Substrate dependence, enzyme activity

The subject of acidity is viewed broadly, and examples are not restricted to IEs on protonation reactions. Among the generalizations are IEs on Lewis acidity and basicity, IEs on conformational and tautomeric equilibria that can be converted into IEs on acidity, and IEs in chromatographic separations that depend on IEs on acidity. IEs on enzyme-catalyzed reactions are omitted, because their emphasis is ordinarily on kinetic IEs, which are used to determine mechanisms.4 However, it should be recognized that equilibrium IEs are operative in the association of substrates with enzyme active sites.5,6... 

Mackenzie RE and Baugh CM (1980) Tetrahydropterolypolyglutamate derivatives as substrates of two multifunctional proteins with folate-dependent enzyme activities. Biochimica et Biophysica Acta 611,187-95. 

Paracatalytic enzyme modification is a new type of catalysis-linked and, hence, substrate-dependent enzyme modification. In all instances in which the substrate promotes inactivation of an enzyme by a chemical reagent, particularly by an oxidant, paracatalsrtic modification should he considered to be the underlying mechanism. In contrast to ligand-induced and syncatalytic modifications, paracatalytic modification involves a direct chemical interaction between enzyme-activated substrate and extrinsic reagent. In this respect, it is similar to the chemical trapping of covalent enzyme-substrate intermediates, e.g., the reduction of enzyme-substrate Schiff bases by sodium borohydride in class I fructose-l,6-bis-phosphate aldolases - or in acetoacetate decarboxylase. ... 

FIGURE 19.9 Fructose-2,6-bisphosphate activates phosphofructokinase, iucreasiug the affinity of the enzyme for fructose-6-phosphate and restoring the hyperbolic dependence of enzyme activity on substrate. 

Ornithine decarboxylase is a pyridoxal dependent enzyme. In its catalytic cycle, it normally converts ornithine (7) to putrisine by decarboxylation. If it starts the process with eflornithine instead, the key imine anion (11) produced by decarboxylation can either alkylate the enzyme directly by displacement of either fluorine atom or it can eject a fluorine atom to produce viny-logue 12 which can alkylate the enzyme by conjugate addidon. In either case, 13 results in which the active site of the enzyme is alkylated and unable to continue processing substrate. The net result is a downturn in the synthesis of cellular polyamine production and a decrease in growth rate. Eflornithine is described as being useful in the treatment of benign prostatic hyperplasia, as an antiprotozoal or an antineoplastic substance [3,4]. 

Acyloins (a-hydroxy ketones) are formed enzymatically by a mechanism similar to the classical benzoin condensation. The enzymes that can catalyze reactions of this type arc thiamine dependent. In this sense, the cofactor thiamine pyrophosphate may be regarded as a natural- equivalent of the cyanide catalyst needed for the umpolung step in benzoin condensations. Thus, a suitable carbonyl compound (a -synthon) reacts with thiamine pyrophosphate to form an enzyme-substrate complex that subsequently cleaves to the corresponding a-carbanion (d1-synthon). The latter adds to a carbonyl group resulting in an a-hydroxy ketone after elimination of thiamine pyrophosphate. Stereoselectivity of the addition step (i.e., addition to the Stand Re-face of the carbonyl group, respectively) is achieved by adjustment of a preferred active center conformation. A detailed discussion of the mechanisms involved in thiamine-dependent enzymes, as well as a comparison of the structural similarities, is found in references 1 -4. 

FIGURE 6-3 Dependence of the velocity of an enzyme-catalyzed reaction upon the substrate concentration (at a constant level of enzyme activity). 

Enzyme activity in organic solvents depends on parameters such as water activity, pH control, substrate-product solvation, enzyme form, and nature of the solvent. 

So far, it has been established from in vitro studies that the enzyme undergoes phosphorylation, a process that changes the conformation of the enzyme protein and leads to an increase in its activity. This involves Ca +/calmodulin-dependent protein kinase II and cAMP-dependent protein kinase which suggests a role for both intracellular Ca + and enzyme phosphorylation in the activation of tryptophan hydroxylase. Indeed, enzyme purified from brain tissue innervated by rostrally projecting 5-HT neurons, that have been stimulated previously in vivo, has a higher activity than that derived from unstimulated tissue but this increase rests on the presence of Ca + in the incubation medium. Also, when incubated under conditions which are appropriate for phosphorylation, the of tryptophan hydroxylase for its co-factor and substrate is reduced whereas its Fmax is increased unless the enzyme is purified from neurons that have been stimulated in vivo, suggesting that the neuronal depolarisation in vivo has already caused phosphorylation of the enzyme. This is supported by evidence that the enzyme activation caused by neuronal depolarisation is blocked by a Ca +/calmodulin protein kinase inhibitor. However, whereas depolarisation... 

The enzyme had a requirement for calcium. The addition of EDTA to the reaction mixtures, resulted in complete loss of activity, whereas the addition of CaCl2 increased the activity (figure 8). Presumably, sufficient contaminating calcium ions were present in the dialyzed enzyme and substrate mixture to permit the limited activity of the controls, but apparently these were removed by chelation with EDTA. The optimum concentration was in the range of 5 to 15 M, and higher concentration resulted in a decrease in activity. Phoma medicaginis var. pinodella synthesizes a pectin lyase that lacked an absolute requirement for calcium ions but maximum enzyme activity required the presence of 1 mM Ca [25]. The lyase from Fusarium solani f sp. phaseoli, that is active on pectin and pectic acid, is calcium-dependent [30]. Most of the pectate lyases characterized are calcium-dependent the pectate lyase from Rhizoctonia solani [34] and the endopectate lyase fi om Fusarium solani f sp. pisi [31]. 

The diagnosis of PK deficiency depends on the determination of quantitative enzyme activity or qualitative abnormalities of the enzyme. In 1979, the International Committee for Standardization in Haematology (ICSH) established methods for the biochemical characterization of red blood cell PK variants (M22). Since the establishment of these methods, many PK-deficient cases have been characterized, including 13 cases of homozygous PK deficiency. Residual red blood cell PK activity is not usually associated with phenotypic severity,whereas enzymatic characteristics such as decreased substrate affinity, thermal instability, or impaired response to the allosteric activator fructose-1,6-diphosphate (F-1,6-DP) correspond to a more severe phenotype. 

The specificity of substrate utilization depends on the well-defined arrangement of atoms in the enzyme active site that in some way complements the structure of the substrate molecule. 

Approximation refers to the bringing together of the substrate molecules and reactive functionalities of the enzyme active site into the required proximity and orientation for rapid reaction. Consider the reaction of two molecules, A and B, to form a covalent product A-B. For this reaction to occur in solution, the two molecules would need to encounter each other through diffusion-controlled collisions. The rate of collision is dependent on the temperature of the solution and molar concentrations of reactants. The physiological conditions that support human life, however, do not allow for significant variations in temperature or molarity of substrates. For a collision to lead to bond formation, the two molecules would need to encounter one another in a precise orientation to effect the molecular orbitial distortions necessary for transition state attainment. The chemical reaction would also require... 

Because mechanism-based inactivators behave as alternative substrates for the enzyme, they must bind in the enzyme active site. Binding of a mechanism-based inactivator is therefore mutually exclusive with binding of the cognate substrate of the normal enzymatic reaction (we say cognate substrate here because for bisubstrate reactions, the mechanism-based inactivator could be competitive with one substrate and noncompetitive or uncompetitive with the other substrate of the reaction, depending on the details of the reaction mechanism). Thus, as the substrate concentration is increased, the observed rate of inactivation should decrease (Figure 8.10) as... 

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