Proteolysis
Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Protein degradation is a major regulatory mechanism of gene expression and contributes substantially to shaping mammalian proteomes. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion.
Proteolysis in organisms serves many purposes; for example, digestive enzymes break down proteins in food to provide amino acids for the organism, while proteolytic processing of a polypeptide chain after its synthesis may be necessary for the production of an active protein. It is also important in the regulation of some physiological and cellular processes including apoptosis, as well as preventing the accumulation of unwanted or misfolded proteins in cells. Consequently, abnormality in the regulation of proteolysis can cause diseases.
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 translation in protein synthesis often occurs for many proteins. This may involve removal of the N-terminal methionine, signal peptide, and/or the conversion of an inactive or non-functional protein to an active one. The precursor to the final functional form of protein is termed proprotein, and these proproteins may be first synthesized as preproprotein. For example, albumin is first synthesized as preproalbumin and contains an uncleaved signal peptide. This forms the proalbumin after the signal peptide is cleaved, and a further processing to remove the N-terminal 6-residue propeptide yields the mature form of the protein.Removal of N-terminal methionine
The initiating methionine may be removed during translation of the nascent protein. For E. coli, fMet is efficiently removed if the second residue is small and uncharged, but not if the second residue is bulky and charged. In both prokaryotes and eukaryotes, the exposed N-terminal residue may determine the half-life of the protein according to the N-end rule.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 pro-opiomelanocortin contains many polypeptide hormones. The cleavage pattern of POMC, however, may vary between different tissues, yielding different sets of polypeptide hormones from the same polyprotein.Many viruses also produce their proteins initially as a single polypeptide chain that were translated from a polycistronic mRNA. This polypeptide is subsequently cleaved into individual polypeptide chains. Common names for the polyprotein include gag in retroviruses and ORF1ab in Nidovirales. The latter name refers to the fact that a slippery sequence in the mRNA that codes for the polypeptide causes ribosomal frameshifting, leading to two different lengths of peptidic chains at an approximately fixed ratio.
Cleavage of precursor proteins
Many proteins and hormones are synthesized in the form of their precursors - zymogens, proenzymes, and prehormones. These proteins are cleaved to form their final active structures. Insulin, for example, is synthesized as preproinsulin, which yields proinsulin after the signal peptide has been cleaved. The proinsulin is then cleaved at two positions to yield two polypeptide chains linked by two disulfide bonds. Removal of two C-terminal residues from the B-chain then yields the mature insulin. Protein folding occurs in the single-chain proinsulin form which facilitates formation of the ultimate inter-peptide disulfide bonds, and the ultimate intra-peptide disulfide bond, found in the native structure of insulin.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 blood clotting cascade whereby an initial event triggers a cascade of sequential proteolytic activation of many specific proteases, resulting in blood coagulation. The complement system of the immune response also involves a complex sequential proteolytic activation and interaction that result in an attack on invading pathogens.
Protein degradation
Protein degradation may take place intracellularly or extracellularly. In digestion of food, digestive enzymes may be released into the environment for extracellular digestion whereby proteolytic cleavage breaks proteins into smaller peptides and amino acids so that they may be absorbed and used. In animals the food may be processed extracellularly in specialized organs or guts, but in many bacteria the food may be internalized via phagocytosis. Microbial degradation of protein in the environment can be regulated by nutrient availability. For example, limitation for major elements in proteins induces proteolytic activity in the fungus Neurospora crassa as well as in of soil organism communities.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 lysosome, or a ubiquitin-dependent process that targets unwanted proteins to proteasome. The autophagy-lysosomal pathway is normally a non-selective process, but it may become selective upon starvation whereby proteins with peptide sequence KFERQ or similar are selectively broken down. The lysosome contains a large number of proteases such as cathepsins.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 ornithine decarboxylase, which has a half-life of 11 minutes. In contrast, other proteins like actin and myosin have a half-life of a month or more, while, in essence, haemoglobin lasts for the entire life-time of an erythrocyte.The N-end rule may partially determine the half-life of a protein, and proteins with segments rich in proline, glutamic acid, serine, and threonine have short half-life. Other factors suspected to affect degradation rate include the rate deamination of glutamine and asparagine and oxidation of cystein, histidine, and methionine, the absence of stabilizing ligands, the presence of attached carbohydrate or phosphate groups, the presence of free α-amino group, the negative charge of protein, and the flexibility and stability of the protein. Proteins with larger degrees of intrinsic disorder also tend to have short cellular half-life, with disordered segments having been proposed to facilitate efficient initiation of degradation by the proteasome.
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 digestion, proteins in food are broken down into smaller peptide chains by digestive enzymes such as pepsin, trypsin, chymotrypsin, and elastase, and into amino acids by various enzymes such as carboxypeptidase, aminopeptidase, and dipeptidase. It is necessary to break down proteins into small peptides and amino acids so they can be absorbed by the intestines, and the absorbed tripeptides and dipeptides are also further broken into amino acids intracellularly before they enter the bloodstream. Different enzymes have different specificity for their substrate; trypsin, for example, cleaves the peptide bond after a positively charged residue ; chymotrypsin cleaves the bond after an aromatic residue ; elastase cleaves the bond after a small non-polar residue such as alanine or glycine.In order to prevent inappropriate or premature activation of the digestive enzymes, these enzymes are secreted as inactive zymogen. The precursor of pepsin, pepsinogen, is secreted by the stomach, and is activated only in the acidic environment found in stomach. The pancreas secretes the precursors of a number of proteases such as trypsin and chymotrypsin. The zymogen of trypsin is trypsinogen, which is activated by a very specific protease, enterokinase, secreted by the mucosa of the duodenum. The trypsin, once activated, can also cleave other trypsinogens as well as the precursors of other proteases such as chymotrypsin and carboxypeptidase to activate them.
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.