Peptide

Last updated
A tetrapeptide (example Val-Gly-Ser-Ala) with green marked amino end (L-valine) and
blue marked carboxyl end (L-alanine) Tetrapeptide structural formulae v.1.png
A tetrapeptide (example Val-Gly-Ser-Ala) with green marked amino end (L-valine) and
blue marked carboxyl end (L-alanine)

Peptides (from Ancient Greek πεπτός (peptós) 'digested', from πέσσειν (péssein) 'to digest') are short chains of amino acids linked by peptide bonds. [1] [2] Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides.

Contents

A polypeptide is a longer, continuous, unbranched peptide chain. [3] Hence, peptides fall under the broad chemical classes of biological polymers and oligomers, alongside nucleic acids, oligosaccharides, polysaccharides, and others.

A polypeptide that contains more than approximately 50 amino acids is known as a protein. [3] [4] [5] Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule such as DNA or RNA, or to complex macromolecular assemblies. [6]

Amino acids that have been incorporated into peptides are termed residues. A water molecule is released during formation of each amide bond. [7] 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).

Classes

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, opiate peptides, neurotrophic peptides, and blood–brain peptides. [8]

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. [9]

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. [10] More exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom. [11]

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. [12] Other nonribosomal peptides are most common in unicellular organisms, plants, and fungi and are synthesized by modular enzyme complexes called nonribosomal peptide synthetases. [13]

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. [14] 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. [15]

Peptones are derived from animal milk or meat digested by proteolysis. [16] 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. [17]

Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein. [18] 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. [19] [20]

Chemical synthesis

Solid-phase peptide synthesis on a rink amide resin using Fmoc-a-amine-protected amino acid Peptide Synthesis.svg
Solid-phase peptide synthesis on a rink amide resin using Fmoc-α-amine-protected amino acid

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

Vasoactive intestinal peptides

Opioid peptides

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:

Number of amino acids

A tripeptide (example Val-Gly-Ala) with
green marked amino end (L-valine) and
blue marked carboxyl end (L-alanine) Tripeptide Val-Gly-Ala Formula V1.svg
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

See also

Related Research Articles

<span class="mw-page-title-main">Amino acid</span> Organic compounds containing amine and carboxylic groups

Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha amino acids appear in the genetic code.

<span class="mw-page-title-main">Alpha helix</span> Type of secondary structure of proteins

The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues earlier along the protein sequence.

<span class="mw-page-title-main">Peptide bond</span> Covalent chemical bond between amino acids in a peptide or protein chain

In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 of one alpha-amino acid and N2 of another, along a peptide or protein chain.

<span class="mw-page-title-main">Protein primary structure</span> Linear sequence of amino acids in a peptide or protein

Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequences.

<span class="mw-page-title-main">Proteolysis</span> Breakdown of proteins into smaller polypeptides or amino acids

Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. 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.

<span class="mw-page-title-main">Post-translational modification</span> Biological processes

Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. PTMs are important components in cell signaling, as for example when prohormones are converted to hormones.

<span class="mw-page-title-main">Oligopeptide</span>

An oligopeptide, often just called peptide, consists of two to twenty amino acids and can include dipeptides, tripeptides, tetrapeptides, and pentapeptides. Some of the major classes of naturally occurring oligopeptides include aeruginosins, cyanopeptolins, microcystins, microviridins, microginins, anabaenopeptins, and cyclamides. Microcystins are best studied, because of their potential toxicity impact in drinking water. A review of some oligopeptides found that the largest class are the cyanopeptolins (40.1%), followed by microcystins (13.4%).

<span class="mw-page-title-main">Proteinogenic amino acid</span> Amino acid that is incorporated biosynthetically into proteins during translation

Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word "proteinogenic" means "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms.

Nonribosomal peptides (NRP) are a class of peptide secondary metabolites, usually produced by microorganisms like bacteria and fungi. Nonribosomal peptides are also found in higher organisms, such as nudibranchs, but are thought to be made by bacteria inside these organisms. While there exist a wide range of peptides that are not synthesized by ribosomes, the term nonribosomal peptide typically refers to a very specific set of these as discussed in this article.

