PROTEASE (PROTEAZ)
PROTEASE
SYNONYMS; PROTEASE; PEPTIDASE; PROTEASE-ACTIVATED; PROTEOLYTIC ENZYME; PROTEASES; ENZYME; PROTEASE INHIBITORS; PROTEASE INHIBITOR; PROTEASE ENZYME; PROTEAZ; PROTEASE; PROTEAS; CYSTEINE PROTEASE; PROTEASE DOMAIN; SERINE PROTEASE; INSULIN PROTEASE; PROTEOLYTIC ENZYMES; PROTEIN CLEAVING ENZYME; PECTOLYTIC ENZYME; PROTEASE-RESISTANT; CYSTEINE PROTEINASE; PROTEASE; protease; proteinase; proteolytic enzyme; peptidase; PROTEAZ; PROTEAS; ENZYM OF PROTEASE; PROTEASE ENZYM; PROTEAZ ENZM; PROTEAS ENZYM; PROTEAZ NHBTÖRÜ; INHIBITOR OF PROTEASE; INHIBITORS; PROTEAZ; PROTEASE; PEPTIDASE; PROTEASE-ACTIVATED; PROTEOLYTIC ENZYME; PROTEASES; ENZYME; PROTEASE INHIBITORS; PROTEASE INHIBITOR; PROTEASE ENZYME; PROTEAZ; PROTEASE; PROTEAS; CYSTEINE PROTEASE; PROTEASE DOMAIN; SERINE PROTEASE; INSULIN PROTEASE; PROTEOLYTIC ENZYMES; PROTEIN CLEAVING ENZYME; PECTOLYTIC ENZYME; PROTEASE-RESISTANT; CYSTEINE PROTEINASE; PROTEASE; protease; proteinase; proteolytic enzyme; peptidase; PROTEAZ; PROTEAS; ENZYM OF PROTEASE; PROTEASE ENZYM; PROTEAZ ENZM; PROTEAS ENZYM; PROTEAZ NHBTÖRÜ; INHIBITOR OF PROTEASE; INHIBITORS; PROTEAZ; ACE; ANGIOTENSIN-C; PROTEOLYTIC E; RENIN; PEPTIDASE; PEPTIDAS; UROKINASE; PROTEOLYTIC-ENZYME; PROTEASE; PROTEAZ; ENZYME; UROKINASE; RENIN; PROTEOLYTIC ENZYME; PEPTIDASE; CASPASE; ACE; PEPTIDS; PROTEINS; PROTEASE; protease; proteinase; proteolytic enzyme; peptidase; PROTEOLTK; ENZM; NHBTÖR; CATALYST; ADIPOSE; AMINO ACID; ARNICA; AMNO AST; AMNOAST; FATTY ACID; LANOLIN; FORMIC ACID; PEPSIN; PEPTID; ADRENALIN; AMYLASE; ENZYME; FLAVONOID; FRUCTOSE; ; PROTEASE; PEPTIDASE; PROTEASE-ACTIVATED; PROTEOLYTIC ENZYME; PROTEASES; ENZYME; PROTEASE INHIBITORS; PROTEASE INHIBITOR; PROTEASE ENZYME; PROTEAZ; PROTEASE; PROTEAS; CYSTEINE PROTEASE; PROTEASE DOMAIN; SERINE PROTEASE; INSULIN PROTEASE; PROTEOLYTIC ENZYMES; PROTEIN CLEAVING ENZYME; PECTOLYTIC ENZYME; PROTEASE-RESISTANT; CYSTEINE PROTEINASE; PROTEASE; protease; proteinase; proteolytic enzyme; peptidase; PROTEAZ; PROTEAS; ENZYM OF PROTEASE; PROTEASE ENZYM; PROTEAZ ENZM; PROTEAS ENZYM; PROTEAZ NHBTÖRÜ; INHIBITOR OF PROTEASE; INHIBITORS; PROTEAZ; PROTEASE; PEPTIDASE; PROTEASE-ACTIVATED; PROTEOLYTIC ENZYME; PROTEASES; ENZYME; PROTEASE INHIBITORS; PROTEASE INHIBITOR; PROTEASE ENZYME; PROTEAZ; PROTEASE; PROTEAS; CYSTEINE PROTEASE; PROTEASE DOMAIN; SERINE PROTEASE; INSULIN PROTEASE; PROTEOLYTIC ENZYMES; PROTEIN CLEAVING ENZYME; PECTOLYTIC ENZYME; PROTEASE-RESISTANT; CYSTEINE PROTEINASE; PROTEASE; protease; proteinase; proteolytic enzyme; peptidase; PROTEAZ; PROTEAS; ENZYM OF PROTEASE; PROTEASE ENZYM; PROTEAZ ENZM; PROTEAS ENZYM; PROTEAZ NHBTÖRÜ; INHIBITOR OF PROTEASE; INHIBITORS; PROTEAZ; ACE; ANGIOTENSIN-C; PROTEOLYTIC E; RENIN; PEPTIDASE; PEPTIDAS; UROKINASE; PROTEOLYTIC-ENZYME; PROTEASE; PROTEAZ; ENZYME; UROKINASE; RENIN; PROTEOLYTIC ENZYME; PEPTIDASE; CASPASE; ACE; PEPTIDS; PROTEINS; PROTEASE; protease; proteinase; proteolytic enzyme; peptidase; PROTEOLTK; ENZM; NHBTÖR; CATALYST; ADIPOSE; AMINO ACID; ARNICA; AMNO AST; AMNOAST; FATTY ACID; LANOLIN; FORMIC ACID; PEPSIN; PEPTID; ADRENALIN; AMYLASE; ENZYME; FLAVONOID; FRUCTOSE;
Thermo Scientific Proteinase K is a broad-range endolytic protease widely used for digestion of proteins in nucleic acid preparations. It degrades proteins even in the presence of detergents. Proteinase K cleaves peptide bonds at the carboxylic sides of aliphatic, aromatic, or hydrophobic amino acids. The Proteinase K is classified as a serine protease. The smallest peptide to be hydrolyzed by this enzyme is a tetrapeptide.
