Specificity of serine proteases

The actual reaction mechanism is very similar for the different members of the family, but the specificity toward the different side chain, R, differs most strikingly. For example, trypsin cleaves bonds only after positively charged Lys or Arg residues, while chymotrypsin cleaves bonds after large hydrophobic residues. The specificity of serine proteases is usually designated by labeling the residues relative to the peptide bond that is being cleaved, using the notation... 

The specificities of serine proteases are exceedingly diverse.16 Occupation of the S rather S subsites is important (terminology from Schechter and Berger 17 Fig. 11.3). 

Change ofSubstrate Specificity with Change of ReactionM Specificity of Serine Proteases... 

Eiectrostatics piays an important role also in substrate specificity of serine proteases. We formulated the similis simili gaudet principle stating that electrostatically similar regions of interacting partners, characterized by MEF values of the same order of magnitude, tend to associate more readily than dissimilar ones. Point mutation experiments on subtilisin support this hypothesis. ... 

Finally, coumarin derivatives may act as general inhibitors of serine proteases or as specific inhibitors of human leukocyte elastase, depending on the nature of the substituents, through two distinct mechanisms, suicide substrates (a-chymotrypsin)... 

Hydrogen bonds appear to be essential in all enzyme-catalyzed reactions, although why they are essential and how they promote function is an open question. In recent years a specific hypothesis for their involvement in catalysis has emerged so-called low-barrier hydrogen bonds (LBHB) have been proposed to lower the transition state energy for many enzymatic reactions, including those of serine protease, citrate... 

Several extracellular proteases have been purified and characterized from entomopathogenic fungi. Molecular weights, isoelectric points and specific inhibitors of some of these enzymes are summarized in Table 1. The majority of them belong to the family of serine proteases. 

An alkaline Ca2+-dependent protease was purified from B. brongniartii, the other main insect pathogenic Beauveria species, by Erlacher et al. (2006). The enzyme hydrolyzed the chromogenic substrates A-succinyl-Ala-Ala-Pro-Phe-pNA and A-succinyl-Ala-Ala-Pro-Leu-/ NA. Both of these substrates are specific for serine proteases which is in contrast to the fact... 

Induction of mRNAs for several other specific rat hepatic proteins by GH has also been demonstrated [81-83]. The effect could be demonstrated in vivo and in vitro and involved a relatively rapid induction with a 5-fold increase in mRNA levels within 4 h of the administration of GH, although synergism with cortisol (possibly and/or thyroxine) was necessary for a maximal response [83]. cDNAs corresponding to two of the induced proteins have been cloned [82,83] and found to have sequences homologous to those of a known family of serine protease inhibitors. One of these proteins was shown to be secreted as a heavily glycosylated serum protein, and to have potent anti-trypsin activity [83]. Regulation of the production of this protein by GH was shown to occur mainly at the transcriptional level [83]. 

As with all complex biological systems we should not forget the close interplay between oxidative and proteolytic systems (see Fig. 2). For example, it has been shown that at a localised inflammatory site, oxidative inactivation of protease inhibitors may lead to a proteolytic cascade resulting in down-stream MMP activation through the localised action of serine proteinases activating previously latent MMPs (see Fig. 2). Equally, the generation of active MMPs (post-oxidant exposure) may be involved in the site-specific catalytic inactivation of serine-protease inhibitors [59] at an inflammatory site with the consequent generation of an elevated serine protease load and connective tissue proteolysis (see Fig. 2). 

Ecotin (eco) is a potent inhibitor of serine proteases that is derived from Escherichia coli. It was originally named for its ability to inhibit trypsin (E. coli trypsin inhibitor), but it is known to interact with and inhibit virtually all characterized tryp-sin-fold serine proteases. It is insensitive to the active site PI preference of the protease (the amino acid N-terminal to the cleaved or scissile bond ) and inhibits proteases with specificity towards basic, large hydrophobic, small aliphatic and acidic amino acids [2]. This remarkable breadth of inhibition classifies eco as a fold-specific inhibitor. It forms a unique tetrameric complex consisting of two protease molecules and two inhibitor molecules (the E2P2 complex), binding in a bi-dentate manner with two surface loop regions known as the primary and secondary sites (3) (Fig. 7.1). Eco itself is a 142 amino acid protein that forms a stable... 

