Serine proteases specificity

Pham CT (2006) Neutrophil serine proteases specific regulators of inflammation. Nat Rev Immunol 6 541-550... 

With one recent exception, which is mentioned later, serine protease specificities tend to be related to the nature of the amino acid residue which contributes the carbonyl group to a bond which is susceptible to cleavage, le., to residue Pi of, for example, the polypeptide ... 

Koepke, J. U. Ermler E. Warkentin G. Wenzl P. Flecker. Crystal structure of cancer chemopre-ventive Bowman-Birk inhibitor in ternary complex with bovine trypsin at 2.3 A resolution. Structural basis of Janus faced serine protease specificity./. Mol Biol 2000, 298, 477—481. 

Engineering Substrate Specificity. Although the serine proteases use a common catalytic mechanism, the enzymes have a wide variety of substrate specificities. For example, the natural variant subtiHsins of B. amyloliquefaciens (subtiHsin BPN J and B. licheniformis (subtiHsin Carlsberg) possess very similar stmctures and sequences where 86 of 275 amino acids are identical, but have different catalytic efficiencies, toward tetraamino acid -nitroanilide substrates (67). 

Protein G. This vitamin K-dependent glycoproteia serine protease zymogen is produced ia the Hver. It is an anticoagulant with species specificity (19—21). Proteia C is activated to Proteia by thrombomodulin, a proteia that resides on the surface of endothefial cells, plus thrombin ia the presence of calcium. In its active form, Proteia selectively iaactivates, by proteolytic degradation. Factors V, Va, VIII, and Villa. In this reaction the efficiency of Proteia is enhanced by complex formation with free Proteia S. la additioa, Proteia activates tissue plasminogen activator, which... 

Antibiotic Resistance. Figure 1 According to Bush, Jacoby and Medeiros [2] four molecular classes of (3-lactamases can be discriminated based upon biochemical and molecular features. Classes 1, 2, and 4 included serine-proteases, while metallo enzymes are included in class 3. The substrate spectrum varies between different subclasses and the corresponding genes can be part of an R-plasmid leading to a wider distribution or are encoded chromosomally in cells of specific species. 

More than 50 endogenous and exogenous inhibitors of the calpains have been described as either transition-state reversible or irreversible inhibitors. The first transition-state inhibitors were the peptide aldehydes (e.g., leupeptin). Using this compound, new ones were synthesized that exhibited improved membrane permeability and calpain specificity (e.g., calpeptin). Other groups of inhibitors have since been discovered a-dicarbonyls (originally developed as serine protease inhibitors), nonpeptide quinolinecarboxamides,... 

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 considerations presented above were based on the specific assumption that the catalytic reaction of the serine proteases involves mechanism a of Fig. 7.2. However, one can argue that the relevant mechanism is mechanism b (the so-called charge-relay mechanism ). In principle the proper procedure, in case of uncertainty about the actual mechanism, is to perform the calculations for the different alternative mechanisms and to find out which of the calculated activation barriers reproduces the observed one. This procedure, however, can be used with confidence only if the calculations are sufficiently reliable. Fortunately, in many cases one can judge the feasibility of different mechanisms without fully quantitative calculations by a simple conceptual consideration based on the EVB philosophy. To see this point let us consider the feasibility of the charge-relay mechanism (mechanism b) as an alternative to mechanism a. Starting from Fig. 7.2 we note that the energetics of route b can be obtained from the difference between the activation barriers of route b and route a by... 

Catalysis, specific acid, 163 Catalytic triad, 171,173 Cavity radius, of solute, 48-49 Charge-relay mechanism, see Serine proteases, charge-relay mechanism Charging processes, in solutions, 82, 83 Chemical bonding, 1,14 Chemical bonds, see also Valence bond model... 

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). 

Serine proteases usually show primary specificity (occupation of subsite Si) for positively charged arginine or lysine (trypsin, plasmin, plasminogen activators, thrombin), large hydrophobic side chains of phenylalanine, tyrosine, and tryptophan (chymotrypsin, cathepsin G, chymase, and subtilisin), or small aliphatic side chains (elastases). Nevertheless, there are a large number of variations and in many cases, other subsites like S2 and S3 are more discriminating while maintaining the... 

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)... 

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