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Peptide

(Redirected from Polypeptide)
"Peptides" redirects here. For the journal, see Peptides (journal).

Peptides are short chains of amino acids linked by peptide bonds.[1][2] A polypeptide is a longer, continuous, unbranched peptide chain.[3] Polypeptides that have a molecular mass of 10,000 Da or more are called proteins.[4] Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides.

Drosomycin, an example of a peptide

Peptides fall under the broad chemical classes of biological polymers and oligomers, alongside nucleic acids, oligosaccharides, polysaccharides, and others.

Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, to another protein or other macromolecule such as DNA or RNA, or to complex macromolecular assemblies.[5]

Amino acids that have been incorporated into peptides are termed residues. A water molecule is released during formation of each amide bond.[6] All peptides except cyclic peptides have an N-terminal (amine group) and C-terminal (carboxyl group) residue at the end of the peptide (as shown for the tetrapeptide in the image).

Classification

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There are numerous types of peptides that have been classified according to their sources and functions. According to the Handbook of Biologically Active Peptides, some groups of peptides include plant peptides, bacterial/antibiotic peptides, fungal peptides, invertebrate peptides, amphibian/skin peptides, venom peptides, cancer/anticancer peptides, vaccine peptides, immune/inflammatory peptides, brain peptides, endocrine peptides, ingestive peptides, gastrointestinal peptides, cardiovascular peptides, renal peptides, respiratory peptides, opioid peptides, neurotrophic peptides, and blood–brain peptides.[7]

Some ribosomal peptides are subject to proteolysis. These function, typically in higher organisms, as hormones and signaling molecules. Some microbes produce peptides as antibiotics, such as microcins and bacteriocins.[8]

Peptides frequently have post-translational modifications such as phosphorylation, hydroxylation, sulfonation, palmitoylation, glycosylation, and disulfide formation. In general, peptides are linear, although lariat structures have been observed.[9] More exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom.[10]

Nonribosomal peptides are assembled by enzymes, not the ribosome. A common non-ribosomal peptide is glutathione, a component of the antioxidant defenses of most aerobic organisms.[11] Other nonribosomal peptides are most common in unicellular organisms, plants, and fungi and are synthesized by modular enzyme complexes called nonribosomal peptide synthetases.[12]

These complexes are often laid out in a similar fashion, and they can contain many different modules to perform a diverse set of chemical manipulations on the developing product.[13] These peptides are often cyclic and can have highly complex cyclic structures, although linear nonribosomal peptides are also common. Since the system is closely related to the machinery for building fatty acids and polyketides, hybrid compounds are often found. The presence of oxazoles or thiazoles often indicates that the compound was synthesized in this fashion.[14]

Peptones are derived from animal milk or meat digested by proteolysis.[15] In addition to containing small peptides, the resulting material includes fats, metals, salts, vitamins, and many other biological compounds. Peptones are used in nutrient media for growing bacteria and fungi.[16]

Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein.[17] Often these are the products of enzymatic degradation performed in the laboratory on a controlled sample, but can also be forensic or paleontological samples that have been degraded by natural effects.[18][19]

Chemical synthesis

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Main article: Peptide synthesis
 
Solid-phase peptide synthesis on a rink amide resin using Fmoc-α-amine-protected amino acid

Protein-peptide interactions

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Example of a protein (orange) and peptide (green) interaction. Obtained from Propedia: a peptide-protein interactions database.[20]

Peptides can perform interactions with proteins and other macromolecules. They are responsible for numerous important functions in human cells, such as cell signaling, and act as immune modulators.[21] Indeed, studies have reported that 15-40% of all protein-protein interactions in human cells are mediated by peptides.[22] Additionally, it is estimated that at least 10% of the pharmaceutical market is based on peptide products.[21]

Example families

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The peptide families in this section are ribosomal peptides, usually with hormonal activity. All of these peptides are synthesized by cells as longer "propeptides" or "proproteins" and truncated prior to exiting the cell. They are released into the bloodstream where they perform their signaling functions.

Antimicrobial peptides

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Tachykinin peptides

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Main article: Tachykinin peptides

Vasoactive intestinal peptides

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Main article: Secretin family
  • VIP (Vasoactive Intestinal Peptide; PHM27)
  • PACAP Pituitary Adenylate Cyclase Activating Peptide
  • Peptide PHI 27 (Peptide Histidine Isoleucine 27)
  • GHRH 1-24 (Growth Hormone Releasing Hormone 1-24)
  • Glucagon
  • Secretin
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  • NPY (NeuroPeptide Y)
  • PYY (Peptide YY)
  • APP (Avian Pancreatic Polypeptide)
  • PPY Pancreatic PolYpeptide

Opioid peptides

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Main article: Opioid peptide

Calcitonin peptides

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Self-assembling peptides

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Other peptides

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Terminology

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Length

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Several terms related to peptides have no strict length definitions, and there is often overlap in their usage:

  • A polypeptide is a single linear chain of many amino acids (any length), held together by amide bonds.
  • A protein consists of one or more polypeptides (more than about 50 amino acids long).
  • An oligopeptide consists of only a few amino acids (between two and twenty).

