Metabolism allosteric interactions

In the following, we mainly use variants of the functional form given in Eq. (56) to describe cooperativity and allosteric regulation in metabolic systems. In particular, within Section VII.C, we discuss a general functional form of rate equations, including allosteric interaction... 

The metabolic functions of living organisms are maintained by a complex interplay of regulatory networks. Enzymatic activity and gene expression are permanently adapted for an optimum performance and may be completely switched on and off in a reversible manner. Typical mechanisms involved in biological systems include the stimulation and inhibition by control proteins or metabolite molecules, allosteric interactions, proteolytic activation, redox transformations, and reversible covalent bond modifications such as phosphorylation and dephosphorylation (5). 

Allosteric interactions. The flow of molecules in most metabolic pathways is determined primarily by the activities of certain enzymes rather than by the amount of substrate available. Enzymes that catalyze essentially irreversible reactions are likely control sites, and the first irreversible reaction in a pathway (the committed step) is nearly always tightly controlled. Enzymes catalyzing committed steps are allosterically regulated, as exemplified by phosphofructokinase in glycolysis and acetyl CoA carboxylase in fatty acid synthesis. Allosteric interactions enable such enzymes to rapidly detect diverse signals and to adjust their activity accordingly. 

A fourth fate of pyruvate is its oxidative decarboxylation to acetyl CoA. This irreversible reaction inside mitochondria is a decisive reaction in metabolism it commits the carbon atoms of carbohydrates and amino acids to oxidation by the citric acid cycle or to the synthesis of lipids. The pyruvate dehydrogenase complex, which catalyzes this irreversible funneling, is stringently regulated by multiple allosteric interactions and covalent modifications. Pyruvate is rapidly converted into acetyl CoA only if ATP is needed or if two-carbon fragments are required for the synthesis of lipids. 

The presence of a suitable chromophore, such as the PLP cofactor, makes it possible to investigate protein structure-function relationships that may be far removed from the chromophoric site. Tryptophan synthase is considered to be a prototype multienzyme complex in which metabolites are channeled directly between successive metabolic enzymes. As described above, allosteric interactions serve to coordinate catalytic events between the heterologous active sites in the complex. Such close interactions suggest that mutations in one enzyme may affect the reactivity of the other. We have found it possible to study the consequences of mutations in the a-subunit by looking for changes in the presteady state behavior of reactions catalyzed at the (3-site (88, 89). Since amino acid replacements in the a-subunit will not affect the primary amino acid sequence of the P-subunit, alterations in the reactivity of the a2P2 complex will be due primarily to differences in the reactivity of the a-subunit and/or aP-subunit interactions. 

Enzyme activity in secondary metabolism may be influenced not only by the accessibility of precursors but also by the accumulation of products (product inhibition by allosteric interaction or competition with the substrates at the binding sites). Table 8 shows results of in vitro experiments which demonstrate that product inhibition is a property of many secondary metabolic enzymes. In living cells, however, enzymes and secondary products usually are separated by compartmentalization (A 3). It is thus difficult to decide whether product inhibition in vivo occurs as frequently as in vitro. 

Under normal conditions the inductor is a diffusible substance or group of substances, metabolic products of the neighboring tissue. The closer the contact, the higher the concentration of these products. For this reason the reaction of the receptor systems has not developed very narrow specificity in the course of evolution. A reaction has developed to a signal, which could be an individual compound. However, this does not mean that other compounds cannot act as such signals. Under normal conditions other compounds simply are not present, and the receptor systems have not therefore developed very narrow specificity of reaction such as occurs during the allosteric interaction of specific proteins in the phenomena of substrate induction in bacteria (see Chapter 3). 

In die metabolic pathway to an amino add several steps are involved. Each step is die result of an enzymatic activity. The key enzymatic activity (usually die first enzyme in the synthesis) is regulated by one of its products (usually die end product, eg die amino add). If die concentration of die amino add is too high die enzymatic activity is decreased by interaction of die inhibitor with the regulatory site of die enzyme (allosteric enzyme). This phenomenon is called feedback inhibition. 

While the ddNs and ANPs must be converted intracellularly to their 5 -triphosphates (ddNTPs) or diphosphate derivatives before they can interact as competitive inhibitors/alternate substrates with regard to the natural substrates (dNTPs), the NNRTIs do not need any metabolic conversion to interact, noncompetitively with respect to the dNTPs, at an allosteric, non-substrate binding site of the HIV-1 RT. Through the analysis of NNRTI-resistant mutants, combined with site-directed mutagenesis studies, it has become increasingly clear which amino acid residues are involved in the interaction of the NNRTIs with HIV-1 RT, and, since the conformation of the HIV-1 RT has been resolved at 3.0 A resolution [73], it is now possible to visualize the binding site of the NNRTIs [74],... 

Metabolic activators and inhibitors are structurally dissimilar to substrates. These effectors exert regulatory control over catalysis by binding at an allosteric site quite distinct from the catalytic site. Such heterotropic interactions are mediated through conformational changes, often involving subunit interactions. Allosteric effectors can alter the catalytic rate by changing the apparent substrate affinity (K system) or by altering the... 

The enzyme has been partially purified (70-fold) from 38,000 X 9 supernatant fluid from sheep brain homogenates by Ipata (55-58). Thq enzyme (MW 140,000) is reported to be specific for 5 -AMP and 5 -IMP although the substrate specificity does not appear to have been examined closely. 2 - and 3 -AMP are not hydrolyzed (56). Unlike the enzyme from many sources the brain enzyme does not require divalent cations and indeed Co2+, which stimulates several other 5 -nucleotidases, was inhibitory at 5 mM. The enzyme is strongly inhibited by very low concentrations of ATP, UTP, and CTP (50% inhibition by 0.3 pM ATP) but not by GTP. 2 -AMP, 3 -AMP, and a variety of other nucleoside monophosphates, nucleosides, and sugar phosphates do not inhibit. A kinetic examination of ATP, UTP, and CTP inhibition (56-58) revealed that inhibition curves were sigmoidal, indicating cooperativity between inhibitor molecules and an allosteric type of interaction between inhibitor and protein. The metabolic significance of ATP inhibition is... 

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