<span class="mw-page-title-main">Daptomycin</span> Antibiotic

Daptomycin, sold under the brand name Cubicin among others, is a lipopeptide antibiotic used in the treatment of systemic and life-threatening infections caused by Gram-positive organisms.

A tetrapeptide is a peptide, classified as an oligopeptide, since it only consists of four amino acids joined by peptide bonds. Many tetrapeptides are pharmacologically active, often showing affinity and specificity for a variety of receptors in protein-protein signaling. Present in nature are both linear and cyclic tetrapeptides (CTPs), the latter of which mimics protein reverse turns which are often present on the surface of proteins and druggable targets. Tetrapeptides may be cyclized by a fourth peptide bond or other covalent bonds.

A peptide library is a tool for studying proteins. A peptide library contains a great number of peptides that have a systematic combination of amino acids. Usually, the peptide library is synthesized on a solid phase, mostly on resin, which can be made as a flat surface or beads. The peptide library provides a powerful tool for drug design, protein–protein interactions, and other biochemical and pharmaceutical applications.

The discovery of an orally inactive peptide from snake venom established the unimportant role of angiotensin converting enzyme (ACE) inhibitors in regulating blood pressure. This led to the development of Captopril, the first ACE inhibitor. When the adverse effects of Captopril became apparent new derivates were designed. Then after the discovery of two active sites of ACE: N-domain and C-domain, the development of domain-specific ACE inhibitors began.

Peptide signaling plays a significant role in various aspects of plant growth and development and specific receptors for various peptides have been identified as being membrane-localized receptor kinases, the largest family of receptor-like molecules in plants. Signaling peptides include members of the following protein families.

Lysine carboxypeptidase is an enzyme. This enzyme catalyses the following chemical reaction:

<span class="mw-page-title-main">Catgrip</span>

Catgrips are small cation-binding molecular features of proteins and peptides. Each consists of the main chain atoms only of three consecutive amino acid residues. The first and third main chain CO groups bind the cations, often calcium, magnesium, potassium or sodium, with no side chain involvement. Many catgrips bind a water molecule instead of a cation; it is hydrogen-bonded to the first and third main chain CO groups. Catgrips are found as calcium-binding features in annexins, matrix metalloproteinases (e.g.serralysins), subtilisins and phospholipase A2. They are also observed in synthetic peptides and in cyclic hexapeptides made from alternating D,L amino acids.

Ribosomally synthesized and post-translationally modified peptides (RiPPs), also known as ribosomal natural products, are a diverse class of natural products of ribosomal origin. Consisting of more than 20 sub-classes, RiPPs are produced by a variety of organisms, including prokaryotes, eukaryotes, and archaea, and they possess a wide range of biological functions.

<span class="mw-page-title-main">Beta bulge loop</span>

Beta bulge loops are commonly occurring motifs in proteins and polypeptides consisting of five to six amino acids. There are two types: type 1, which is a pentapeptide; and type 2, with six amino acids. They are regarded as a type of beta bulge, and have the alternative name of type G1 beta bulge. Compared to other beta bulges, beta bulge loops give rise to chain reversal such that they often occur at the loop ends of beta hairpins; hairpins of this sort can be described as 3:5 or 4:6. Two websites are available for finding and examining β bulge loops in proteins, Motivated Proteins: and PDBeMotif:.

A proteolipid is a protein covalently linked to lipid molecules, which can be fatty acids, isoprenoids or sterols. The process of such a linkage is known as protein lipidation, and falls into the wider category of acylation and post-translational modification. Proteolipids are abundant in brain tissue, and are also present in many other animal and plant tissues. They are proteins covalenently bound to fatty acid chains, often granting them an interface for interacting with biological membranes. They are not to be confused with lipoproteins, a kind of spherical assembly made up of many molecules of lipids and some apolipoproteins.

<span class="mw-page-title-main">Halovir</span> Group of chemical compounds

Halovir refers to a multi-analogue compound belonging to a group of oligopeptides designated as lipopeptaibols which have membrane-modifying capacity and are fungal in origin. These peptides display interesting microheterogeneity; slight variation in encoding amino acids gives rise to a mixture of closely related analogues and have been shown to have antibacterial/antiviral properties.

