 | This articleneeds additional citations forverification. Please helpimprove this article byadding citations to reliable sources. Unsourced material may be challenged and removed. Find sources: "Protease" – news ·newspapers ·books ·scholar ·JSTOR(December 2024) (Learn how and when to remove this message) |
Aprotease (also called apeptidase,proteinase, orproteolytic enzyme)[1] is anenzyme thatcatalyzesproteolysis, breaking downproteins into smallerpolypeptides or singleamino acids, and spurring the formation of new protein products.[2] They do this by cleaving thepeptide bonds within proteins byhydrolysis, a reaction wherewater breaksbonds. Proteases are involved in numerous biological pathways, includingdigestion of ingested proteins,protein catabolism (breakdown of old proteins),[3][4] andcell signaling.
In the absence of functional accelerants, proteolysis would be very slow, taking hundreds ofyears.[5] Proteases can be found in all forms of life andviruses. They have independentlyevolved multiple times, and different classes of protease can perform the same reaction by completely differentcatalytic mechanisms.
Proteases can be classified into seven broad groups:[6]
Proteases were first grouped into 84 families according to their evolutionary relationship in 1993, and classified under four catalytic types:serine,cysteine,aspartic, andmetallo proteases.[7] Thethreonine andglutamic proteases were not described until 1995 and 2004 respectively. The mechanism used to cleave apeptide bond involves making anamino acid residue that has the cysteine and threonine (proteases) or a water molecule (aspartic, glutamic and metalloproteases) nucleophilic so that it can attack the peptidecarbonyl group. One way to make anucleophile is by acatalytic triad, where ahistidine residue is used to activateserine,cysteine, orthreonine as a nucleophile. This is not an evolutionary grouping, however, as the nucleophile types haveevolved convergently in differentsuperfamilies, and some superfamilies show divergent evolution to multiple different nucleophiles. Metalloproteases, aspartic, and glutamic proteases utilize their active site residues to activate a water molecule, which then attacks the scissile bond.[8]
A seventh catalytic type of proteolytic enzymes,asparagine peptide lyase, was described in 2011. Its proteolytic mechanism is unusual since, rather thanhydrolysis, it performs anelimination reaction.[9] During this reaction, the catalyticasparagine forms a cyclic chemical structure that cleaves itself at asparagine residues in proteins under the right conditions. Given its fundamentally different mechanism, its inclusion as a peptidase may be debatable.[9]
An up-to-date classification of protease evolutionarysuperfamilies is found in the MEROPS database.[10] In this database, proteases are classified firstly by 'clan' (superfamily) based on structure, mechanism and catalytic residue order (e.g. thePA clan where P indicates a mixture of nucleophile families). Within each 'clan', proteases are classified intofamilies based on sequence similarity (e.g. the S1 and C3 families within the PA clan). Each family may contain many hundreds of related proteases (e.g.trypsin,elastase,thrombin andstreptogrisin within the S1 family).
Currently more than 50 clans are known, each indicating an independent evolutionary origin of proteolysis.[10]
Alternatively, proteases may be classified by the optimalpH in which they are active:
Proteases are involved indigesting long protein chains into shorter fragments by splitting thepeptide bonds that linkamino acid residues. Some detach the terminal amino acids from the protein chain (exopeptidases, such asaminopeptidases,carboxypeptidase A); others attack internal peptide bonds of a protein (endopeptidases, such astrypsin,chymotrypsin,pepsin,papain,elastase).
Catalysis is achieved by one of two mechanisms:
Proteolysis can be highlypromiscuous such that a wide range of protein substrates are hydrolyzed. This is the case for digestive enzymes such astrypsin, which have to be able to cleave the array of proteins ingested into smaller peptide fragments. Promiscuous proteases typically bind to a singleamino acid on the substrate and so only have specificity for that residue. For example,trypsin is specific for the sequences ...K\... or ...R\... ('\'=cleavage site).[12]
Conversely some proteases are highly specific and only cleave substrates with a certain sequence. Blood clotting (such asthrombin) and viral polyprotein processing (such asTEV protease) requires this level of specificity in order to achieve precise cleavage events. This is achieved by proteases having a long binding cleft or tunnel with several pockets that bind to specified residues. For example,TEV protease is specific for the sequence ...ENLYFQ\S... ('\'=cleavage site).[13]
Proteases, being themselves proteins, are cleaved by other protease molecules, sometimes of the same variety. This acts as a method of regulation of protease activity. Some proteases are less active after autolysis (e.g.TEV protease) whilst others are more active (e.g.trypsinogen).
Proteases occur in all organisms, fromprokaryotes toeukaryotes toviruses. These enzymes are involved in a multitude of physiological reactions from simple digestion of food proteins to highly regulated cascades (e.g., theblood-clotting cascade, thecomplement system,apoptosis pathways, and the invertebrate prophenoloxidase-activating cascade). Proteases can either break specific peptide bonds (limited proteolysis), depending on theamino acid sequence of a protein, or completely break down a peptide to amino acids (unlimited proteolysis). The activity can be a destructive change (abolishing a protein's function or digesting it to its principal components), it can be an activation of a function, or it can be a signal in a signalling pathway.