Eco is a powerful tool for defining the active sites of serine protease due to the extended substrate-like interaction that it makes with the protease. The three-dimensional structure of a complex with eco has many advantages that a structure of a protease alone or bound to a small molecule inhibitor does not have. Eco can be used to take a molecular impression of the serine protease active site and reveal features that determine substrate preference. These features are used to design specific inhibitors with therapeutic prospects. Often, a small molecule inhibitor is used to define a protease active site cleft, but the resulting structures have particular drawbacks. Typically, a small molecule inhibitor lacks the prime side interac-... 

DCI was developed by James C. Powers and coworkers at Georgia Institute of Technology (Harper, J.W., Hemmi, K., and Powers, J.C., Reaction of serine proteases with substituted isocoumarins discovery of 3,4-dichloroisocoumatin, a new general mechanism-based serine protease inhibitor, Biochemistry 24,1831-1841,1985). This inhibitor is reasonably specific, although side reactions have been described. As with the sulfonyl fluorides and DFR the modification is slowly reversible and enhanced by basic solvent conditions and/or nucleophiles. DCI has been used as a proteosome inhibitor. See Rusbridge, N.M. and... 

Serine residues occurring in the active sites of serine proteases (e.g., chymotryp-sin) or other hydrolyases (e.g., acetylcholinesterase) are specifically modified by diisopropylfluorophosphate in a reaction that is essentially irreversible. 

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 most thoroughly studied mechanism of protein protease inhibitors is that of the standard mechanism (or Canonical or Laskowski mechanism) inhibitors of serine proteases (1) (Fig. 2). Standard mechanism inhibitors include the Kazal, Kunitz, and Bowman-Birk family of inhibitors and bind in a lock-and-key fashion. Ah standard mechanism inhibitors insert a reactive loop into the active site of the protease, which is complementary to the substrate specificity of the target protease and binds in an extended fi-sheet with the enzyme in a substrate-like manner. WhUe bound to the protease, the scissile bond of standard mechaiusm inhibitors is hydrolyzed very slowly, but products are not released and the amide bond is re-ligated. The standard mechanism is an efficient way to inhibit serine proteases, and it is thus used by many structurally... 

Figure 8 Irreversible inhibitors of proteases. Serine and cysteine proteases can be acylated by aza-peptides, which release an alcohol, but cannot be deacylated due to the relative unreactivity of the (thio) acyl-enzyme intermediate. Reactive carbons, such as the epoxide of E64, can alkylate the thiol of cysteine proteases. Phosphonate inhibitors form covalent bonds with the active site serine of serine proteases. Phosphonates are specific for serine proteases as a result of the rigid and well-defined oxyanion hole of the protease, which can stabilize the resulting negative charge. Mechanism-based inhibitors make two covalent bonds with their target protease. The cephalosporin above inhibits elastase [23]. After an initial acylation event that opens the p-lactam ring, there are a number of isomerization steps that eventually lead to a Michael addition to His57. Therefore, even if the serine is deacylated, the enzyme is completely inactive.

Phosphonates (Fig. 8) and sulfonates represent a third class of covalent irreversible inhibitors. These inhibitors adopt a stable tetrahedral geometry and are covalently bound transition-state analogs. They often have a peptide-like specificity element, and the electrophilicity of the leaving groups can be modified to mne the reactivity of the inhibitor. These inhibitors are specific for serine proteases, because the serine protease active site has a well-defined oxyanion hole, which stabilizes the transition-state mimic. 

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