Allosteric, effectors mechanisms

Stereochemical probes of the specificity of substrates, products, and effectors in enzyme-catalyzed reactions, receptor-ligand interactions, nucleic acid-ligand interactions, etc. Most chirality probe studies attempt to address the stereospecificity of the substrates or ligands or even allosteric effectors. However, upon use of specific kinetic probes, isotopic labeling of achiral centers, chronfium-or cobalt-nucleotide complexes, etc., other stereospecific characteristics can be identified, aU of which will assist in the delineation of the kinetic mechanism as well as the active-site topology. A few examples of chirality probes include ... 

Fig. 9. A schematic drawing of a possible mechanism for the reaction catalyzed by the pyruvate dehydrogenase complex. The three enzymes Elf E2, and E3 are located so that lipoic acid covalently linked to E2 can rotate between the active sites containing thiamine pyrophosphate (TPP) and pyruvate (Pyr) on Elt CoA on E2, and FAD on E3. Acetyl-CoA and GTP are allosteric effectors of E, and NAD+ is an inhibitor of the overall reaction.

A relative of the kinases is adenylate cyclase, whose role in forming the allosteric effector 3, 5 -cyclic AMP (cAMP) was considered in Chapter 11. This enzyme catalyzes a displacement on Pa of ATP by the 3 -hydroxyl group of its ribose ring (see Eq. 11-8, step a). The structure of the active site is known.905 Studies with ATPaS suggest an in-line mechanism resembling that of ribonuclease (step a, Eq. 12-25). However, it is Mg2+ dependent, does not utilize the two-histidine mechanism of ribonuclease A, and involves an aspartate carboxylate as catalytic base.906 All isoforms of adenylate cyclase are activated by the a subunits of some G proteins (Chapter 11). The structures907 of Gsa and of its complex with adenylate kinase905 have been determined. The Gsa activator appears to serve as an allosteric effector. 

Possible mechanisms of hormone action, (a) The hormone (H) theoretically activates an enzyme (E) directly as an allosteric effector. (b) Alternatively, a separate binding protein for the hormone, called a receptor (R), may then activate an enzyme, (c) Another possibility interposes an acceptor protein (A) between the receptor and the enzyme. Each interaction is reversible. 

Just as the auto mechanic sometimes has parts left over, electron-density maps occasionally show clear, empty density after all known contents of the crystal have been located. Apparent density can appear as an artifact of missing Fourier terms, but this density disappears when a more complete set of data is obtained. Among the possible explanations for density that is not artifactual are ions like phosphate and sulfate from the mother liquor reagents like mercaptoethanol, dithiothreitol, or detergents used in purification or crystallization or cofactors, inhibitors, allosteric effectors, or other small molecules that survived the protein purification. Later discovery of previously unknown but important ligands has sometimes resulted in subsequent interpretation of empty density. 

Structural Insights, Glycogen Phosphorylase, looks closely at the structural mechanisms of phosphorylase regulation, examining the efects of allosteric effectors and serine phosphorylation. 

CO2 reduction to formyl-MFR in cell extracts. Cell extracts of Methanobacterium thermoautotrophicum catalyze the formation of formyl-MFR from H2, CO2 and MFR. The rates of formation of formyl-MFR were stimulated by CH3-S-CoM [170,171] or CoM-S-S-HTP [172], suggesting that CO2 activation is coupled with the terminal steps of methane formation ( RPG effect [170], for literature see [173]). The mechanism of that coupling is far from clear. The heterodisulfide may act as an allosteric effector in the activation of low-potential electron carriers in electron flow from H2 to formyl-MFR [173]. It should be pointed out that the RPG effect was not observed in cell extracts of Methanosarcina barkeri[ 14],... 

It is important to distinguish clearly between a covalent modification for activation and an allosteric activation. A covalent modification remains with the enzyme until the modification is enzymatically reversed. For example, phosphorylase kinase and phosphorylase will remain active after phosphorylation until the enzymes are dephosphorylated as catalyzed by phosphoprotein phosphatase. In the case of allosteric activation, the enzyme will remain active as long as there is an elevated allosteric effector such as calcium. As soon as calcium is reconcentrated in subcellular fractions or subcellular organelles and/or extruded from the cell, the enzyme becomes relatively inactive because there is no longer an allosteric activator present. The same is true for allosteric inhibitors. Thus, it is advantageous that both of these mechanisms are available to the cell. 

Lipogenesis is controlled by a number of mechanisms, including allosteric effectors, covalent modification, and availability of substrate. Pyruvate is an excellent potential precursor for fatty acids, particularly in the liver. One of the difficulties encountered is that pyruvate can proceed to acetyl CoA in the mitochondrion, however, acetyl CoA in the mitochondrion will not directly produce fatty-acid synthesis because this process occurs in the cytosol. 

Central to elucidating the mechanism of qE is to understand the role of the xanthophyll cycle. Eirst it is necessary to obtain information on where within the LHCII system the active xanthophyll carotenoids are bound. Information on the structural features of violaxanthin and zeaxanthin that determine their binding to LHCII is needed, just as such information is vital to understanding other allosteric effectors in... 

While developed as possible therapeutics, bisubstrate analogs have found great utility in the dissection and characterization of enzyme structure and mechanism. As discussed below, bisubstrate analogs have been used extensively in structural studies, where the use of natural substrates would result in catalysis, to investigate the architecture of the active site at the Michaelis complex, and to define structural changes at the active site produced by allosteric effectors. In some cases, bisubstrate analogs that are formed during the reaction (a type of mechanism-based inhibitor) can help to support or eliminate proposed chemical mechanisms. 

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