Mammalian serine proteases

J Greer. Comparative modelling methods Application to the family of the mammalian serine proteases. Proteins 7 317-334, 1990. 

The starting point for much of the work described in this article is the idea that quinone methides (QMs) are the electrophilic species that are generated from ortho-hydro-xybenzyl halides during the relatively selective modification of tryptophan residues in proteins. Therefore, a series of suicide substrates (a subtype of mechanism-based inhibitors) that produce quinone or quinonimine methides (QIMs) have been designed to inhibit enzymes. The concept of mechanism-based inhibitors was very appealing and has been widely applied. The present review will be focused on the inhibition of mammalian serine proteases and bacterial serine (3-lactamases by suicide inhibitors. These very different classes of enzymes have however an analogous step in their catalytic mechanism, the formation of an acyl-enzyme intermediate. Several studies have examined the possible use of quinone or quinonimine methides as the latent... 

The mammalian serine proteases have a common tertiary structure as well as a common function. The enzymes are so called because they have a uniquely reactive serine residue that reacts irreversibly with organophosphates such as diisopropyl fluorophosphate. The major pancreatic enzymes—trypsin, chymotrypsin, and elastase—are kinetically very similar, catalyzing the hydrolysis of peptides... 

The mammalian serine proteases appear to represent a classic case of divergent evolution. All were presumably derived from a common ancestral serine protease.23 Proteins derived from a common ancestor are said to be homologous. Some nonmammalian serine proteases are 20 to 50% identical in sequence with their mammalian counterparts. The crystal structure of the elastase-like protease from Streptomyces griseus has two-thirds of the residues in a conformation similar to those in the mammalian enzymes, despite having only 186 amino acids in its sequence, compared with 245 in a-chymotrypsin. The bacterial enzymes and the pancreatic ones have probably evolved from a common precursor. 

The first crystal structure of a bacterial serine protease to be solved—subtilisin, from Bacillus amyloliquefaciens—revealed an enzyme of apparently totally different construction from the mammalian serine proteases (Figure 1.17). This was not unexpected, since there is no sequence homology between them. But closer examination shows that they are functionally identical in terms of substrate binding and catalysis. Subtilisin has the same catalytic triad, the same system of hydrogen bonds for binding the carbonyl oxygen and the acetamido NH of the substrate, and the same series of subsites for binding the acyl portion of... 

For instance, the mammalian serine proteases — trypsin, chymotrypsin, and elastase—are very similar in structure and conformation. If a new mammalian serine protease is discovered, and sequence homology with known proteases... 

The serine proteases are divided into at least two genetic families the mammalian serine proteases, such as trypsin, chymotrypsin, elastase, the enzymes of the blood clotting system, and many other proteases with specific roles in control of systems and the bacterial proteases called subtilisins (first to be isolated from Bacillus amyloliquefaciens), which are genetically unrelated to the mammalian enzymes but independently evolved the same mechanism (evolutionary convergence). 

Greer, J., Comparative model-building of the mammalian serine proteases, J. Mol. Biol, 153, 1027, 1981. 

The polymer passes the tests of compostability, provided that the thickness of the parts do not exceed around 2-3 mm. The extracellular enzymatic degradation consists of two steps a) the enzyme is adsorbed on the polymer surface, through its binding site and b) ester bonds are cleaved through the catalytic site of the enzyme [61]. The polymer chain ends are attacked preferentially. The biodegradation rate is a function of the crystallinity and the content of L-monomers [68]. Some enzymes (proteases) that may degrade PLA are proteinase K, pronase and bromelain. Subtilisin, a microbial serine protease, and some mammalian serine proteases, such as a-chymotrypsin, tr)rpsm and elastase, could also degrade PLA [20, 61, 67]. 

Modeling Methods Application to the Family of the Mammalian Serine Proteases. 

The catalytic mechanism of the subtilisins is the same as that of the digestive enzymes trypsin and chymotrypsin as well as that of enzymes in the blood clotting cascade, reproduction and other mammalian enzymes. The enzymes are known as serine proteases due to the serine residue which is crucial for catalysis (Kraut, 1977 and Polgar, 1987)... 

Inhibits serine proteases such as trypsin and chymotrypsin. Also inhibits cysteine proteases (reversible by reduced thiols) and mammalian acetylcholinesterase Inhibits ATPase, alkaline phosphatase and tyrosine phosphatase Reagent for maintaining -SH groups in the reduced state. Effective for reducing protein disulfide bonds prior to SDS-PAGE... 

Mammalian PCs, just like kexin, cleave their substrates carboxy-terminal of paired basic residues and they share a conserved catalytic domain resembling that of bacterial subtilisins. The catalytically important residues Asp, His, and Ser are arranged in the catalytic triad in a way that is typical for subtilisins but distinct from the arrangement found within the (chymo)trypsin clan of serine proteases. The subtilisins and (chymo)trypsins have thus served as a prime example of convergent evolution [140,141],... 

The serine proteases are a large family of proteolytic ( enzymes that use the reaction mechanism for nucleophilic catalysis outlined in equations (3) and (4), with a serine residue as the reactive nucleophile. The best known members of the family are three closely related digestive enzymes trypsin, chymotrypsin, and elastase. These enzymes are synthesized in the mammalian pancreas as inactive precursors termed zymogens. They are secreted into the small intestine, where they are activated by proteolytic cleavage in a manner discussed in chapter 9. 

Recently discovered antitumor monocyclic and bicyclic (3-lactam systems [40-42] are, in general, in good agreement with the phenomenon of azetidin-2-one pharmacophore of inexhaustible pharmacological potential on account of the specific ability of its numerous derivatives to inhibit not only bacterial transpeptidase, but also mammalian serin and cystein proteases [43]. As a measure of cytotoxicity, some compounds have been assayed against nine human cancer cell lines. 

The strategy used by the cysteine proteases is most similar to that used by the chymotrypsin family. In these enzymes, a cysteine residue, activated by a histidine residue, plays the role of the nucleophile that attacks the peptide bond (see Figure 9.18). in a manner quite analogous to that of the serine residue in serine proteases. An ideal example of these proteins is papain, an enzyme purified from the fruit of the papaya. Mammalian proteases homologous to papain have been discovered, most notably the cathepsins, proteins having a role in the immune and other systems. The cysteine-based active site arose independently at least twice in the course of evolution the caspases, enzymes that play a major role in apoptosis (Section 2.4.3). have active sites similar to that of papain, but their overall structures are unrelated. 

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