Enzymes linear free energy relationships

Linear free-energy relationships 58, 62-65,86,87,599 protein engineering of enzymes and 442-444... 

Hydrolysis of phosphate esters is one of the fundamental biochemical reactions and a vast amount of research has been devoted to the study of phosphoryl transfer reactions [57-60], both in solution and in enzymes. Despite these efforts there are still ambiguities regarding the interpretation of experimental data (e.g., linear free energy relationships, kinetic isotope effects, crystal structures of enzyme-inhibitor complexes etc.) in terms of detailed reaction mechanisms [21,25,59,60]. Of particular interest has been to determine... 

The study of Fersht et al. (1985) provided an interesting Linear Free Energy Relationship (LFER) between the catalytic effect of the enzyme with its effect on the free energy of the reaction. The theoretical basis of this effect has been provided by a recent work (Warshel et al., 1994). 

Warshel, A., Schweins, T. and Fothergill, M. (1994). Linear free energy relationships in enzymes. Theoretical analysis of the reaction of tyrosyl-tRNA synthetase. J. Am. Chem. Soc. 116, 8437-8442... 

Since the coordinates log/Cf and log/<,- are independent of each other, a correlation between log/cf and log/ ,- as in Equation (29) would demonstrate the existence of a linear free energy relationship The demonstration of a linear free energy relationship by this means is not necessary for chemical systems because these usually involve substituent change directly adjacent to the reaction centre the correlation is thus chemically reasonable. Application of Equation (29) is significant when the substituent changes may not be so obviously connected with the reaction centre as in the case of the effect of point mutation on conformational changes in enzymes. 

Application of linear free energy relationships to enzyme mechanisms has, naturally, been attempted but the influence of the substituent may... 

Variation of Substrate Structure. Whereas linear free energy relationships play a central role in the determination of non-enzymic mechanisms, they are much less important for enzymes, for two reasons. First, enzymes have evolved to bind their natural substrates, and substituents introduced in an attempt merely to alter electron demand at the transition state may have many other interactions with the enzyme protein. The result is very noisy Hammett and Bronsted plots. Whereas conclusions can be drawn from non-enzymic rates varying over a factor of 3, with enzyme reactions, to see any trend above the noise it is usually necessary to have rates ranging over several orders of magnitude. 

The existence of a linear free energy relationship between two enzymes acting on the same library of substrates can give an indication of common mechanism. Thus, a plot of log(kcat/Ani) for hydrolysis of a series of p-nitrophenyl glycosides and aryl glucosides by the GH 1 enzyme from the mesophile Agrobacterium... 

Barberis S, Quiroga E, Morcelle S et al. (2006) Study of phytoproteases stability in aqueous-organic biphasic systems using linear free energy relationships. J Mol Catal B Enzym 38 95-103... 

A simple procedure reported for the isolation of jack-bean a-D-mannosidase was based on affinity chromatography on agarose-immobilized benzidine. The influence of substituents on the hydrolysis of substituted phenyl a-D-mannopyranosides by a-D-mannosidase from Medicago sativa seeds has been investigated. As indicated by structure-activity relations, the electronic effect of the substituent has an influence on the rate of formation of the intermediate D-mannosyl-enzyme complex. This effect depends not only on the nature of the substituent, but also on its position meta or para) and on the temperature of the experiment. Hammett-type linear free energy relationships show that the reaction constant p changes its sign at ca. 27 °C. Substrates... 

This procedure is far less reliable than that used for the diagonal energies and can benefit from ab initio calculations on the gas phase reaction (see [9]), which can be used as extra constraints on the parameters of eqn. (5.6). However, the calculated difference between the free energy surface in solution and in the enzyme is not very sensitive to the exact value of the It has previously been demonstrated [9] that the dependence of on the reaction free energy is almost linear. Moreover, the relation between and AG is virtually independent of the magnitude of the particular Hy (this is why linear free energy relationships were found to be so powerful in physical organic chemistry [10]). 

Halo-3-deoxychloramphenicols, the derivatives of Cm in which the 3-OH is replaced by a halogen, are competitive inhibitors. The affinity of the inhibitors to the enzyme shows a linear free energy relationship with hydrophobicity (17). 

Finally, it is interesting to note that the free energy relationships elicited in this work might have quite general implications for other enzyme reactions. In fact, the validity of such relationships in enzymes and solutions can be examined by computer simulation methods as has been illustrated in several preliminary studies from this laboratory [9,12b]. It appears that polar sites in enzymes obey to some extent the linear response approximation (the system polarisation is proportional to the applied local field) and therefore follow linear free energy relations. 

Michaelis-Menten equation shows that the enzyme reactions in certain regions can be approximated by linear kinetics. Stucki (1984) demonstrated that variation of the phosphate potential at constant oxidation potential yields linear flow-force relationships in the mitochondria. Through linear flow-force relationships, cells may optimize their free energy production and utilization by lowering their entropy production and hence exergy losses at stationary states. 

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