References

  1. Hamley, I. W. (September 2020). introduction to Peptide Science. Wiley. ISBN   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. 1 2 Saladin, K. (13 January 2011). Anatomy & physiology: the unity of form and function (6th ed.). McGraw-Hill. p. 67. ISBN   9780073378251.
  4. IUPAC , Compendium of Chemical Terminology , 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006) " proteins ". doi : 10.1351/goldbook.P04898.
  5. "What are peptides". Zealand Pharma A/S. Archived from the original on 2019-04-29.
  6. 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.
  7. 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.
  8. Abba J. Kastin, ed. (2013). Handbook of Biologically Active Peptides (2nd ed.). ISBN   978-0-12-385095-9.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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. Bibcode:2004PNAS..10115585H. doi: 10.1073/pnas.0404932101 . PMC   524835 . PMID   15498872.
  14. 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.
  15. 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.
  16. "UsvPeptides- USVPeptides is a leading pharmaceutical company in India". USVPeptides.
  17. Payne, J. W.; Rose, Anthony H.; Tempest, D. W. (27 September 1974). "Peptides and micro-organisms". Advances in Microbial Physiology, Volume 13. Advances in Microbial Physiology. Vol. 13. Oxford, England: Elsevier Science. pp. 55–160. doi:10.1016/S0065-2911(08)60038-7. ISBN   9780080579719. OCLC   1049559483. PMID   775944.
  18. Hummel J, Niemann M, Wienkoop S, Schulze W, Steinhauser D, Selbig J, Walther D, Weckwerth W (2007). "ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites". BMC Bioinformatics. 8 (1): 216. doi:10.1186/1471-2105-8-216. PMC   1920535 . PMID   17587460.
  19. Webster J, Oxley D; Oxley (2005). Peptide mass fingerprinting: protein identification using MALDI-TOF mass spectrometry . 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.
  20. 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.
  21. Tao, Kai; Makam, Pandeeswar; Aizen, Ruth; Gazit, Ehud (17 Nov 2017). "Self-assembling peptide semiconductors". Science. 358 (6365): eaam9756. doi:10.1126/science.aam9756. PMC   5712217 . PMID   29146781.
  22. 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.
  23. 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.
  24. Ian Hamley (2011). "Self-Assembly of Amphiphilic Peptides" (PDF). Soft Matter. 7 (9): 4122–4138. Bibcode:2011SMat....7.4122H. doi:10.1039/C0SM01218A.{{cite journal}}: CS1 maint: uses authors parameter (link)
  25. 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.{{cite journal}}: CS1 maint: uses authors parameter (link)
  26. 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.{{cite journal}}: CS1 maint: uses authors parameter (link)
  27. Donghui Jia, Kai Tao, Jiqian Wang, Chengdong Wang, Xiubo Zhao, Mohammed Yaseen, Hai Xu, Guohe Que, John R. P. Webster, Jian R. Lu (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.{{cite journal}}: CS1 maint: uses authors parameter (link)
  28. Heitz, Marc; Javor, Sacha; Darbre, Tamis; Reymond, Jean-Louis (2019-08-21). "Stereoselective pH Responsive Peptide Dendrimers for siRNA Transfection". Bioconjugate Chemistry. 30 (8): 2165–2182. doi:10.1021/acs.bioconjchem.9b00403. ISSN   1043-1802. PMID   31398014. S2CID   199519310.
  29. 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.
  30. Xu JY, Qin LQ, Wang PY, Li W, Chang C (October 2008). "Effect of milk tripeptides on blood pressure: a meta-analysis of randomized controlled trials". Nutrition. 24 (10): 933–40. doi:10.1016/j.nut.2008.04.004. PMID   18562172.
  31. 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. PMC   2596738 . PMID   19109662.
  32. Engberink MF, Schouten EG, Kok FJ, van Mierlo LA, Brouwer IA, Geleijnse JM (February 2008). "Lactotripeptides show no effect on human blood pressure: results from a double-blind randomized controlled trial". Hypertension. 51 (2): 399–405. doi: 10.1161/HYPERTENSIONAHA.107.098988 . PMID   18086944.
  33. 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.

{{Authority control}