PROTEASE
ThermoA protease (also called a peptidase or proteinase) is a Trypsin that catalyzes (increases the rate of) proteolysis, the breakdown of proteins into smaller polypeptides or single amino acids. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks bonds. Proteases are involved in many biological functions, including digestion of ingested proteins, protein catabolism (breakdown of old proteins),[1][2] and cell signalling.
Without additional helping mechanisms, proteolysis would be very slow, taking hundreds of years. Proteases can be found in all forms of life and viruses. They have independently evolved multiple times, and different classes of protease can perform the same reaction by completely different catalytic mechanisms.
Scientific Protease K is a broad-range endolytic protease widely used for digestion of proteins in nucleic acid preparations. It degrades proteins even in the presence of detergents. Protease K cleaves peptide bonds at the carboxylic sides of aliphatic, aromatic, or hydrophobic amino acids. The Protease K is classified as a serine protease. The smallest peptide to be hydrolyzed by this enzyme is a tetrapeptide.
A seventh catalytic type of proteolytic enzymes, asparagine peptide lyase, was described in 2011. Its proteolytic mechanism is unusual since, rather than hydrolysis, it performs an elimination reaction.[5] During this reaction, the catalytic asparagine 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.[5]
Without additional helping mechanisms, proteolysis would be very slow, taking hundreds of years. Protease can be found in all forms of life and viruses. They have independently evolved multiple times, and different classes of protease can perform the same reaction by completely different catalytic mechanisms.
An up-to-date classification of protease evolutionary superfamilies is found in the MEROPS database.[6] In this database, proteases are classified firstly by ‘clan’ (superfamily) based on structure, mechanism and catalytic residue order (e.g. the PA clan where P indicates a mixture of nucleophile families). Within each ‘clan’, proteases are classified into families 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 and streptogrisin within the S1 family).
Currently more than 50 clans are known, each indicating an independent evolutionary origin of proteolysis
Proteases are involved in digesting long protein chains into shorter fragments by splitting the peptide bonds that link amino acid residues. Some detach the terminal amino acids from the protein chain (exopeptidases, such as aminopeptidases, carboxypeptidase A); others attack internal peptide bonds of a protein (endopeptidases, such as trypsin, chymotrypsin, pepsin, papain, elastase).
Catalysis is achieved by one of two mechanisms:
• Aspartic, glutamic and metallo- proteases activate a water molecule which performs a nucleophilic attack on the peptide bond to hydrolyse it.
• Serine, threonine and cysteine proteases use a nucleophilic residue (usually in a catalytic triad). That residue performs a nucleophilic attack to covalently link the protease to the substrate protein, releasing the first half of the product. This covalent acyl-enzyme intermediate is then hydrolysed by activated water to complete catalysis by releasing the second half of the product and regenerating the free enzyme.
Proteases were first grouped into 84 families according to their evolutionary relationship in 1993, and classified under four catalytic types: serine, cysteine, aspartic, and metallo proteases.[4] The threonine and glutamic-acid proteases were not described until 1995 and 2004 respectively. The mechanism used to cleave a peptide bond involves making an amino acid residue that has the cysteine and threonine (proteases) or a water molecule (aspartic acid, metallo- and acid proteases) nucleophilic so that it can attack the peptide carboxyl group. One way to make a nucleophile is by a catalytic triad, where a histidine residue is used to activate serine, cysteine, or threonine as a nucleophile. This is not an evolutionary grouping, however, as the nucleophile types have evolved convergently in different superfamilies, and some superfamilies show divergent evolution to multiple different nucleophiles.
