Chemistry:Peptide

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Short description: Short chains of 2–50 amino acids
A tetrapeptide (example Val-Gly-Ser-Ala) with green marked amino end (L-valine) and
blue marked carboxyl end (L-alanine)

Peptides are short chains of amino acids linked by peptide bonds.[1][2] A polypeptide is a longer, continuous, unbranched peptide chain.[3] Polypeptides which 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.

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

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

Main page: Biology:Peptide synthesis
Table of amino acids
Solid-phase peptide synthesis on a rink amide resin using Fmoc-α-amine-protected amino acid

Protein-peptide interactions

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 several 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

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

Tachykinin peptides

Main page: Biology:Tachykinin peptides

Vasoactive intestinal peptides

Main page: Biology: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

Pancreatic polypeptide-related peptides

  • NPY (NeuroPeptide Y)
  • PYY (Peptide YY)
  • APP (Avian Pancreatic Polypeptide)
  • PPY Pancreatic PolYpeptide

Opioid peptides

Main page: Biology:Opioid peptide

Calcitonin peptides

Self-assembling peptides

Other peptides

Terminology

Length

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

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

  • 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


References

  1. ↑ Hamley, I. W. (September 2020). introduction to Peptide Science. Wiley. ISBN 978-1-119-69817-3. https://www.wiley.com/en-ai/Introduction+to+Peptide+Science-p-9781119698173. 
  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. doi:10.1126/science.1237708. ISSN 0036-8075. PMID 23641105. Bibcode: 2013Sci...340..561A. 
  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. ↑ "Microcins, gene-encoded antibacterial peptides from enterobacteria". Natural Product Reports 24 (4): 708–34. August 2007. doi:10.1039/b516237h. PMID 17653356. 
  9. ↑ "Conformational analysis of bacitracin A, a naturally occurring lariat". Biopolymers 31 (6): 605–12. May 1991. doi:10.1002/bip.360310604. PMID 1932561. 
  10. ↑ "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. July 2002. doi:10.1016/S0014-5793(02)03050-8. PMID 12135762. 
  11. ↑ Meister A, Anderson ME; Anderson (1983). "Glutathione". Annual Review of Biochemistry 52 (1): 711–60. doi:10.1146/annurev.bi.52.070183.003431. PMID 6137189. 
  12. ↑ Hahn M, Stachelhaus T; Stachelhaus (November 2004). "Selective interaction between nonribosomal peptide synthetases is facilitated by short communication-mediating domains". Proceedings of the National Academy of Sciences of the United States of America 101 (44): 15585–90. doi:10.1073/pnas.0404932101. PMID 15498872. Bibcode: 2004PNAS..10115585H. 
  13. ↑ Finking R, Marahiel MA; Marahiel (2004). "Biosynthesis of nonribosomal peptides1". Annual Review of Microbiology 58 (1): 453–88. doi:10.1146/annurev.micro.58.030603.123615. PMID 15487945. 
  14. ↑ Du L, Shen B; Shen (March 2001). "Biosynthesis of hybrid peptide-polyketide natural products". Current Opinion in Drug Discovery & Development 4 (2): 215–28. PMID 11378961. 
  15. ↑ "UsvPeptides- USVPeptides is a leading pharmaceutical company in India". http://www.usvpeptides.com. 
  16. ↑ Payne, J. W.; Rose, Anthony H.; Tempest, D. W. (27 September 1974). "Peptides and micro-organisms". Advances in Microbial Physiology, Volume 13. 13. Oxford, England: Elsevier Science. pp. 55–160. doi:10.1016/S0065-2911(08)60038-7. ISBN 978-0-08-057971-9. OCLC 1049559483. https://books.google.com/books?id=QgQuTYSW8A4C&dq=peptides&pg=PA147. 
  17. ↑ "ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites". BMC Bioinformatics 8 (1): 216. 2007. doi:10.1186/1471-2105-8-216. PMID 17587460. 
  18. ↑ Webster J, Oxley D; Oxley (2005). "Peptide Mass Fingerprinting". Chemical Genomics. Methods in Molecular Biology. 310. pp. 227–40. doi:10.1007/978-1-59259-948-6_16. ISBN 978-1-58829-399-2. https://archive.org/details/chemicalgenomics00zand_0/page/227. 