Plant genomes encode hundreds of proteases, largely of unknown function. Those with known function are largely involved indevelopmental regulation.[14] Plant proteases also play a role in regulation ofphotosynthesis.[15]
Proteases are used throughout an organism for various metabolic processes. Acid proteases secreted into the stomach (such aspepsin) and serine proteases present in theduodenum (trypsin andchymotrypsin) enable the digestion of protein in food. Proteases present in blood serum (thrombin,plasmin,Hageman factor, etc.) play an important role in blood-clotting, as well as lysis of the clots, and the correct action of the immune system. Other proteases are present in leukocytes (elastase,cathepsin G) and play several different roles in metabolic control. Somesnake venoms are also proteases, such aspit viperhaemotoxin and interfere with the victim's blood clotting cascade. Proteases determine the lifetime of other proteins playing important physiological roles like hormones, antibodies, or other enzymes. This is one of the fastest "switching on" and "switching off" regulatory mechanisms in the physiology of an organism.
By a complex cooperative action, proteases can catalyzecascade reactions, which result in rapid and efficient amplification of an organism's response to a physiological signal.
Bacteria secrete proteases tohydrolyse the peptide bonds in proteins and therefore break the proteins down into their constituentamino acids. Bacterial and fungal proteases are particularly important to the globalcarbon andnitrogen cycles in the recycling of proteins, and such activity tends to be regulated by nutritional signals in these organisms.[16] The net impact of nutritional regulation of protease activity among the thousands of species present in soil can be observed at the overall microbial community level as proteins are broken down in response to carbon, nitrogen, or sulfur limitation.[17]
Bacteria contain proteases responsible for general protein quality control (e.g. the AAA+proteasome) by degradingunfolded or misfolded proteins.
A secreted bacterial protease may also act as an exotoxin, and be an example of avirulence factor in bacterialpathogenesis (for example,exfoliative toxin). Bacterial exotoxic proteases destroy extracellular structures.
The genomes of someviruses encode one massivepolyprotein, which needs a protease to cleave this into functional units (e.g. thehepatitis C virus and thepicornaviruses).[18] These proteases (e.g.TEV protease) have high specificity and only cleave a very restricted set of substrate sequences. They are therefore a common target forprotease inhibitors.[19][20]
Archaea use proteases to regulate various cellular processes fromcell-signaling,metabolism,secretion and protein quality control.[21][22] Only two ATP-dependent proteases are found in archaea: the membrane associated LonB protease and a soluble20S proteosome complex .[21]
Proteases are associated withcancer progression due to their ability to degradeextracellular matrices, which facilitatesinvasion andmetastasis; these enzymes target a diversity of substrates and favour all steps of tumour production; some proteases havetumour-suppressive effects, associated with more than 30 different enzymes that belong to three distinct protease classes.[23]
The field of protease research is enormous. Since 2004, approximately 8000papers related to this field were published each year.[24] Proteases are used in industry,medicine and as a basic biological research tool.[25][26]
Digestive proteases are part of manylaundry detergents and are also used extensively in the bread industry inbread improver. A variety of proteases are used medically both for their native function (e.g. controlling blood clotting) or for completely artificial functions (e.g. for the targeted degradation of pathogenic proteins). Highly specific proteases such asTEV protease andthrombin are commonly used to cleavefusion proteins andaffinity tags in a controlled fashion.Protease-containing plant-solutions calledvegetarian rennet have been in use for hundreds of years inEurope and theMiddle East for makingkosher and halal Cheeses. Vegetarian rennet fromWithania coagulans has been in use for thousands of years as aAyurvedic remedy for digestion and diabetes in the Indian subcontinent. It is also used to makePaneer.
The activity of proteases is inhibited byprotease inhibitors.[27] One example of protease inhibitors is theserpin superfamily. It includesalpha 1-antitrypsin (which protects the body from excessive effects of its owninflammatory proteases),alpha 1-antichymotrypsin (which does likewise),C1-inhibitor (which protects the body from excessive protease-triggered activation of its owncomplement system),antithrombin (which protects the body from excessivecoagulation),plasminogen activator inhibitor-1 (which protects the body from inadequate coagulation by blocking protease-triggeredfibrinolysis), andneuroserpin.[28]
Natural protease inhibitors include the family oflipocalin proteins, which play a role in cell regulation and differentiation.Lipophilic ligands, attached to lipocalin proteins, have been found to possess tumor protease inhibiting properties. The naturalprotease inhibitors are not to be confused with theprotease inhibitors used in antiretroviral therapy. Someviruses, withHIV/AIDS among them, depend on proteases in their reproductive cycle. Thus,protease inhibitors are developed asantiviral therapeutic agents.
Other natural protease inhibitors are used as defense mechanisms. Common examples are thetrypsin inhibitors found in the seeds of some plants, most notable for humans being soybeans, a major food crop, where they act to discourage predators. Raw soybeans aretoxic to many animals, including humans, until the protease inhibitors they contain have been denatured.
To assess the relative proficiencies of enzymes that catalyze the hydrolysis of internal and C-terminal peptide bonds [...]