Protease is can be classified into seven broad groups:
• Serine protease – using a serine alcohol
• Cysteine protease – using a cysteine thiol
• Threonine protease – using a threonine secondary alcohol
• Aspartic protease – using an aspartate carboxylic acid
• Glutamic protease – using a glutamate carboxylic acid
• Metalloprotease – using a metal, usually zinc
• Asparagine peptide lyases – using an asparagine to perform an elimination reaction (not requiring water)
Proteases were first grouped into 84 families according to their evolutionary relationship in 1993, and classified under four catalytic types: serine, cysteine, aspartic, and metallo proteases. The threonine and glutamic-acid proteases were not described until 1995 and 2004 respectively. The mechanism used to cleave a peptide bond involves making an amino acid residue that has the cysteine and threonine (proteases) or a water molecule (aspartic acid, metallo- and acid proteases) nucleophilic so that it can attack the peptide carboxyl group. One way to make a nucleophile is by a catalytic triad, where a histidine residue is used to activate serine, cysteine, or threonine as a nucleophile. This is not an evolutionary grouping, however, as the nucleophile types have evolved convergently in different superfamilies, and some superfamilies show divergent evolution to multiple different nucleophiles.
Proteolysis can be highly promiscuous such that a wide range of protein substrates are hydrolysed. This is the case for digestive enzymes such as trypsin which have to be able to cleave the array of proteins ingested into smaller peptide fragments. Promiscuous proteases typically bind to a single amino 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).[8]
Conversely some proteases are highly specific and only cleave substrates with a certain sequence. Blood clotting (such as thrombin) and viral polyprotein processing (such as TEV 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 along it which bind the specified residues.
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
Proteases occur in all organisms, from prokaryotes to eukaryotes to viruses. These enzymes are involved in a multitude of physiological reactions from simple digestion of food proteins to highly regulated cascades (e.g., the blood-clotting cascade, the complement system, apoptosis pathways, and the invertebrate prophenoloxidase-activating cascade). Proteases can either break specific peptide bonds (limited proteolysis), depending on the amino 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.
Peptide lyases
A seventh catalytic type of proteolytic enzymes, asparagine peptide lyase, was described in 2011. Its proteolytic mechanism is unusual since, rather than hydrolysis, it performs an elimination reaction. During this reaction, the catalytic asparagine 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.
Evolutionary phylogeny
An up-to-date classification of protease evolutionary superfamilies is found in the MEROPS database. In this database, proteases are classified firstly by ‘clan’ (superfamily) based on structure, mechanism and catalytic residue order (e.g. the PA clan where P indicates a mixture of nucleophile families). Within each ‘clan’, proteases are classified into families 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 and streptogrisin within the S1 family).
Currently more than 50 clans are known, each indicating an independent evolutionary origin of proteolysis.
Proteolysis can be highly promiscuous such that a wide range of protein substrates are hydrolysed. This is the case for digestive enzymes such as trypsin which have to be able to cleave the array of proteins ingested into smaller peptide fragments. Promiscuous proteases typically bind to a single amino acid on the substrate and so only have specificity for that residue.
Conversely some protease s are highly specific and only cleave substrates with a certain sequence. Blood clotting (such as thrombin) and viral polyprotein processing (such as TEV 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 along it which bind the specified residues.
Protease is occur in all organisms, from prokaryotes to eukaryotes to viruses. These enzymes are involved in a multitude of physiological reactions from simple digestion of food proteins to highly regulated cascades (e.g., the blood-clotting cascade, the complement system, apoptosis pathways, and the invertebrate prophenoloxidase-activating cascade). Protease is can either break specific peptide bonds (limited proteolysis), depending on the amino 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.
Protease containing plant-solutions called vegetarian rennet has been in use for hundreds of years in Europe and middle-east for making kosher and halal Cheeses. Vegetarian rennet from Withania coagulans has been in use for thousands of years as Ayurvedic remedy for digestion and diabetes in the Indian subcontinent. It is also used to make Paneer.
Plant genomes encode hundreds of protease is, largely of unknown function. Those with known function are largely involved in developmental regulation. Plant protease is also play a role in regulation of photosynthesis.
Protease s are used throughout an organism for various metabolic processes. Acid proteases secreted into the stomach (such as pepsin) and serine protease s present in duodenum (trypsin and chymotrypsin) enable us to digest the protein in food. Protease s present in blood serum (thrombin, plasmin, Hageman factor, etc.) play 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. Some snake venoms are also protease s, such as pit viper haemotoxin and interfere with the victim’s blood clotting cascade. Protease s determine the lifetime of other proteins playing important physiological role 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 complex cooperative action the proteases may proceed as cascade reactions, which result in rapid and efficient amplification of an organism’s response to a physiological signal.
Bacteria secrete proteases to hydrolyse the peptide bonds in proteins and therefore break the proteins down into their constituent amino acids. Bacterial and fungal proteases are particularly important to the global carbon and nitrogen cycles in the recycling of proteins, and such activity tends to be regulated by nutritional signals in these organisms. 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.[13]
Bacteria contain proteases responsible for general protein quality control (e.g. the AAA+ proteasome) by degrading unfolded or misfolded proteins.
A secreted bacterial protease may also act as an exotoxin, and be an example of a virulence factor in bacterial pathogenesis (for example, exfoliative toxin). Bacterial exotoxic protease s destroy extracellular structures.
