Proteolysis
Proteolysis is the breakdown of
, but may also occur by intra-molecular digestion.Proteolysis in organisms serves many purposes; for example,
Proteolysis can also be used as an analytical tool for studying proteins in the laboratory, and it may also be used in industry, for example in food processing and stain removal.
Biological functions
Post-translational proteolytic processing
Limited proteolysis of a polypeptide during or after
Removal of N-terminal methionine
The initiating methionine (and, in prokaryotes,
Removal of the signal sequence
Proteins that are to be targeted to a particular organelle or for secretion have an N-terminal signal peptide that directs the protein to its final destination. This signal peptide is removed by proteolysis after their transport through a membrane.
Cleavage of polyproteins
Some proteins and most eukaryotic polypeptide hormones are synthesized as a large precursor polypeptide known as a polyprotein that requires proteolytic cleavage into individual smaller polypeptide chains. The polyprotein
Many
Cleavage of precursor proteins
Many proteins and hormones are synthesized in the form of their precursors -
Proteases in particular are synthesized in the inactive form so that they may be safely stored in cells, and ready for release in sufficient quantity when required. This is to ensure that the protease is activated only in the correct location or context, as inappropriate activation of these proteases can be very destructive for an organism. Proteolysis of the zymogen yields an active protein; for example, when trypsinogen is cleaved to form trypsin, a slight rearrangement of the protein structure that completes the active site of the protease occurs, thereby activating the protein.
Proteolysis can, therefore, be a method of regulating biological processes by turning inactive proteins into active ones. A good example is the
Protein degradation
Protein degradation may take place intracellularly or extracellularly. In digestion of food, digestive enzymes may be released into the environment for
Proteins in cells are broken into amino acids. This intracellular degradation of protein serves multiple functions: It removes damaged and abnormal proteins and prevents their accumulation. It also serves to regulate cellular processes by removing enzymes and regulatory proteins that are no longer needed. The amino acids may then be reused for protein synthesis.
Lysosome and proteasome
The intracellular degradation of protein may be achieved in two ways - proteolysis in
The ubiquitin-mediated process is selective. Proteins marked for degradation are covalently linked to ubiquitin. Many molecules of ubiquitin may be linked in tandem to a protein destined for degradation. The polyubiquinated protein is targeted to an ATP-dependent protease complex, the proteasome. The ubiquitin is released and reused, while the targeted protein is degraded.
Rate of intracellular protein degradation
Different proteins are degraded at different rates. Abnormal proteins are quickly degraded, whereas the rate of degradation of normal proteins may vary widely depending on their functions. Enzymes at important metabolic control points may be degraded much faster than those enzymes whose activity is largely constant under all physiological conditions. One of the most rapidly degraded proteins is
The
The rate of proteolysis may also depend on the physiological state of the organism, such as its hormonal state as well as nutritional status. In time of starvation, the rate of protein degradation increases.
Digestion
In human
In order to prevent inappropriate or premature activation of the digestive enzymes (they may, for example, trigger pancreatic self-digestion causing
In bacteria, a similar strategy of employing an inactive zymogen or prezymogen is used. Subtilisin, which is produced by Bacillus subtilis, is produced as preprosubtilisin, and is released only if the signal peptide is cleaved and autocatalytic proteolytic activation has occurred.
Cellular regulation
Proteolysis is also involved in the regulation of many cellular processes by activating or deactivating enzymes, transcription factors, and receptors, for example in the biosynthesis of cholesterol,[11] or the mediation of thrombin signalling through protease-activated receptors.[12]
Some enzymes at important metabolic control points such as ornithine decarboxylase is regulated entirely by its rate of synthesis and its rate of degradation. Other rapidly degraded proteins include the protein products of proto-oncogenes, which play central roles in the regulation of cell growth.
Cell cycle regulation
Apoptosis
Autoproteolysis
Autoproteolysis takes place in some proteins, whereby the peptide bond is cleaved in a self-catalyzed intramolecular reaction. Unlike zymogens, these autoproteolytic proteins participate in a "single turnover" reaction and do not catalyze further reactions post-cleavage. Examples include cleavage of the Asp-Pro bond in a subset of von Willebrand factor type D (VWD) domains[14][15] and Neisseria meningitidis FrpC self-processing domain,[16] cleavage of the Asn-Pro bond in Salmonella FlhB protein,[17] Yersinia YscU protein,[18] as well as cleavage of the Gly-Ser bond in a subset of sea urchin sperm protein, enterokinase, and agrin (SEA) domains.[19] In some cases, the autoproteolytic cleavage is promoted by conformational strain of the peptide bond.[19]
Proteolysis and diseases
Abnormal proteolytic activity is associated with many diseases.
