Peptide: Wikis

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From Wikipedia, the free encyclopedia

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 called 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.

Contents

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 Native chemical ligation has given access to even longer proteins, so this convention seems to be outdated.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). 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:

Milk peptides 
Milk peptides are formed from milk proteins by enzymatic breakdown by digestive enzymes or by the proteinases formed by lactobacilli during the fermentation of milk. Several milk peptides have been shown to have antihypertensive effects in animal and in clinical studies (see also Lactotripeptides).
Ribosomal peptides 
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.[1] 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.[2] More exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom.[3]
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.[4] Other nonribosomal peptides are most common in unicellular organisms, plants, and fungi and are synthesized by modular enzyme complexes called nonribosomal peptide synthetases.[5] 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.[6] 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.[7]
Peptones
See also Tryptone
Peptones are derived from animal milk or 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.[8]
Peptide fragments 
Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein.[9] 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.[10][11]

Peptide Synthesis

See also peptide synthesis
Table of Amino Acids.
Solid-Phase Peptide Syntesis on a Rink amide resin using Fmoc-α-amine-protected amino acid

Peptides in molecular biology

Peptides have recently received prominence in molecular biology 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.[12] 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 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.

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The Tachykinin peptides

Vasoactive intestinal peptides

  • 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

Calcitonin peptides

Other peptides

Notes on terminology

See also

References

  1. ^ 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.  
  2. ^ 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.  
  3. ^ 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.  
  4. ^ Meister A, Anderson ME (1983). "Glutathione". Annual Review of Biochemistry 52: 711–60. doi:10.1146/annurev.bi.52.070183.003431. PMID 6137189.  
  5. ^ Hahn M, Stachelhaus T (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.  
  6. ^ Finking R, Marahiel MA (2004). "Biosynthesis of nonribosomal peptides1". Annual Review of Microbiology 58: 453–88. doi:10.1146/annurev.micro.58.030603.123615. PMID 15487945.  
  7. ^ Du L, Shen B (March 2001). "Biosynthesis of hybrid peptide-polyketide natural products". Current Opinion in Drug Discovery & Development 4 (2): 215–28. PMID 11378961.  
  8. ^ Payne JW (1976). "Peptides and micro-organisms". Advances in Microbial Physiology 13: 55–113. doi:10.1016/S0065-2911(08)60038-7. PMID 775944.  
  9. ^ 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. doi:10.1186/1471-2105-8-216. PMID 17587460.  
  10. ^ Webster J, Oxley D (2005). "Peptide mass fingerprinting: protein identification using MALDI-TOF mass spectrometry". Methods in Molecular Biology 310: 227–40. doi:10.1007/978-1-59259-948-6_16. PMID 16350956.  
  11. ^ Marquet P, Lachâtre G (October 1999). "Liquid chromatography-mass spectrometry: potential in forensic and clinical toxicology". Journal of Chromatography. B, Biomedical Sciences and Applications 733 (1-2): 93–118. doi:10.1016/S0378-4347(99)00147-4. PMID 10572976.  
  12. ^ Bulinski JC (1986). "Peptide antibodies: new tools for cell biology". International Review of Cytology 103: 281–302. doi:10.1016/S0074-7696(08)60838-4. PMID 2427468.  
  13. ^ Boelsma E, Kloek J (March 2009). "Lactotripeptides and antihypertensive effects: a critical review". The British Journal of Nutrition 101 (6): 776–86. doi:10.1017/S0007114508137722. PMID 19061526.  
  14. ^ 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.  
  15. ^ Pripp AH (2008). "Effect of peptides derived from food proteins on blood pressure: a meta-analysis of randomized controlled trials". Food & Nutrition Research 52. doi:10.3402/fnr.v52i0.1641. PMID 19109662.  
  16. ^ 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.  

Simple English

Peptides are organic chemical molecules. They are polymers made from linking amino acids together in a certain order. The link between one amino acid residue and the next is known as an amide bond or a peptide bond.

Linking peptides together gives proteins, which are also known as Polypeptides.



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