Some viruses express their entire genome as one massive polyprotein and use a protease to cleave this into functional units (e.g. polio, norovirus, and TEV protease s).[14] 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 for protease inhibitors.
The field of protease research is enormous. Since 2004, approximately 8000 papers related to this field were published each year.[17] Proteases are used in industry, medicine and as a basic biological research tool.[18][19]
Digestive proteases are part of many laundry detergents and are also used extensively in the bread industry in bread 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 as TEV protease and thrombin are commonly used to cleave fusion proteins and affinity tags in a controlled fashion.
The activity of proteases is inhibited by protease inhibitors.[20] One example of protease inhibitors is the serpin superfamily. It includes alpha 1-antitrypsin (which protects the body from excessive effects of its own inflammatory proteases), alpha 1-antichymotrypsin (which does likewise), C1-inhibitor (which protects the body from excessive protease-triggered activation of its own complement system), antithrombin (which protects the body from excessive coagulation), plasminogen activator inhibitor-1 (which protects the body from inadequate coagulation by blocking protease-triggered fibrinolysis), and neuroserpin.[21]
Natural protease inhibitors include the family of lipocalin 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 natural protease inhibitors are not to be confused with the protease inhibitors used in antiretroviral therapy. Some viruses, with HIV/AIDS among them, depend on proteases in their reproductive cycle. Thus, protease inhibitors are developed as antiviral means.
Other natural protease inhibitors are used as defense mechanisms. Common examples are the trypsin 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 are toxic to many animals, including humans, until the protease inhibitors they contain have been denatured.
Our view of protease s has come a long way since P. A. Levene reported his studies on “The Cleavage Products of Proteose s” in the first issue of The Journal of Biological Chemistry published October 1, 1905 (1). Today, after more than 100 years and 350,000 articles on these enzymes in the scientific literature, protease s remain at the cutting edge of biological research.
Proteases likely arose at the earliest stages of protein evolution as simple destructive enzymes necessary for protein catabolism and the generation of amino acids in primitive organisms. For many years, studies on proteases focused on their original roles as blunt aggressors associated with protein demolition. However, the realization that, beyond these nonspecific degradative functions, proteases act as sharp scissors and catalyze highly specific reactions of proteolytic processing, producing new protein products, inaugurated a new era in protease research (2). The current success of research in this group of ancient enzymes derives mainly from the large collection of findings demonstrating their relevance in the control of multiple biological processes in all living organisms (3–11). Thus, proteases regulate the fate, localization, and activity of many proteins, modulate protein-protein interactions, create new bioactive molecules, contribute to the processing of cellular information, and generate, transduce, and amplify molecular signals. As a direct result of these multiple actions, proteases influence DNA replication and transcription, cell proliferation and differentiation, tissue morphogenesis and remodeling, heat shock and unfolded protein responses, angiogenesis, neurogenesis, ovulation, fertilization, wound repair, stem cell mobilization, hemostasis, blood coagulation, inflammation, immunity, autophagy, senescence, necrosis, and apoptosis. Consistent with these essential roles of proteases in cell behavior and survival and death of all organisms, alterations in proteolytic systems underlie multiple pathological conditions such as cancer, neurodegenerative disorders, and inflammatory and cardiovascular diseases. Accordingly, many proteases are a major focus of attention for the pharmaceutical industry as potential drug targets or as diagnostic and prognostic biomarkers (12). Proteases also play key roles in plants and contribute to the processing, maturation, or destruction of specific sets of proteins in response to developmental cues or to variations in environmental conditions (13). Likewise, many infectious microorganisms require proteases for replication or use proteases as virulence factors, which has facilitated the development of protease-targeted therapies for diseases of great relevance to human life such as AIDS (12). Finally, proteases are also important tools of the biotechnological industry because of their usefulness as biochemical reagents or in the manufacture of numerous products (e.g. Ref. 14).
This outstanding diversity in protease functions directly results from the evolutionary invention of a multiplicity of enzymes that exhibit a variety of sizes and shapes. Thus, the architectural design of proteases ranges from small enzymes made up of simple catalytic units (~20 kDa) to sophisticated protein-processing and degradation machines, like the proteasome and meprin metalloproteinase isoforms (0.7–6 MDa) (15). In terms of specificity, diversity is also a common rule. Thus, some proteases exhibit an exquisite specificity toward a unique peptide bond of a single protein (e.g. angiotensin-converting enzyme); however, most proteases are relatively nonspecific for substrates, and some are overtly promiscuous and target multiple substrates in an indiscriminate manner (e.g. proteinase K). Proteases also follow different strategies to establish their appropriate location in the cellular geography and, in most cases, operate in the context of complex networks comprising distinct proteases, substrates, cofactors, inhibitors, adaptors, receptors, and binding proteins, which provide an additional level of interest but also complexity to the study of proteolytic enzymes.
