Enzymes thermodynamic reactions

By protodetritiation of the thiazolium salt (152) and of 2 tritiothiamine (153) Kemp and O Brien (432) measured a kinetic isotope effect, of 2.7 for (152). They evaluated the rate of protonation of the corresponding yiides and found that the enzyme-mediated reaction of thiamine with pyruvate is at least 10 times faster than the maximum rate possible with 152. The scale of this rate ratio establishes the presence within the enzyme of a higher concentration of thiamine ylide than can be realized in water. Thus a major role of the enzyme might be to change the relative thermodynamic stabilities of thiamine and its ylide (432). 

NIST [195] Thermodynamics of Enzyme Catalyzed Reactions http //xpdb.nist.gov/enzyme thermodynamics/... 

R. N. Goldberg, Y. B.Tewari, andT. N. Bhat. Thermodynamics of enzyme catalyzed reactions A database for quantitative biochemistry. Bioinformatics 20(16), 2874 2877 (2004). 

The thermodynamic activation parameters for the enzyme-catalysed reaction are very different from those for the uncatalysed process (Albers et at., 1990). For the isomerization of succinyl-alanyl-leucyl-prolylphenylalanyl-p-nitroanilide catalysed by recombinant human FK binding protein AH = 5.85 kcal mol"1 and AS = -44. e.u. This compares with figures of 18.9 kcal mol 1 and — l.lbe.u. for the uncatalysed reaction of the same substrate. Probably a different step is rate determining in the enzyme-catalysed reaction. 

In the last decade there were many papers published on the study of enzyme catalyzed reactions performed in so-called chromatographic reactors. The attractive feature of such systems is that during the course of the reaction the compounds are already separated, which can drive the reaction beyond the thermodynamic equilibrium as well as remove putative inhibitors. In this chapter, an overview of such chromatographic bioreactor systems is given. Besides, some immobilization techniques to improve enzyme activity are discussed together with modern chromatographic supports with improved hydrodynamic characteristics to be used in this context. 

Burbaum et al. considered how kinetic/thermodynamic features of present-day enzyme-catalyzed reactions suggest that enzyme evolution tends to maximize catalytic effectiveness. They analyzed Uni Uni enzymes in terms of reaction energetics. Catalytically optimized enzymes... 

Biochemical reactions are basically the same as other chemical organic reactions with their thermodynamic and mechanistic characteristics, but they have the enzyme stage. Laws of thermodynamics, standard energy status and standard free energy change, reduction-oxidation (redox) and electrochemical potential equations are applicable to these reactions. Enzymes catalyse reactions and induce them to be much faster . Enzymes are classified by international... 

Fig. 4 Free energy diagram for the two possible situations in enzyme-triggered formation of supramolecular assembly. Left. The enzyme-catalysed reaction and self-assembly process are both favoured independently and therefore uncoupled. Right. Enzyme-triggered self-assembly under thermodynamic control formation of the building blocks is thermodynamically unfavoured in isolation and occurs in reversible fashion when coupled to a sufficiently stable self-assembled structure formation...

Tewari, Y.B. (1990) Thermodynamics of indnstrially-important, enzyme catalysed reactions. Biochem. Biotechnol., 23, 187-203. 

Ideally, thermodynamic activities of the reactants should be used in the equation, but since concentrations are normally easier to measure these are often used instead. The use of the activity of water (which can be measured fairly easily) and the concentrations of the other reactants has been recommended for studies of enzyme catalyzed reactions in organic media (Hailing, 1984). In order to increase the synthesis of the ester, the water concentration (or activity) should be reduced. This can be achieved by replacing part of the water with a water miscible solvent. 

The natural cycles of the bioelements carbon, oxygen, hydrogen, nitrogen and sulphur) are subjected to various discrimination effects, such as thermodynamic isotope effects during water evaporation and condensation or isotope equilibration between water and CO2. On the other hand, the processes of photosynthesis and secondary plant metabolism are characterised by kinetic isotope effects, caused by defined enzyme-catalysed reactions [46]. 

Miller and Wolfenden6 compared the rates of decarboxylation of the substrate of orotidine-5 -monophosphate decarboxylase (OMPDC) in quantitative detail, on and off the enzyme. They showed that the apparent unimolecular rate constant of decarboxylation of the substrate when bound to the enzyme is about 1015 times greater than the decarboxylation process in the absence of the enzyme. Further studies confirm that the enzyme-promoted reaction does not involve additional intermediates or covalent alterations of the substrate. The reaction consists of carbon dioxide being formed and the resulting carbanion becoming protonated. Since thermodynamic barriers are not altered by catalysis, the energy of the carbanion must be a component that reflects the energy of the environment in which it is created, one in which the carbanion that is formed is selectively stabilized. 

The procedure for calculating standard formation properties of species at zero ionic strength from measurements of apparent equilibrium constants is discussed in the next chapter. The future of the thermodynamics of species in aqueous solutions depends largely on the use of enzyme-catalyzed reactions. The reason that more complicated ions in aqueous solutions were not included in the NBS Tables (1992) is that it is difficult to determine equilibrium constants in systems where a number of reactions occur simultaneously. Since many enzymes catalyze clean-cut reactions, they make it possible to determine apparent equilibrium constants and heats of reaction between very complicated organic reactants that could not have been studied classically. 

The semigrand partition function F corresponds with a system of enzyme-catalyzed reactions in contact with a reservoir of hydrogen ions at a specified pH. The semigrand partition function can be written for an aqueous solution of a biochemical reactant at specified pH or a system involving many biochemical reations. The other thermodynamic properties of the system can be calculated from F. 

This book is about the thermodynamics of enzyme-catalyzed reactions that make up the metabolism of living organisms, ft is not an introductory text, but the fundamental principles of thermodynamics are reviewed. The reader does need some background in thermodynamics, such as that provided by a first course in physical chemistry. The book uses a generalized approach to thermodynamics that makes it possible to calculate the effects of changing pH, free concenrations of metal ions that are bound by reactants, and steady-state concentrations of coenzymes. This approach can be extended to other types of work that may be involved in a living organism. 

This field owes a tremendous debt to the experimentalists who have measured apparent equilibrium constants and heats of enzyme-catalyzed reactions and to those who have made previous thermodynamic tables that contain information needed in biochemical thermodynamics. 

The explanation of Ql(l effects just presented is rather typical of treatments found in most textbooks, in which a relatively simplified thermodynamic explanation, based on energy distribution patterns, is developed to account for effects of temperature on reaction rates. Such treatments of temperature effects, while correct overall, are abstract and nonmecha-nistic—a necessary property of thermodynamic explanations—and will be seen to be incomplete in important ways. In particular, thermodynamic treatments that eschew discussions of underlying mechanisms are unable to provide an explicit account of what steps in an enzyme-catalyzed reaction are rate limiting and, thus, responsible for Qio effects. 

While enzymes, as a rule, essentially lose their normal activity and specificity, they possess new useful features 1) utilization of substrates non-soluble in water 2) their ability to change substrate and inhibitor selectivity and specificity 3) they alternate of reactions thermodynamics and kinetics reactions so that desirable products are favoured 4) improvements of enzyme stability and 5) the possibility to fix enzymes and reaction intermediates at states of certain pH and ionic strength in both solution and crystal form ( molecular memory effects ). 

R. A. Alberty. Thermodynamic properties of weak acids involved in enzyme-catalyzed reactions. J. Phys. Chem. B, 110 5012-5016, 2006. 

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