Proteolytic enzymes specificity

Like all catalysts, proteolytic enzymes (specific proteins obtained from animals, vegetables, or, more extensively, from microbial cultures) do not shift the reaction equilibrium. Enzymes are able to open an alternative pathway, with a lower energy barrier, and accelerate the hydrolysis by lowering the free energy of the transition state (Fig. 5) (11). 

FIGURE 5.20 Trypsin is a proteolytic enzyme, or protease, that specifically cleaves only those peptide bonds in which arginine or lysine contributes the carbonyl function. The products of the reaction are a mixture of peptide fragments with C-terminal Arg or Lys residues and a single peptide derived from the polypeptide s C-terminal end. 

Mammals, fungi, and higher plants produce a family of proteolytic enzymes known as aspartic proteases. These enzymes are active at acidic (or sometimes neutral) pH, and each possesses two aspartic acid residues at the active site. Aspartic proteases carry out a variety of functions (Table 16.3), including digestion pepsin and ehymosin), lysosomal protein degradation eathepsin D and E), and regulation of blood pressure renin is an aspartic protease involved in the production of an otensin, a hormone that stimulates smooth muscle contraction and reduces excretion of salts and fluid). The aspartic proteases display a variety of substrate specificities, but normally they are most active in the cleavage of peptide bonds between two hydrophobic amino acid residues. The preferred substrates of pepsin, for example, contain aromatic residues on both sides of the peptide bond to be cleaved. 

Proteolytic enzyme from the latex of Carica papaya with an approximate molecular weight of 27000. It is differentiated from papain in electrophoresis behavior, in solubility and in substrate specifity. Isolation by acidify of papaya-latex with HCl, salting out with NaCl and following chromatographic purification. The formulation contains L-cysteine as reducing agent. 

The granules contain two types of proteins that result in death. First, compounds that produce holes (pores) in the membrane of the cells these are the proteins, perforin and granulysin. Both insert into the membrane to produce the pores. These were once considered to result in death by lysis (i.e. exchange of ions with extracellular space and entry of water into the cell). However, it is now considered that the role of the pores is to enable enzymes in the granules, known as granzymes, to enter the cell. These granzymes contain proteolytic enzymes. They result in death of the cell by proteolysis but, more importantly, activation of specific proteolytic enzymes, known as caspases. These enzymes initiate reactions that result in programmed cell death , i.e. apoptosis (Chapter 20). 

Figure 20.35 Mechanisms by which external or internal stress leads to cell damage resulting in apoptosis. The stress leads to activation of initiator proteolytic enzymes (caspases) that initiate activation of effector caspases. These enzymes cause proteolytic damage to the cytoskeleton, plasma membrane and DNA. The activation of DNAases in the nucleus results in cleavage of DNA chains between histones that produces a specific pattern of DNA damage which, upon electrophoresis, gives a specific pattern of DNA fragments. The major endproduct of apoptosis are the apoptolic bodies which are removed by the phagocytes.

The proteolytic enzymes are classified into endopeptidases and exopeptidases, according to their site of attack in the substrate molecule. The endopeptidases or proteinases cleave peptide bonds inside peptide chains. They recognize and bind to short sections of the substrate s sequence, and then hydrolyze bonds between particular amino acid residues in a relatively specific way (see p. 94). The proteinases are classified according to their reaction mechanism. In serine proteinases, for example (see C), a serine residue in the enzyme is important for catalysis, while in cysteine proteinases, it is a cysteine residue, and so on. 

Recently, proteolytic enzymes that cleave peptide bonds only adjacent to proline were introduced (Lopez and Edens, 2005). Since proline is involved in the polyphenol-binding sites and there is little proline in the foam-active proteins, these enzymes are specific for haze proteins and do little damage to foam proteins. 

Highly specific proteolytic enzymes cleave a single peptide bond in a naturally occurring substrate. These proteases appear to be Integral parts of many biologic processes and may be contrasted with less specific proteases Isolated from the gastrointestinal tract. 

This chapter aims to summarize our efforts to investigate the effects of fluorinated amino acid substitutes on the interactions with natural protein environments. In addition to a rather specific example concerning the interactions of small peptides with a proteolytic enzyme, we present a simple polypeptide model that aids for a systematic investigation of the interaction pattern of amino acids that differ in side chain length as well as fluorine content within both a hydrophobic and hydrophilic protein environment. Amino acid side chain fluoiination highly affects polypeptide folding due to steric effects, polarization, and fluorous interactions. 

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