This work aims at serving as a primer to a minireview series on proteases to be published in forthcoming issues of this Journal. This introductory article will focus on the discussion of the large and growing complexity of proteolytic enzymes present in all organisms, from bacteria to man. We will first show the results of comparative genomic analysis that have shed light on the real dimensions of the proteolytic space. The levels of protease complexity and mechanisms of protease regulation will then be addressed. Finally, we will discuss current frontiers and future perspectives in protease research. Proteases are the efficient executioners of a common chemical reaction: the hydrolysis of peptide bonds protease Most proteolytic enzymes cleave ?-peptide bonds between naturally occurring amino acids, but there are some protease s that perform slightly different reactions. Thus, a large group of enzymes known as DUBs (deubiquitylating enzymes) can hydrolyze isopeptide bonds in ubiquitin and ubiquitin-like protein conjugates; ?-glutamyl hydrolase and glutamate carboxypeptidase target ?-glutamyl bonds; ?-glutamyltransferases both transfer and cleave peptide bonds; and intramolecular autoproteases (such as nucleoporin and polycystin-1) hydrolyze only a single bond on their own polypeptide chain but then lose their proteolytic activity. Notably and under some conditions, protease s can also synthesize peptide bonds.
Protease s were initially classified into endopeptidases, which target internal peptide bonds, and exopeptidases (aminopeptidases and carboxypeptidases), the action of which is directed by the NH2 and COOH termini of their corresponding substrates. However, the availability of structural and mechanistic information on these enzymes facilitated new classification schemes. Based on the mechanism of catalysis, protease s are classified into six distinct classes, aspartic, glutamic, and metalloproteases, cysteine, serine, and threonine protease s, although glutamic protease s have not been found in mammals so far. The first three classes utilize an activated water molecule as a nucleophile to attack the peptide bond of the substrate, whereas in the remaining enzymes, the nucleophile is an amino acid residue (Cys, Ser, or Thr, respectively) located in the active site from which the class names derive (supplemental Fig. 1). Protease s of the different classes can be further grouped into families on the basis of amino acid sequence comparison, and families can be assembled into clans based on similarities in their three-dimensional structures. Bioinformatic analysis of genome sequences has been decisive for establishingthedimensionsofthe complexity of proteolytic systems operating in different organisms The last release of MEROPS a comprehensive data base of proteases and inhibitors, annotates 1008 entries for human proteases and homologs, although it includes a large number of pseudogenes and protease-related sequences derived from endogenous retroviral elements embedded in our genome. A highly curated data base, the Degradome Database, which does not incorporate protease pseudogenes or these retrovirus-derived sequences, lists 569 human proteases and homologs classified into 68 families Metalloproteases and serine proteases are the most densely populated classes, with 194 and 176 members, respectively, followed by 150 cysteine proteases, whereas threonine and aspartic proteases contain only 28 and 21 members, respectively. The recent availability of the genome sequence of different mammals has allowed the identification of their entire protease complement (termed degradome) and their detailed comparison with humans (The chimpanzee degradome is very similar to the human degradome, although it exhibits some remarkable differences in immune defense proteases like caspase-12 Interestingly, mice and rats contain more protease genes (644 and 629, respectively) compared with humans despite the fact that their genomes are smaller These differences derive mainly from the expansion in rodents or the inactivation in humans of members of protease families (such as kallikreins and placental cathepsins) involved in immunological and reproductive functions The recent analysis of the degradome of other mammals such as the duck-billed platypus (Ornithorhynchus anatinus) has revealed some interesting findings on protease evolution. This fascinating monotreme also has more than 500 protease genes but lacks all genes encoding gastric pepsins, which are the archetypal digestive protease s widely conserved in all mammals Birds, amphibians, and fish also contain large numbers of protease genes (382 in Gallus gallus, 278 in Xenopus tropicalis, and 503 in Danio rerio), although the protease annotation work in these species has not been as detailed as in mammals. Surprisingly, analysis of the protease content of invertebrates such as Drosophila melanogaster (a model organism with a gene content considerably lower than that in vertebrates) has shown the presence of more than 600 protease The model plant Arabidopsis thaliana contains at least 723 protease-encoding genes, whereas a total of 955 protease genes have been annotated in the tree Populus trichocarpa. These marked differences are linked to the expansion of some protease families in Populus, especially the copia transposon endopeptidase family of aspartic proteases, which has 20 components in Arabidopsis and 123 in Populus Genomic analyses have also shown that plants share with prokaryotes a set of serine proteases absent in other eukaryotes, which may be an indication of ancient endosymbiotic events leading to evolution of chloroplasts . Finally, there is a growing interest in analyzing the degradome of bacteria, viruses, fungi, and parasites as part of strategies aimed to define novel targets for therapeutic intervention In this regard, the MEROPS Database annotates more than 100 protease genes in the genome of bacteria such as Yersinia pestis and Legionella pneumophila or in the malaria parasite Plasmodium falciparum, which cause devastating human diseases.
In summary, the emerging pattern derived from the global analysis of proteolytic systems is one of diversity and multiplicity. These comparative genomic studies have also provided valuable insights into the conservation, evolution, and functional relevance of this group of enzymes. Thus, it has become evident that, in addition to proteolytic routines conserved in all organisms, there are also specific roles played by unique proteases in different species. Nevertheless, further studies will be necessary to clarify the genetic and molecular basis underlying the evolutionary differences in the complex protease repertoire of all living forms.
