Binding of charged substrates

The Use of Extramlcellar Probe Luminescence Quenching to Monitor Binding of Charged Substrates to Micelles... 

Residue 189 is at the bottom of the specificity pocket. In trypsin the Asp residue at this position interacts with the positively charged side chains Lys or Arg of a substrate. This accounts for the preference of trypsin to cleave adjacent to these residues. In chymotrypsin there is a Ser residue at position 189, which does not interfere with the binding of the substrate. Bulky aromatic groups are therefore preferred by chymotrypsin since such side chains fill up the mainly hydrophobic specificity pocket. It has now become clear, however, from site-directed mutagenesis experiments that this simple picture does not tell the whole story. 

Monoamine oxidase catalyzes the deamination of primary amines and some secondary amines, with some notable exceptions. Aromatic amines with unsubstituted a-carbon atoms are preferred, but aromatic substituents influence the binding of these substrates. For example, m-iodobenzylamine is a good substrate, whereas the o-iodo analog is an inhibitor. The mechanism of deamination is as follows hydrolysis of the Schiff base that results from loss of a hydride ion on an a-proton yields an aldehyde, which is then normally oxidized to the carboxylic acid. Aromatic substrates are probably preferred because they can form a charge-transfer complex with the FAD at the active site, properly... 

The majority of useful lyase families utilize anionically functionalized substrates such as pyruvate or dihydroxyacetone phosphate which remain unaltered during catalysis. The charged group thereby introduced into the products (phosphate, carboxylate) not only constitutes a handle for binding of the substrates by the enzymes but also can facilitate the preparative isolation from... 

After switching from the active conformation that might be concerned in the binding of the substrate of the MDR P-gp to an inactive conformation, the transient charging-current of the capacitor-like P-gp could be neutralized, or the direction of charge flow could be modified in the system. 

The redox states of the flavin cofactor in a purified flavoenzyme can be conveniently studied by optical spectroscopy (see also Elavoprotein Protocols article). Oxidized (yellow) flavin has characteristic absorption maxima around 375 and 450 nm (Fig. lb and Ic). The anionic (red) and neutral (blue) semiquinone show typical absorption maxima around 370 nm and 580 nm, respectively (Fig. lb and Ic). During two-electron reduction to the (anionic) hydroquinone state, the flavin turns pale, and the absorption at 450 nm almost completely disappears (Fig. lb and Ic). The optical properties of the flavin can be influenced through the binding of ligands (substrates, coenzymes, inhibitors) or the interaction with certain amino acid residues. In many cases, these interactions result in so-called charge-transfer complexes that give the protein a peculiar color. 

FiGDRE 2.S3 Catalytic mechanism for hydrolysis of a peptide bond by chymotrypsin. fa) Four amino adds in the polypeptide chain of chymotrypsin have been shown ro participate in the chemLiitry of catalysis His S7, Asp 102, Gly 193, and Ser 195. (b Binding of the substrate a dietary polypeptide, to the active site of chymotrypsin. (c> The carbonyl group of the target peptide bond of the substrate becomes more polarized. (dl A charge relay... 

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