Bonding pockets

As a compromise, host 6.66 was designed. This species uses a napthyl spacer and incorporates a hydrogen-bond accepting pyridyl moiety at the core of its bonding pocket. One of the hexadiyne bridges has also been replaced by a shorter p-xylyl spacer, which results in additional edge-to-face Jt-Jt interactions. The association constant of this host for p-nitrophenol is much larger ... 

A crystal structure of the peroxidase-substrate complex has been determined at 2.0 A resolution and demonstrated the existence of an aromatic bonding pocket. This hydrophobic distal pocket, containing a benzhydroxamic acid, is created by several phenylalanine residues (Phe-68, Phe-142, Phe-143, and Phe-179) and is close to His-42 and Arg-38. The shape of the distal cavity has been... 

Most medium voltage cables are made with insulation shield layers that are bonded but easily stripped from the insulation in order to avoid pockets of air at the interface and at the same time to allow easy field handling for termination and splicing (during installation). 

The quality of bonding is related direcdy to the size and distribution of solidified melt pockets along the interface, especially for dissimilar metal systems that form intermetaUic compounds. The pockets of solidified melt are brittle and contain localized defects which do not affect the composite properties. Explosion-bonding parameters for dissimilar metal systems normally are chosen to minimize the pockets of melt associated with the interface. 

Cell Construction. Nickel—2iac batteries are housed ia molded plastic cell jars of styrene, SAN, or ABS material for maximum weight savings. Nickel electrodes can be of the siatered or pocket type, however, these types are not cost effective and several different types of plastic-bonded nickel electrodes (78—80) have been developed. 

Even though these enzymes have no absolute specificity, many of them show a preference for a particular side chain before the scissile bond as seen from the amino end of the polypeptide chain. The preference of chymotrypsin to cleave after large aromatic side chains and of trypsin to cleave after Lys or Arg side chains is exploited when these enzymes are used to produce peptides suitable for amino acid sequence determination and fingerprinting. In each case, the preferred side chain is oriented so as to fit into a pocket of the enzyme called the specificity pocket. 

This inhibitor does not form a covalent bond to Ser 195 but one of its carboxy oxygen atoms is in the oxyanion hole forming hydrogen bonds to the main-chain NH groups of residues 193 and 195. The tyrosyl side chain is positioned in the specificity pocket, which derives its specificity mainly from three residues, 216, 226, and 189, as we shall see later. The main chain of... 

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 11.11 Schematic diagrams of the specificity pockets of chymotrypsin, trypsin and elastase, illustrating the preference for a side chain adjacent to the scisslle bond In polypeptide substrates. Chymotrypsin prefers aromatic side chains and trypsin prefers positively charged side chains that can interact with Asp 189 at the bottom of the specificity pocket. The pocket is blocked in elastase, which therefore prefers small uncharged side chains.

Figure 11.14 Schematic diagram of the active site of subtilisin. A region (residues 42-45) of a bound polypeptide inhibitor, eglin, is shown in red. The four essential features of the active site— the catalytic triad, the oxyanion hole, the specificity pocket, and the region for nonspecific binding of substrate—are highlighted in yellow. Important hydrogen bonds between enzyme and inhibitor are striped. This figure should be compared to Figure 11.9, which shows the same features for chymotrypsin. (Adapted from W. Bode et al., EMBO /.

Serine proteinases such as chymotrypsin and subtilisin catalyze the cleavage of peptide bonds. Four features essential for catalysis are present in the three-dimensional structures of all serine proteinases a catalytic triad, an oxyanion binding site, a substrate specificity pocket, and a nonspecific binding site for polypeptide substrates. These four features, in a very similar arrangement, are present in both chymotrypsin and subtilisin even though they are achieved in the two enzymes in completely different ways by quite different three-dimensional structures. Chymotrypsin is built up from two p-barrel domains, whereas the subtilisin structure is of the a/p type. These two enzymes provide an example of convergent evolution where completely different loop regions, attached to different framework structures, form similar active sites. 

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