Proteaz (protease)
Proteinlerin parçalanmasndan sorumlu enzim grubu. Proteazlar (protease) veya peptidazlar peptid balarnn hidroliz reaksiyonu ile ykmn katalizler. Proteaz (protease) enzimleri hayvan, bitki, bakteri, arkea ve virüslerde bulunur.
Katalitik mekanizmalarna göre 6 ana snfa ayrlrlar; serin, treonin, sistein, aspartat, glutamik asit ve metallo proteazlar. Treonin (1995) ve glutamik asit (2004) proteazlar nispeten daha sonra karakteriz edilmistir. Peptid bann ykm, proteazn katalitik sistein veya treonin amino asitinin veya bir su molekülünün peptidteki karboksil (C=O) grubuyla nükleofil yer deitirme tepkimesi sonucu olur. Nükleofil oluumunu katalitik üçlüde yer alan histidinin salar.
Proteazlar (protease) ayrca en aktif olduklar pH derecelerine göre de snflandrlrlar: asidik, nötr ve bazik (alkali) proteazlar.
Proteolitik reaksiyonlar basit veya karmak biyolojik proseslerdir ve iyi ekilde düzenlenmeleri gerekir. Doada bunu salayan proteaz regülasyon mekanizmalar görülmektedir, örnein; yüksek substrat özgüllüü. Baz proteazlar (protease) yüksek substrat özgüllüü gostermez ve nerdeyse bütün proteinleri parçalayabilir. Ornein sindirimde rol alan tripsin.
Hücrede protein sentezi ve ykm hücresel bileenlerin ihtiyaç duyduu homeostasisi salar. Yapsnda selüloz bulunur.
PROTEAZ(protease)
Proteazlar (protease), doada bitkisel, hayvansal ve mikrobiyal kalntlarn dekompozisyonunda önemli rol oynamaktadrlar ve böylece besin döngüsünü salamakta ve ayrca bitkilerin besinleri alabilmelerini salamaktadr. Proteazlar (protease) enzimlerin oldukça kompleks bir grubunu oluturular ve oldukça farkl fizikokimyasal ve katalitik özelliklere sahiptirler. Proteaz (protease) sentezinin hücresel kontrolünden sorumlu mekanizma henüz tam olarak bilinmemekle beraber alkali proteazlarn üretimi amino asit veya amonyum gibi hzl bir ekilde metabolize edilebilen azot kaynaklar ile basklanmaktadr. Dier ortam bileenleri küçük ekerler ve mineraller enzim sentezini etkilemektedir. Potansiyel proteaz (protease) kullanm ve maksimum enzim üretimi ile endüstriyel ilemlerin maliyetini düürmek amaçlanmaktadr. Proteazlar (protease), toplam endüstriyel enzim ticaretinin yaklak % 60’n oluturmaktadr. Proteazlar (protease), çamar deterjanlar, deri, et, süt, ilaç, bira, fotoraf, organik sentezlerde ve atklarn muamelesinde kullanlmaktadr. Proteazlar (protease) arasnda bakteriyel proteazlar, hayvan ve fungal proteazlar ile karlatrld zaman daha etkin olduu görülmektedir. Bu nedenle ticari ilgiden dolay endüstriyel olarak uygun proteazlar üreten mikroplar çok çeitli habitatlardan aratrclar tarafndan çallmtr. Alkali proteazlar, bakteri, küf, maya gibi çeitli kaynaklardan elde edilse de alkalifilik Bacillus biyoteknolojide en fazla kullanlan mikroorganizmadr, çünkü çok geni çeitli ortamlardan izolasyonu nispeten kolaydr. Bununla birlikte Bacillus, hem kompleks hem de sentetik mediumda geliebilmektedir. Termofilik ve alkalifilik Bacillus tarafndan üretilen alkalifilik proteazlar yüksek scaklk ve pH’ya dayanmaktadr. Ayrca Bacillus türleri post-eksponansiyal ve durgunluk fazlarnda da ekstrasellüler proteazlar üretebilmektedir. Mikroorganizmalardan elde edilen proteolitik enzimler dünya çapnda deterjan endüstrilerinde en fazla kullanm bulan enzimlerdir. 30 yl boyunca deterjanlardaki proteazlarn önemi küçük katk maddesinden, anahtar bileenlere deimitir. yi bir deterjan enzimi oksitleme ajan ve aartclarla beraber stabilitesini koruyabilmelidir. Ticari olarak kullanlan enzimlerin büyük bir ksm aartma/oksitleme ajanlarnn varlnda stabilitesini koruyamamaktadr. Bu nedenle enzim tabanl deterjanlarn daha iyi stabiliteye sahip olmas için rekombinant DNA teknolojisi kullanlmaktadr. Bununla birlikte mikrobiyal çeitlilii derinlemesine inceleyerek ticari olarak daha kullanl enzimler üretebilen mikroorganizmalarn bulunma ans da daima vardr. Klasik olarak deterjanlar yüksek ykama scaklklarnda kullanlmaktadr. imdilerde alkalin proteazlarn tanmlanmasnda geni scaklk aralklarnda etkili olmas oldukça ilgi çekmektedir. Dier taraftan günümüzde deterjan endüstrisi, ykama scaklnn