Protease

Proteases, also called peptidase or proteinase, are a kind of simple destructive enzymes necessary for protein catabolism and the generation of amino acids in primitive organisms by hydrolyzing peptide bonds. Proteases are likely to arise at the earliest stages of protein evolution and have been applied for multiple times. Different classes of protease usually perform the same proteolysis reaction through completely different catalytic mechanisms. Proteases can be found in a wild of sources like animalia, plantae, fungi, bacteria, archaea and viruses and they participate in many body processes including digestion, immune system function, and blood circulation.

Classification

Based on catalytic residue, proteases can be classified into seven broad groups: serine proteases, cysteine proteases, threonine proteases, aspartic proteases, glutamic proteases, metalloproteases, and asparagine peptide lyases with an asparagine to perform an elimination reaction (no need of water).

Actually, proteases are primarily grouped into 84 families according to their evolutionary relationship and classified under four catalytic types: serine, cysteine, aspartic, and metallo proteases. It is until 1995 and 2004 respectively that the threonine and glutamic-acid proteases are described. Asparagine peptide lyase as the seventh catalytic type of proteolytic enzymes is described in 2011. Its proteolytic mechanism is unusual since it executes an elimination reaction, during which the catalytic asparagine forms a cyclic chemical structure that cleaves itself at asparagine residues in proteins under the appropriate conditions. Thanks to the fundamentally different mechanism, it is debatable to include peptide lyase as a peptidase. Alternatively, proteases may also be classified based on the optimal pH at which they are active. Acid proteases, basic proteases (or alkaline proteases) and neutral proteases involved in type 1 hypersensitivity can be found according to this classification method. Another up-to-date classification of protease evolutionary superfamilies could be found in the MEROPS database, where proteases are classified firstly by 'clan' (superfamily) based on structure, mechanism and catalytic residue order. Within each 'clan', proteases are further classified into families on the basis of sequence similarity and each family may have hundreds of related proteases. Up to now, more than 50 clans are known, each one of which indicates an independent evolutionary origin of proteolysis.

Catalytic Mechanism

Proteases are implicated in cutting long protein chains into shorter fragments by splitting the peptide bonds linking amino acid residues. Some could detach the terminal amino acids from the protein chain and others might attack internal peptide bonds of a protein. The process of catalysis is achieved by one of the two following mechanisms. Aspartic, glutamic and metallo-proteases activate a water molecule performing a nucleophilic to directly attack and hydrolyze the peptide bond. Serine, threonine and cysteine proteases adopt a nucleophilic residue (usually in a catalytic triad), which attack the substrate protein to covalently link it with the protease, thus releasing the first half of the product. This covalent acyl-enzyme intermediate is further degraded by the activated water to finish catalysis by liberating the second half of the product and regenerating the free enzyme. Proteolysis might be so promiscuous that a wide range of protein substrates are hydrolyzed. This is the case for digestive enzyme trypsin, which is able to cleave the array of ingested proteins into smaller peptide fragments. However, promiscuous proteases could typically bind to a single amino acid on the substrate and so only have specificity for that residue. Some proteases are quite specific and merely digest substrates with a certain sequence. This level of specificity is a prerequisite for blood clotting and viral polyprotein in order to achieve precise cleavage events. Proteases, being themselves proteins, can also be hydrolyzed by other protease molecules, sometimes of the same variety, which functions as protease activity regulating method. Some proteases behave less active after autolysis while others are more active.

Functions

It has been a long time that studies on proteases have mainly focused on their original roles as blunt aggressors for protein demolition. Beyond these nonspecific degradative functions, proteases also catalyze highly specific reactions of proteolytic processing to produce new protein products, which inaugurates a new era in protease research. A large collection of findings have demonstrated the relevance of proteases in the control of multiple biological processes in all living organisms through regulating the fate, localization, and activity of many proteins, modulating protein-protein interactions, creating new bioactive molecules, contributing to the processing of cellular information, and generating, transducing, and amplifying molecular signals. As a result of these multiple actions, proteases could thereby influence replication and transcription of DNA, proliferation and differentiation of cell, morphogenesis and remodeling of tissue, heat shock and unfolded protein responses, inflammation, immunity, apoptosis, and so on.

Applications

The research value of protease is enormous and proteases have been widely applied in industry, medicine and biological technology. In compliance with the essential roles of proteases in living organisms, minor alterations in proteolytic systems would underlie multiple pathological conditions such as neurodegenerative disorder, cancer, cardiovascular and inflammatory diseases. Therefore, proteases accordingly play significant roles in pharmaceutical industry as potential drug targets or as diagnostic and prognostic biomarkers. A variety of proteases are applied medically both for their native function or completely artificial functions. Proteases also contribute to the processing, maturation, or destruction of specific sets of plant proteins as a reflection of developmental cues or environmental variations. Similarly, many infectious microorganisms take proteases as necessities for replication or treat them as virulence factors, which expedited the development of protease-targeted therapies for the administration of diseases with great relevance to human life. Proteases are also the major focus in the biotechnological industry owing to their usefulness as biochemical reagents or in the manufacture of numerous products. Digestive proteases as part of many laundry detergents can also be used extensively in the bread industry as bread improver.

Biodiversity

Proteases are present in all organisms from prokaryotes to eukaryotes to viruses and involved in a multitude of physiological reactions from simple digestion of food proteins to highly regulated cascades. Proteases in plants with known function are largely involved in developmental regulation and also play a role in regulation of photosynthesis. Animal proteases are helpful to digest the protein in food and control the metabolism. Proteases secreted by bacteria are particularly important to the global carbon and nitrogen cycles in the recycling of proteins, which tends to be regulated by nutritional signals in these organisms. A bacterial protease may also function as an exotoxin or a virulence factor leading to bacterial pathogenesis. Proteases from viruses exhibit high specificity and only split very restricted set of substrate sequences. Proteases can either perform limited proteolysis by breaking specific peptide bonds, depending on the amino acid sequence of a protein, or carry out unlimited proteolysis through completely degrading a peptide to amino acids. The activity can be a destructive change through abolishing a protein's function or digesting it to its principal components, and can also be an activation of a function, and even a signal in a signaling pathway.

Reference

1. López-Otín C, Bond J S. Proteases: multifunctional enzymes in life and disease. J Biol Chem, 2008, 283(45):30433–30437.