyme to be 1.4x10, corresponding to a reduction of AG of 24 kcal/mol [1]. He also reported the catalytic proficiency to be 2x10 meaning that the enzyme-transition state complex is an impressive 32 kcal/mol more stable than the fi-ee enzyme and transition state in water (i.e., the effective binding free energy of the transition state out of water is 32 kcal/mol) [1] The experimental free energy of activation is 15 kcal/mol for this decarboxylation in ODCase. 

Keywords Orotidine 5 -phosphate decarboxylase Catalytic proficiency ... 

Many DNAzymes catalyse RNA ligation reactions to yield linear, branched, and lariat-type reaction products. The ligation of DNA strands as well as the phosphorylation of DNA or RNA oligonucleotides was described. Some notable extensions beyond phosphodiester chemistry include a photoreversion reaction, a deglycosylation, porphyrin metalation, nucleopeptide bond formation, and finally a Diels-Alder reaction. This latter reaction is essentially the same studied by the Jaschke lab with RNA as a catalyst (as discussed below in more detail), and the information published to-date indicates that the catalytic proficiency of DNA and RNA enzymes for Diels-Alder reactions is very similar. 

We were able to experimentally demonstrate a functional interaction between the two domains, through reconstitution of cleavage activity (14). Success of this experiment depended on having previously solved the misfolding problems described above. The separated domains are able to associate in solution to assemble a catalytically-proficient complex. The observed rate of the reaction approaches cat of the unmodified ribozyme, but only at very high RNA concentrations. This demonstrates the presence of tertiary interactions between the two domains, but suggests that they are quite weak. The identity of these interactions has not yet been determined. 

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