Proteases may be regulated by
Other diseases linked to aberrant proteolysis include muscular dystrophy, degenerative skin disorders, respiratory and gastrointestinal diseases, and malignancy.
Non-enzymatic processes
Protein backbones are very stable in water at neutral pH and room temperature, although the rate of hydrolysis of different peptide bonds can vary. The half life of a peptide bond under normal conditions can range from 7 years to 350 years, even higher for peptides protected by modified terminus or within the protein interior.[23][24][25] The rate of hydrolysis however can be significantly increased by extremes of pH and heat. Spontaneous cleavage of proteins may also involve catalysis by zinc on serine and threonine.[26]
Strong
Certain chemicals cause proteolysis only after specific residues, and these can be used to selectively break down a protein into smaller polypeptides for laboratory analysis.
Like other biomolecules, proteins can also be broken down by high heat alone. At 250 °C, the peptide bond may be easily hydrolyzed, with its half-life dropping to about a minute.[27][30] Protein may also be broken down without hydrolysis through pyrolysis; small heterocyclic compounds may start to form upon degradation. Above 500 °C, polycyclic aromatic hydrocarbons may also form,[31][32] which is of interest in the study of generation of carcinogens in tobacco smoke and cooking at high heat.[33][34]
Laboratory applications
Proteolysis is also used in research and diagnostic applications:
- Cleavage of enterokinase, and TEV protease, so that only the targeted sequence may be cleaved.
- Complete inactivation of undesirable enzymatic activity or removal of unwanted proteins. For example,
- Partial inactivation, or changing the functionality, of specific protein. For example, treatment of DNA polymerase I with subtilisin yields the Klenow fragment, which retains its polymerase function but lacks 5'-exonuclease activity.[36]
- Digestion of proteins in solution for proteins after separation by gel electrophoresis for the identification by mass spectrometry.
- Analysis of the stability of folded domain under a wide range of conditions.[37]
- Increasing success rate of crystallisation projects[38]
- Production of digested protein used in growth media to culture bacteria and other organisms, e.g. Lysogeny Broth.
Protease enzymes
Proteases may be classified according to the catalytic group involved in its active site.[39]
- Cysteine protease
- Serine protease
- Threonine protease
- Aspartic protease
- Glutamic protease
- Metalloprotease
- Asparagine peptide lyase
Venoms
Certain types of venom, such as those produced by venomous snakes, can also cause proteolysis. These venoms are, in fact, complex digestive fluids that begin their work outside of the body. Proteolytic venoms cause a wide range of toxic effects,[40] including effects that are:
- cytotoxic(cell-destroying)
- hemotoxic (blood-destroying)
- myotoxic (muscle-destroying)
- hemorrhagic(bleeding)
See also
- The Proteolysis Map
- PROTOMAPa proteomic technology for identifying proteolytic substrates
- Proteasome
- In-gel digestion
- Ubiquitin
References
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- ^ Hanson, M.A., Marzluf, G.A., 1975. Control of the synthesis of a single enzyme by multiple regulatory circuits in Neurospora crassa. Proc. Natl. Acad. Sci. U.S.A. 72, 1240–1244.
- ^ Sims, G. K., and M. M. Wander. 2002. Proteolytic activity under nitrogen or sulfur limitation. Appl. Soil Ecol. 568:1-5.
- ^ ISBN 978-0-7167-2317-2.
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- ^ ISBN 978-0-7167-2317-2.
- ^ "Ribonuclease A". Protein Data Bank.
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- ^ "Chemicals in Meat Cooked at High Temperatures and Cancer Risk". National Cancer Institute. 2 April 2018.
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- ^ Hayes WK. 2005. Research on Biological Roles and Variation of Snake Venoms. Loma Linda University.
Further reading
- Thomas E Creighton (1993). Proteins: Structures and Molecular Properties (2nd ed.). W H Freeman and Company. ISBN 978-0-7167-2317-2.
External links
- The Journal of Proteolysis is an open access journal that provides an international forum for the electronic publication of the whole spectrum of high-quality articles and reviews in all areas of proteolysis and proteolytic pathways.
- Proteolysis MAP from Center on Proteolytic Pathways