Peptide

Peptides (from the Greek πεπτίδια, "small digestibles") are short polymers formed from the linking, in a defined order, of α-amino acids. The link between one amino acid residue and the next is known as an amide bond or a peptide bond.

Proteins are polypeptide molecules (or consist of multiple polypeptide subunits). The distinction is that peptides are short and polypeptides/proteins are long. There are several different conventions to determine these, all of which have caveats and nuances.

Conventions

One convention is that those peptide chains that are short enough to be made synthetically from the constituent amino acids are called peptides rather than proteins. However, with the advent of better synthetic techniques, peptides as long as hundreds of amino acids can be made, including full proteins like ubiquitin. Native chemical ligation has given access to even longer proteins, so this convention seems to be outdated.

Another convention places an informal dividing line at approximately 50 amino acids in length (some people claim shorter lengths). However, this definition is somewhat arbitrary. Long peptides, such as the amyloid beta peptide linked to Alzheimer\'s disease, can be considered proteins; and small proteins, such as insulin, can be considered peptides.

Peptide classes

Here are the major classes of peptides, according to how they are produced:

Ribosomal peptides 

Are synthesized by translation of mRNA. They are often subjected to proteolysis to generate the mature form. These function, typically in higher organisms, as hormones and signaling molecules. Some organisms produce peptides as antibiotics, such as microcins.Duquesne S, Destoumieux-Garzón D, Peduzzi J, Rebuffat S (2007). "Microcins, gene-encoded antibacterial peptides from enterobacteria". Natural product reports 24 (4): 708–34. PMID 17653356.  Since they are translated, the amino acid residues involved are restricted to those utilized by the ribosome. However, these peptides frequently have posttranslational modifications, such as phosphorylation, hydroxylation, sulfonation, palmitylation, glycosylation and disulfide formation. In general, they are linear, although lariat structures have been observed.Pons M, Feliz M, Antònia Molins M, Giralt E (1991). "Conformational analysis of bacitracin A, a naturally occurring lariat". Biopolymers 31 (6): 605–12. PMID 1932561.  More exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom.Torres AM, Menz I, Alewood PF, et al (2002). "D-Amino acid residue in the C-type natriuretic peptide from the venom of the mammal, Ornithorhynchus anatinus, the Australian platypus". FEBS Lett. 524 (1-3): 172–6. PMID 12135762. 

Nonribosomal peptides 

These peptides are assembled by enzymes that are specific to each peptide, rather than by the ribosome. The most common non-ribosomal peptide is glutathione, which is a component of the antioxidant defenses of most aerobic organisms.Meister A, Anderson M (1983). "Glutathione". Annu Rev Biochem 52: 711 – 60. PMID 6137189.  Other nonribosomal peptides are most common in unicellular organisms, plants, and fungi and are synthesized by modular enzyme complexes called nonribosomal peptide synthetases.Hahn M, Stachelhaus T (2004). "Selective interaction between nonribosomal peptide synthetases is facilitated by short communication-mediating domains". Proc. Natl. Acad. Sci. U.S.A. 101 (44): 15585–90. PMID 15498872.  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.Finking R, Marahiel MA (2004). "Biosynthesis of nonribosomal peptides1". Annu. Rev. Microbiol. 58: 453–88. PMID 15487945.  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. Oxazoles, thiazoles often indicate that the compound was synthesized in this fashion.Du L, Shen B (2001). "Biosynthesis of hybrid peptide-polyketide natural products". Current opinion in drug discovery & development 4 (2): 215–28. PMID 11378961. 

Peptones 

Are derived from animal meat digested by proteolytic digestion. In addition to containing small peptides, the resulting spray-dried material includes fats, metals, salts, vitamins and many other biological compounds. Peptone is used in nutrient media for growing bacteria and fungi.Payne JW (1976). "Peptides and micro-organisms". Adv. Microb. Physiol. 13: 55–113. PMID 775944. 

Peptide Fragments 

Refer to fragments of proteins which used to identify or quantify the source protein.Hummel J, Niemann M, Wienkoop S, et al (2007). "ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites". BMC Bioinformatics 8: 216. PMID 17587460.  Often these are the products of enzymatic degradation performed in the laboratory on a controlled sample, but can also be forensic or paleontological samples which have been degraded by natural effects.Webster J, Oxley D (2005). "Peptide mass fingerprinting: protein identification using MALDI-TOF mass spectrometry". Methods Mol. Biol. 310: 227–40. PMID 16350956. Marquet P, Lachâtre G (1999). "Liquid chromatography-mass spectrometry: potential in forensic and clinical toxicology". J. Chromatogr. B Biomed. Sci. Appl. 733 (1-2): 93–118. PMID 10572976. 

Peptides in molecular biology

Peptides have received prominence in molecular biology in recent times for several reasons. The first and most important is that peptides allow the creation of peptide antibodies in animals without the need to purify the protein of interest.Bulinski JC (1986). "Peptide antibodies: new tools for cell biology". Int. Rev. Cytol. 103: 281–302. PMID 2427468.  This involves synthesizing antigenic peptides of sections of the protein of interest. These will then be used to make antibodies in a rabbit or mouse against the protein.

Another reason is that peptides have become instrumental in mass spectrometry, allowing the identification of proteins of interest based on peptide masses and sequence. In this case the peptides are most often generated by in-gel digestion after electrophoretic separation of the proteins.

Peptides have recently been used in the study of protein structure and function. For example, synthetic peptides can be used as probes to see where protein-peptide interactions occur.

Inhibitory peptides are also used in clinical research to examine the effects of peptides on the inhibition of cancer proteins and other diseases.

Well-known peptide families in humans

The peptide families in this section are all 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 signalling functions.

The Tachykinin peptides

• Substance P
• Kassinin
• Neurokinin A
• Eledoisin
• Neurokinin B

Vasoactive intestinal peptides

• VIP Vasoactive intestinal peptide
• PACAP Pituitary adenylate cyclase activating peptide
• PHI 27
• PHM 27
• GHRH 1-24 Growth hormone releasing hormone 1-24
• Glucagon
• Secretin

Pancreatic polypeptide-related peptides

• NPY
• PYY Peptide YY
• APP Avian pancreatic polypeptide
• HPP Human pancreatic polypeptide

Opioid peptides

• Proopiomelanocortin (POMC) Peptides
• The Enkephalin pentapeptides
• The Prodynorphin peptides

Calcitonin peptides

• Calcitonin
• Amylin
• AGG01

Notes on terminology

• A polypeptide is a single linear chain of amino acids.
• A protein is one or more polypeptides more than about 50 amino acids long.
• An oligopeptide or (simply) a peptide is a polypeptide less than 30-50 amino acids long.
• A dipeptide has two amino acids.
• A tripeptide has three amino acids.
• A pentapeptide has five amino acids.
• A nonapeptide has nine amino acids (e.g., oxytocin).
• A neuropeptide is a peptide that is active in association with neural tissue.
• A peptide hormone is a peptide that acts as a hormone.

See also

• Peptidomimetics (such as peptoids and β-peptides) to peptides, but with different properties.
• bis-peptide
• Peptide synthesis
• Translation
• Ribosome

References

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