Molecules, effector

Effector molecules switch allosteric proteins between R and T states... 

Figure 6.25 Schematic diagram of the structure of one dimer of phosphofructokinase. Each polypeptide chain is folded Into two domains (blue and red, and green and brown), each of which has an oi/p structure. Helices are labeled A to M and p strands 1 to 11 from the amino terminus of one polypeptide chain, and respectively from A to M and 1 to 11 for the second polypeptide chain. The binding sites of substrate and effector molecules are schematically marked In gray. The effector site of one subunit is linked to the active site of the other subunit of the dimer through the 6-F loop between helix F and strand 6. (Adapted from T. Schlrmer and P.R. Evans, Nature 343 140-145, 1990.)...

Many biochemical and biophysical studies of CAP-DNA complexes in solution have demonstrated that CAP induces a sharp bend in DNA upon binding. This was confirmed when the group of Thomas Steitz at Yale University determined the crystal structure of cyclic AMP-DNA complex to 3 A resolution. The CAP molecule comprises two identical polypeptide chains of 209 amino acid residues (Figure 8.24). Each chain is folded into two domains that have separate functions (Figure 8.24b). The larger N-terminal domain binds the allosteric effector molecule, cyclic AMP, and provides all the subunit interactions that form the dimer. The C-terminal domain contains the helix-tum-helix motif that binds DNA. 

Some of the procaryotic DNA-binding proteins are activated by the binding of an allosteric effector molecule. This event changes the conformation of the dimeric protein, causing the helix-tum-helix motifs to move so that they are 34 A apart and able to bind to the major groove. The dimeric repressor for purine biosynthesis, PurR, induces a sharp bend in DNA upon binding caused by insertion of a helices in the minor groove between the two... 

Figure 13.2 Activated G protein receptors, here represented as seven red transmembrane helices, catalyze the exchange of GTP for GDP on the Gapy trimer. The then separated Ga-GTP and Gpy molecules activate various effector molecules. The receptor is embedded in the membrane, and Ga, Gpy and G py are attached to the membrane by lipid anchors, and they all therefore move in two dimensions. (Adapted from D. Clapham, Nature 379 297-299, 1996.)...

The Gpy dimer appears to function as a rigid unit with critical residues positioned to interact with Ga-GDP. Whereas Ga activation proceeds through nucleotide-dependent structural reorganization, activation of Gpy occurs solely as a function of its release from Ga. As we will see, the Ga subunit acts as a negative regulator of Gpy by masking sites on the surface of Gpy that interact with downstream effector molecules. 

I IS. Hibbs-. B, Taintor, R. R., Vavrm, Z., and Rachlin, E. M. (1988). Nitric oxide A cytotoxic activated macrophage effector molecule. Biochem. Biophys. Res. Commun. 1.57, 87-99,... 

Regulatory or allosteric enzymes like enzyme 1 are, in some instances, regulated by activation. That is, whereas some effector molecules such as F exert negative effects on enzyme activity, other effectors show stimulatory, or positive, influences on activity. 

We shall first consider those regulatory processes which are distinctive for NCR and which make the expression of permease genes either inducible (i.e., dependent on an inducing effector molecule) or constitutive (i.e., occurring without addition of an exogenous effector). 

Either free Ga-GTP or free G 3y (or sometimes both) interacts with the effector molecule to activate or inhibit it (see below for examples). This activation is persistent unless... 

Oswald, I.P., Wynn, T.A., Sher, A. and James, S.L. (1994) NO as an effector molecule of parasite killing modulation of its synthesis by cytokines. Comparative Biochemistry, Physiology, Pharmacology, Toxicology and Endocrinology 108,11-18. 

Allosterism The binding of an effector molecule to a seperate site on the enzyme affects the Km or Vmax of the enzyme. 

The separation between allosteric effectors and cooperativity lies in the molecule doing the affecting. If the effector molecule acts at another site and the effector is not the substrate, the effect is deemed allosteric and heterotropic. If the effector molecule is the substrate itself, the effect is called cooperative and/or homotropic. 

Substrates can affect the conformation of the other active sites. So can other molecules. Effector molecules other than the substrate can bind to specific effector sites (different from the substrate-binding site) and shift the original T-R equilibrium (see Fig. 8-9). An effector that binds preferentially to the T state decreases the already low concentration of the R state and makes it even more difficult for the substrate to bind. These effectors decrease the velocity of the overall reaction and are referred to as allosteric inhibitors. An example is the effect of ATP or citrate on the activity of phosphofructokinase. Effectors that bind specif-... 

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