Proteolysis

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The hydrolysis of a protein (red) by the nucleophilic attack of water (blue). The uncatalysed half-life is several hundred years.

Proteolysis is the breakdown of

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 disease.

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

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.[1]

Removal of N-terminal methionine

The initiating methionine (and, in prokaryotes,

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
(POMC) 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

polycistronic mRNA. This polypeptide is subsequently cleaved into individual polypeptide chains.[1] Common names for the polyprotein include gag (group-specific antigen) 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 (a and ab) at an approximately fixed ratio.

Cleavage of precursor proteins

Many proteins and hormones are synthesized in the form of their precursors -

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

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 (carbon, nitrogen, and sulfur) induces proteolytic activity in the fungus Neurospora crassa[3] as well as in of soil organism communities.[4]

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.

Structure of a proteasome. Its active sites are inside the tube (blue) where proteins are degraded.

Lysosome and proteasome

The intracellular degradation of protein may be achieved in two ways - proteolysis in

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

erythrocyte.[5]

The

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.[5] Proteins with larger degrees of intrinsic disorder also tend to have short cellular half-life,[7] with disordered segments having been proposed to facilitate efficient initiation of degradation by the proteasome.[8][9]

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

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 (tripeptides and dipeptides) 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.[10] Different enzymes have different specificity for their substrate; trypsin, for example, cleaves the peptide bond after a positively charged residue (arginine and lysine); chymotrypsin cleaves the bond after an aromatic residue (phenylalanine, tyrosine, and tryptophan
); 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 (they may, for example, trigger pancreatic self-digestion causing

. 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.

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

Cyclins are a group of proteins that activate kinases involved in cell division. The degradation of cyclins is the key step that governs the exit from mitosis and progress into the next cell cycle.[13] Cyclins accumulate in the course the cell cycle, then abruptly disappear just before the anaphase
of mitosis. The cyclins are removed via a ubiquitin-mediated proteolytic pathway.

Apoptosis

death receptor
pathways.

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.

Alzheimer's due to generation and ineffective removal of peptides that aggregate in cells.[21]

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

ribonuclease A, which can be purified by treating crude extracts with hot sulfuric acid so that other proteins become degraded while ribonuclease A is left intact.[28]

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.

asparaginyl peptide bonds. Acids such as trifluoroacetic acid and formic acid
may be used for cleavage.

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:

Protease enzymes

Proteases may be classified according to the catalytic group involved in its active site.[39]

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

References

  1. ^ .
  2. .
  3. ^ 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.
  4. ^ Sims, G. K., and M. M. Wander. 2002. Proteolytic activity under nitrogen or sulfur limitation. Appl. Soil Ecol. 568:1-5.
  5. ^ .
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  22. PMID 18371259.{{cite journal}}: CS1 maint: numeric names: authors list (link
    )
  23. .
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  28. ^ "Ribonuclease A". Protein Data Bank.
  29. S2CID 3692961
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  34. ^ "Chemicals in Meat Cooked at High Temperatures and Cancer Risk". National Cancer Institute. 2 April 2018.
  35. PMID 1236799
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  40. ^ Hayes WK. 2005. Research on Biological Roles and Variation of Snake Venoms. Loma Linda University.

Further reading

External links