Number of amino acids

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A tripeptide (example Val-Gly-Ala) with
green marked amino end (L-valine) and
blue marked carboxyl end (L-alanine)

Peptides and proteins are often described by the number of amino acids in their chain, e.g. a protein with 158 amino acids may be described as a "158 amino-acid-long protein". Peptides of specific shorter lengths are named using IUPAC numerical multiplier prefixes:

The same words are also used to describe a group of residues in a larger polypeptide (e.g., RGD motif).

Function

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  • A neuropeptide is a peptide that is active in association with neural tissue.
  • A lipopeptide is a peptide that has a lipid connected to it, and pepducins are lipopeptides that interact with GPCRs.
  • A peptide hormone is a peptide that acts as a hormone.
  • A proteose is a mixture of peptides produced by the hydrolysis of proteins. The term is somewhat archaic.
  • A peptidergic agent (or drug) is a chemical which functions to directly modulate the peptide systems in the body or brain. An example is opioidergics, which are neuropeptidergics.
  • A cell-penetrating peptide is a peptide able to penetrate the cell membrane.

See also

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Wikiquote has quotations related to Peptide.

References

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  1. ^ Hamley, I. W. (September 2020). introduction to Peptide Science. Wiley. ISBN 978-1-119-69817-3.
  2. ^ Nelson, David L.; Cox, Michael M. (2005). Principles of Biochemistry (4th ed.). New York: W. H. Freeman. ISBN 0-7167-4339-6.
  3. ^ Saladin, K. (13 January 2011). Anatomy & physiology: the unity of form and function (6th ed.). McGraw-Hill. p. 67. ISBN 978-0-07-337825-1.
  4. ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "proteins". doi:10.1351/goldbook.P04898.
  5. ^ Ardejani, Maziar S.; Orner, Brendan P. (2013-05-03). "Obey the Peptide Assembly Rules". Science. 340 (6132): 561–562. Bibcode:2013Sci...340..561A. doi:10.1126/science.1237708. ISSN 0036-8075. PMID 23641105. S2CID 206548864.
  6. ^ IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006–) "amino-acid residue in a polypeptide". doi:10.1351/goldbook.A00279.
  7. ^ Abba J. Kastin, ed. (2013). Handbook of Biologically Active Peptides (2nd ed.). Elsevier Science. ISBN 978-0-12-385095-9.
  8. ^ Duquesne S, Destoumieux-Garzón D, Peduzzi J, Rebuffat S (August 2007). "Microcins, gene-encoded antibacterial peptides from enterobacteria". Natural Product Reports. 24 (4): 708–34. doi:10.1039/b516237h. PMID 17653356.
  9. ^ Pons M, Feliz M, Antònia Molins M, Giralt E (May 1991). "Conformational analysis of bacitracin A, a naturally occurring lariat". Biopolymers. 31 (6): 605–12. doi:10.1002/bip.360310604. PMID 1932561. S2CID 10924338.
  10. ^ Torres AM, Menz I, Alewood PF, et al. (July 2002). "D-Amino acid residue in the C-type natriuretic peptide from the venom of the mammal, Ornithorhynchus anatinus, the Australian platypus". FEBS Letters. 524 (1–3): 172–6. doi:10.1016/S0014-5793(02)03050-8. PMID 12135762. S2CID 3015474.
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  16. ^ Payne, J. W.; Rose, Anthony H.; Tempest, D. W. (27 September 1974). "Peptides and micro-organisms". Advances in Microbial Physiology, Volume 13. Vol. 13. Oxford, England: Elsevier Science. pp. 55–160. doi:10.1016/S0065-2911(08)60038-7. ISBN 978-0-08-057971-9. OCLC 1049559483. PMID 775944.
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  18. ^ Webster J, Oxley D; Oxley (2005). "Peptide Mass Fingerprinting". Chemical Genomics. Methods in Molecular Biology. Vol. 310. pp. 227–40. doi:10.1007/978-1-59259-948-6_16. ISBN 978-1-58829-399-2. PMID 16350956.
  19. ^ Marquet P, Lachâtre G; Lachâtre (October 1999). "Liquid chromatography-mass spectrometry: potential in forensic and clinical toxicology". Journal of Chromatography B. 733 (1–2): 93–118. doi:10.1016/S0378-4347(99)00147-4. PMID 10572976.
  20. ^ "Propedia v2.3 - Peptide-Protein Interactions Database". bioinfo.dcc.ufmg.br. Retrieved 2023-03-28.
  21. ^ a b Martins, Pedro M.; Santos, Lucianna H.; Mariano, Diego; Queiroz, Felippe C.; Bastos, Luana L.; Gomes, Isabela de S.; Fischer, Pedro H. C.; Rocha, Rafael E. O.; Silveira, Sabrina A.; de Lima, Leonardo H. F.; de Magalhães, Mariana T. Q.; Oliveira, Maria G. A.; de Melo-Minardi, Raquel C. (December 2021). "Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm". BMC Bioinformatics. 22 (1): 1. doi:10.1186/s12859-020-03881-z. ISSN 1471-2105. PMC 7776311. PMID 33388027.
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