düürülmesi ve deterjan kompozisyonunun deimesi yönünde çalmalar yapmakta, fosfat tabanl deterjanlar uzaklatrarak, deterjan uygulamalar için daha uygun yeni alkali proteazlar üzerinde durmaktadr. Proteazlarn dier ilginç bir kullanm alan ise deniz Crustacea atklarnn deproteinizasyonudur. Kimyasal ilemlerin üstesinden gelmek için mikroorganizmalarn veya proteolitik Enzimlerin kullanlmas üzerine çalmalar yaplmaktadr. Kitin ve türevleri çok yönlü biyolojik aktiviteleri ve zirai kimyasal uygulamalarndan dolay büyük ekonomik deere sahiptir. Deniz crustaceanlar ise kitin bakmndan oldukça zengindir. Klasik olarak deniz atk materyallerinden kitinin hazrlanmas güçlü asit ve bazlar kullanarak demineralizasyonu ve kimyasallarn kullanlmas kitinin deasetilasyonunu ksmi olarak gerçekletirmektedir. Kimyasal uygulamalar ayn zamanda atk sularda nötralizasyon ve detoksifikasyon yaplmasn gerektirmektedir. Bu nedenle kimyasal uygulamalardan doan zararlarn üstesinden gelmek için alternatif olarak mikroorganizmalarn kullanlmas veya proteolitik enzimlerin kullanlmas gündemdedir.
Proteaz (protease) enzimleri virüslerin genom ifadelerinde önemli role sahiptirler. Proteazlar (protease) peptid zincirlerinin hidrolizini katalizleyen enzimlerdir. Bu enzimler hareket alanlarna göre; ekzoproteaz ya da endoproteaz eklinde snflandrlr. Ekzoproteazlar sadece proteinlerin yapsndaki peptid zincirinin sonundaki bölgeye etki eden enzimlerdir ve proteinlerin karboksil ya da amino uçlarndan amino asitlerin uzaklatrlmasnda rol oynamaktadrlar. Endoproteazlar ya da proteinazlar (protease) ise, polipeptid zincirinin N ve C ucundan uzakta veya polipeptid zincirinin iç bölgesindeki peptid zincirlerini açan enzimlere denir (Ryan ve Flint, 1997; Dougherty ve Semler, 1993). Virüsler tarafndan kodlanan proteazlarn (protease) ise virüsün replikasyonu esnasnda iki fonksiyondan birini gerçekletirdii bilinmektedir. lki, virüslerin kodlad proteazlarn (protease) çou fonksiyonel gen ürünleri içinde yüksek moleküler arla sahip moleküllerin ilenmesiyle birlikte gen ifadesinde rol oynamaktadr. Bu polyprotein, genomik RNA’nn translasyonuyla sentezlenmektedir. kinci genel ilem ise, virüs replikasyonu sonunda virionlarn olumas esnasnda yapsal proteinlerin olgunlamasn salamaktr. Doada aminoasitlerin katalitik alann oluturan sekans korunmutur ve bu amino asitler proteaz snflandrlmasnn olumasnda önemli role sahiptir. Proteazlar (protease) aktif bölgelerindeki fonksiyonel amino asit köküne göre dört ana grup altnda snflandrlmaktadrlar. Bunlar; serin proteaz, sistein (thiol) proteaz (protease), aspartik (ya da asidik) proteaz ve metalloproteazlardr. Proteinlerin yapsnda bulunan peptid balarn parçalamakta sistein aminoasitlerini kullananlara sistein proteaz (protease), aspartat aminoasitlerini kullananlara aspartat proteaz (protease) ve metal iyonlarn kullananlara ise metalloproteaz denilmektedir. Virüsler tarafndan kodlanan bu 4 tür proteazn üçü bitki patojeni virüslerde bulunmaktadr. Proteaz Tipleri ve Fonksiyonlar Serin ve serin tipi proteazlar Serin ve serin tipi proteazlar, amino asitlerin peptid balarn parçalamakta ve substrat balanma bölgelerinde bulunan aktif serin rezidülerini kullanan enzimlere denir. Bu tip proteazlar “3C proteaz” ya da “chymotrypsin benzeri proteaz” olarak da ifade edilmektedirler. Çounluu histidin (His), asparajin (Asn) ve serin (Ser) katalitik üçlüsüne Proteaz Tipleri ve Fonksiyonlar Serin ve serin tipi proteazlar Serin ve serin tipi proteazlar, amino asitlerin peptid balarn parçalamakta ve substrat balanma bölgelerinde bulunan aktif serin rezidülerini kullanan enzimlere denir (ekil 1). Bu tip proteazlar “3C proteaz” ya da “chymotrypsin benzeri proteaz” olarak da ifade edilmektedirler. Sistein proteazlar ayn zamanda “papain benzeri” ya da “thiol proteaz” olarak bilinmektedir. Bu proteazlarn, biri dieri ile etkileim halinde olan yakn çevrede histidin (His) ve sistein (Cys) kalntlarndan oluan katalitik iki moleküle sahip olduu bildirilmitir. Bu residüler arasndaki boluk virüslerin kodlad proteazlarda hücresel protezlara oranla daha ksa olduu görülmütür.
