Chymotrypsin substrate binding

Inhibitors as well as substrates bind in this crevice between the domains. From the numerous studies of different inhibitors bound to serine pro-teinases we have chosen as an illustration the binding of a small peptide inhibitor, Ac-Pro-Ala-Pro-Tyr-COOH to a bacterial chymotrypsin (Figure 11.9). The enzyme-peptide complex was formed by adding a large excess of the substrate Ac-Pro-Ala-Pro-Tyr-CO-NHz to crystals of the enzyme. The enzyme molecules within the crystals catalyze cleavage of the terminal amide group to produce the products Ac-Pro-Ala-Pro-Tyr-COOH and NHs. The ammonium ions diffuse away, but the peptide product remains bound as an inhibitor to the active site of the enzyme. 

Figure 11.9 A diagram of the active site of chymotrypsin with a bound inhibitor, Ac-Pro-Ala-Pro-Tyr-COOH. The diagram illustrates how this inhibitor binds in relation to the catalytic triad, the strbstrate specificity pocket, the oxyanion hole and the nonspecific substrate binding region. The Inhibitor is ted. Hydrogen bonds between Inhibitor and enzyme are striped. (Adapted from M.N.G. James et al., /. Mol. Biol. 144 43-88, 1980.)...

Figure 11.10 Topological diagram of the two domains of chymotrypsin, illustrating that the essential active-site residues are part of the same two loop regions (3-4 and 5-6, red) of the two domains. These residues form the catalytic triad, the oxyanion hole (green), and the substrate binding regions (yellow and blue) including essential residues in the specificity pocket.

FIGURE 16.19 The substrate-binding pockets of trypsin, chymotrypsin, and elastase. 

Fig. 2. Model image of a typical substrate bound to ot-Chymotrypsin. (a) Binding of the substrate, (b) Three additional hydrogen bonds stabilize the intermediate oxyanion.

These loops are not part of the Sj binding site or the other direct substrate binding subsites. A further mutation of Tyr-172 — Trp in a third distal loop was required for an additional 50-fold enhancement of binding to give a mutant with about 10% of the kcat/KM of chymotrypsin.140... 

The binding site for a polypeptide substrate consists of a series of subsites across the surface of the enzyme. By convention, they are labeled as in Figure 1.24. The substrate residues are called P (for peptide) the subsites, S. Except at the primary binding site S, for the side chains of the aromatic substrates of chymotrypsin or the basic amino acid substrates of trypsin, there is no obvious, well-defined cleft or groove for substrate binding. The subsites run along the surface of the protein. 

Fiqtire 3.5 (a) Competitive inhibition inhibitor and substrate compete for the same binding site. For example, indole, phenol, and benzene bind in the binding pocket of chymotrypsin and inhibit the hydrolysis of derivatives of tryptophan, tyrosine, and / phenylalanine, (b) Noncompetitive inhibition inhibitor and substrate bind simultaneously to the enzyme. An example is the inhibition of fructose 1,6-diphosphatase by AMP. This type of inhibition is very common with multisubstrate enzymes. A rare example of / uncompetitive inhibition of a single-substrate enzyme is the inhibition of alkaline phosphatase by L-phenylalanine. This enzyme is composed of two identical subunitjs, so presumably the phenylalanine binds at one site and the substrate at the other. [From N. K. Ghosh and W. H. Fishman, J. Biol. Chem. 241, 2516 (1966) see also M. Caswell and M. Caplow, Biochemistry 19, 2907 (1980). 

In this assay, enzymes with chymotrypsin-like specificity readily bind the side chain of Phe at the primary substrate binding site (SI) and subsequently hydrolyze the adjacent amide bond linking the Phe residue to the p-NA moiety. On cleavage, the release of p-NA is measured by the increase in absorbance at 410 nm (e4l0 = 8480 M 1 cm-1) with time, using a recording spectrophotometer. 

Most of the enzymes show extremely strict chiral recognitions, and only one of the enantiomers can be the substrate of the enzyme. For example, chymotrypsin incorporates L-peptides only to the enzyme-substrate binding site to form enzyme-substrate complex, so it shows very high enantioselectivity (Figure 3 (a)). Oxidoreductases also form the enzyme-substrate complex of only one enantiomer, so enantioselectivities are high when isolated enzymes are used for reactions instead of whole cells containing both (R)- and (.S )-specific enzymes, which leads to overall low enantioselectivities. 

Fig. 2. Schematic representation of the substrate-binding sites in the serine proteases (a) trypsin, (b) chymotrypsin and (c) elastase.

Amongst the subnanomolar chymotrypsin inhibitors, modelling of one of the best variants implied a novel inhibitory mechanism for protein serine protease inhibitors, in which two amino acid side chains (arginine and aspartic acid) intrude into the proximity of the catalytic triad of the protease rather than binding in the substrate-binding pockets (see Fig. 4). 

Within each protease family, individual members will differ in their substrate specificity. Most proteases have extended substrate binding sites and will bind to and recognize several amino acid residues of a polypeptide substrate (see Figure 2). Usually one of these will be the primary binding site. For example, in the serine proteases chymotrypsin, trypsin, and elastase, the primary substrate binding site is the Si subsite... 

Essentially, a-chymotrypsin has these characteristics the selectivity in the substrate binding, the charge-relay system in the active center and a contribution of the bound substrate to the catalysis, as cooperativities. 

Blevins and Tulinsky (1985) made the suggestion, based on a 1.67 A resolution structure for qe-chymotrypsin, that several molecules of the specificity-site water are not displaced on substrate binding and may serve to position the substrate. 

Blevins and Tulinsky (1985) suggested two functions for the solvent at the chymotrypsin active site (1) solvation of the Asp—His—Ser catalytic triad, and (2) a guiding effect on the substrate in formation of the enzyme-substrate complex, provided by several waters at the end of the specificity site. X-Ray diffraction results have suggested a role of active-site water in determining the kinetics or equilibria of substrate binding for other proteins (Section IV). 

Serine proteases are widely distributed and have many different functions. They are products of at least two evolutionary pathways, which originate in prokaryotes. Many of them resemble trypsin, chymotrypsin, elastase, or sub-tilisin in specificity, but serine proteases with quite different specificities have been isolated recently. A recent NMR study of a bacterial protease labelled with at carbon 2 of its single imidazole groups implicates a buried side chain of aspartic acid as the ultimate base for proton transfers in catalysis and eliminates a charge separation from reaction schemes for catalysis. Much of the catalytic effectiveness of serine proteases can be attributed to substrate binding, but the interactions which yield a Michaelis complex are supplemented by others which stabilize intermediates on the reaction pathway. 

The Reaction Site (Ser-195). Ser-195 is located immediately adjacent to the substrate binding pocket. It is the serine which is esterified by DFP. It also is acylated during the hydrolysis of substrates such as p-nitrophenyl acetate and, as discussed in detail by Bender and Kill-heflFer (23) in a recent review on chymotrypsin, it was established many years ago that hydrolysis by a serine protease is the result of an acylation and a deacylation at Ser-195 ... 

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