  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". http://bioinfo.dcc.ufmg.br/propedia2/. 
  21. ↑ 21.0 21.1 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. et al. (December 2021). "Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm" (in en). BMC Bioinformatics 22 (1): 1. doi:10.1186/s12859-020-03881-z. ISSN 1471-2105. PMID 33388027. 
  22. ↑ Neduva, Victor; Linding, Rune; Su-Angrand, Isabelle; Stark, Alexander; Masi, Federico de; Gibson, Toby J; Lewis, Joe; Serrano, Luis et al. (2005-11-15). Matthews, Rowena. ed. "Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks" (in en). PLOS Biology 3 (12): e405. doi:10.1371/journal.pbio.0030405. ISSN 1545-7885. PMID 16279839. 
  23. ↑ Tao, Kai; Makam, Pandeeswar; Aizen, Ruth; Gazit, Ehud (17 Nov 2017). "Self-assembling peptide semiconductors". Science 358 (6365): eaam9756. doi:10.1126/science.aam9756. PMID 29146781. 
  24. ↑ Tao, Kai; Levin, Aviad; Adler-Abramovich, Lihi; Gazit, Ehud (26 Apr 2016). "Fmoc-modified amino acids and short peptides: simple bio-inspired building blocks for the fabrication of functional materials". Chem. Soc. Rev. 45 (14): 3935–3953. doi:10.1039/C5CS00889A. PMID 27115033. 
  25. ↑ Tao, Kai; Wang, Jiqian; Zhou, Peng; Wang, Chengdong; Xu, Hai; Zhao, Xiubo; Lu, Jian R. (February 10, 2011). "Self-Assembly of Short Aβ(16−22) Peptides: Effect of Terminal Capping and the Role of Electrostatic Interaction". Langmuir 27 (6): 2723–2730. doi:10.1021/la1034273. PMID 21309606. 
  26. ↑ Ian Hamley (2011). "Self-Assembly of Amphiphilic Peptides". Soft Matter 7 (9): 4122–4138. doi:10.1039/C0SM01218A. Bibcode: 2011SMat....7.4122H. http://centaur.reading.ac.uk/19780/1/AmphPeptReviewRevised.pdf. 
  27. ↑ Kai Tao; Guy Jacoby; Luba Burlaka; Roy Beck; Ehud Gazit (July 26, 2016). "Design of Controllable Bio-Inspired Chiroptic Self-Assemblies". Biomacromolecules 17 (9): 2937–2945. doi:10.1021/acs.biomac.6b00752. PMID 27461453. 
  28. ↑ Kai Tao; Aviad Levin; Guy Jacoby; Roy Beck; Ehud Gazit (23 August 2016). "Entropic Phase Transitions with Stable Twisted Intermediates of Bio‐Inspired Self‐Assembly". Chem. Eur. J. 22 (43): 15237–15241. doi:10.1002/chem.201603882. PMID 27550381. 
  29. ↑ Donghui Jia; Kai Tao; Jiqian Wang; Chengdong Wang; Xiubo Zhao; Mohammed Yaseen; Hai Xu; Guohe Que et al. (June 16, 2011). "Dynamic Adsorption and Structure of Interfacial Bilayers Adsorbed from Lipopeptide Surfactants at the Hydrophilic Silicon/Water Interface: Effect of the Headgroup Length". Langmuir 27 (14): 8798–8809. doi:10.1021/la105129m. PMID 21675796. 
  30. ↑ Heitz, Marc; Javor, Sacha; Darbre, Tamis; Reymond, Jean-Louis (2019-08-21). "Stereoselective pH Responsive Peptide Dendrimers for siRNA Transfection" (in en). Bioconjugate Chemistry 30 (8): 2165–2182. doi:10.1021/acs.bioconjchem.9b00403. ISSN 1043-1802. PMID 31398014. 
  31. ↑ Boelsma E, Kloek J; Kloek (March 2009). "Lactotripeptides and antihypertensive effects: a critical review". The British Journal of Nutrition 101 (6): 776–86. doi:10.1017/S0007114508137722. PMID 19061526. 
  32. ↑ "Effect of milk tripeptides on blood pressure: a meta-analysis of randomized controlled trials". Nutrition 24 (10): 933–40. October 2008. doi:10.1016/j.nut.2008.04.004. PMID 18562172. 
  33. ↑ Pripp AH (2008). "Effect of peptides derived from food proteins on blood pressure: a meta-analysis of randomized controlled trials". Food & Nutrition Research 52: 10.3402/fnr.v52i0.1641. doi:10.3402/fnr.v52i0.1641. PMID 19109662. 
  34. ↑ "Lactotripeptides show no effect on human blood pressure: results from a double-blind randomized controlled trial". Hypertension 51 (2): 399–405. February 2008. doi:10.1161/HYPERTENSIONAHA.107.098988. PMID 18086944. 
  35. ↑ Wu, Hongzhong; Ren, Chunyan; Yang, Fang; Qin, Yufeng; Zhang, Yuanxing; Liu, Jianwen (April 2016). "Extraction and identification of collagen-derived peptides with hematopoietic activity from Colla Corii Asini". Journal of Ethnopharmacology 182: 129–136. doi:10.1016/j.jep.2016.02.019. PMID 26911525. 



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