PROTEAZ (protease) ENZM, undaki proteinlere etki etmektedir. Kuvvetli unlarn yourma ve ileme zorluunu gidermek için kullanlmaktadr.
Proteaz (protease) özellikle bisküvi, kraker ve gofretlik ürünlerde gevreklik ve ktrl arttrmak amacyla kullanlr. Bacillus subtilisbakterisinden üretilir. Unlara uygun proteaz enziminin ilavesi,gluten yap deiiminde mükemmel kontrol,elastikiyet kontrolü salar ve gofret üretiminde yüksek kaliteli enzimdir.
Bisküvi ve kraker üretiminde düük oranda protein içeren ve gluten yaps güçlü olmayan unlar kullanlr. Ancak kullanlan un bu karakteristik özelliklere sahip deil ise, istenilen özellikleri elde etmek için bir takm etken maddeler kullanlr.
PROTEAZ (PROTEASE) GÖRÜNÜM: TOZ
PROTEAZ (PROTEASE) RENK: BEYAZA YAKIN VEYA KAHVERENG
PROTEAZ (PROTEASE) KOKU: HAFF KARAKTERSTK BR KOKUSU VAR.
PROTEAZ (PROTEASE) TEHLHE:
CLDE TEMASTA HAFF BR RRTASYONA NEDEN OLUR. TEMASTA BOL SU LE YIKAYINIZ.
Proteazlar muhtemelen protein evriminin ilk aamalarnda protein katabolizmas ve ilkel organizmalarda amino asitlerin oluumu için gerekli olan basit ykc enzimler olarak ortaya çkt. Uzun yllar boyunca, proteazlar üzerindeki çalmalar, protein ykmyla ilikili kör saldrganlar olarak orijinal rollerine odakland. Bununla birlikte, bu spesifik olmayan bozunma fonksiyonlarnn ötesinde, proteazlarn keskin makas görevi gördüünün ve proteolitik ilemenin oldukça spesifik reaksiyonlarn katalize ederek yeni protein ürünleri ürettiinin anlalmas, proteaz aratrmalarnda yeni bir dönem balatmtr (2). Bu antik enzimler grubundaki aratrmann u anki baars, esas olarak tüm canl organizmalardaki çoklu biyolojik süreçlerin kontrolüyle ilikilerini gösteren geni bulgular koleksiyonundan kaynaklanmaktadr (3-11). Bu nedenle proteazlar, birçok proteinin kaderini, lokalizasyonunu ve aktivitesini düzenler, protein-protein etkileimlerini modüle eder, yeni biyoaktif moleküller oluturur, hücresel bilgilerin ilenmesine katkda bulunur ve moleküler sinyalleri üretir, aktarr ve yükseltir. Bu çoklu eylemlerin dorudan bir sonucu olarak, proteazlar DNA replikasyonu ve transkripsiyonunu, hücre proliferasyonunu ve farkllamasn, doku morfogenezini ve yeniden ekillenmesini, s oku ve katlanmam protein yantlarn, anjiyogenez, nörojenez, yumurtlama, fertilizasyon, yara onarm, kök hücre mobilizasyonu, hemostaz etkiler. kan phtlamas, iltihaplanma, baklk, otofaji, yalanma, nekroz ve apoptoz. Proteazlarn hücre davran ve tüm organizmalarn hayatta kalmas ve ölümündeki bu temel rolleriyle tutarl olarak, proteolitik sistemlerdeki deiiklikler, kanser, nörodejeneratif bozukluklar ve enflamatuar ve kardiyovasküler hastalklar gibi birçok patolojik durumun altnda yatar. Buna göre, birçok proteaz, ilaç endüstrisi için potansiyel ilaç hedefleri veya tansal ve prognostik biyobelirteçler olarak ana ilgi odadr (12). Proteazlar ayrca bitkilerde önemli roller oynar ve geliimsel ipuçlarna veya çevresel koullardaki deiikliklere yant olarak belirli protein setlerinin ilenmesine, olgunlamasna veya yok edilmesine katkda bulunur (13). Benzer ekilde, birçok enfeksiyöz mikroorganizma replikasyon için proteazlara ihtiyaç duyar veya virülans faktörleri olarak proteazlar kullanr, bu da AIDS gibi insan yaam ile büyük önem tayan hastalklar için proteaz hedefli tedavilerin gelitirilmesini kolaylatrmtr (12). Son olarak, proteazlar, biyokimyasal reaktifler olarak veya çok sayda ürünün imalatnda yararl olmalar nedeniyle biyoteknoloji endüstrisinin de önemli araçlardr (ör. Ref. 14).