Peptide



Peptides (from the Greek πεπτός, "digested" from πέσσειν "to digest") are short polymers of amino acids linked by peptide bonds. They have the same peptide bonds as those in proteins, but are commonly shorter in length. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond. There can also be tripeptides, tetrapeptides, pentapeptides, etc. Peptides have an amino end and a carboxyl end, unless they are cyclic peptides. A polypeptide is a single linear chain of amino acids bonded together by peptide bonds. Protein molecules consist of one or more polypeptides put together typically in a biologically functional way and sometimes have non-peptide groups attached, which can be called prosthetic groups or cofactors.

Definitions
One definition is that those 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 Native chemical ligation has given access to even longer proteins, so this convention seems to be outdated.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 definition 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.

Structural flexibility offers a differential feature in regard to proteins, since the latter exhibit a native structure conferred by their tertiary structure and the former do not. Length only is not a differential feature between peptides and proteins, since it can talk about long peptides, with a preferred secondary structure and structural flexibility, like the growth hormone releasing hormone (GHRH) with forty-four residues, or mini-proteins, with a definite tertiary structure, like the Trp cage whose sequence is twenty residues long.

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


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


 * 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.


 * Peptide fragments : Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein. 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.

Peptide synthesis

 * See also Peptide synthesis



Peptides in molecular biology
Peptides have recently received prominence in molecular biology for several reasons. The first is that peptides allow the creation of peptide antibodies in animals without the need to purify the protein of interest. 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. Sulfur is an element that occurs in a number of polypeptides.

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.

The Tachykinin peptides

 * Substance P
 * Kassinin
 * Neurokinin A
 * Eledoisin
 * Neurokinin B

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

 * Proopiomelanocortin (POMC) peptides
 * Enkephalin pentapeptides
 * Prodynorphin peptides

Calcitonin peptides

 * Calcitonin
 * Amylin
 * AGG01

Other peptides

 * B-type Natriuretic Peptide (BNP) - produced in myocardium & useful in medical diagnosis
 * Lactotripeptides - Lactotripeptides might reduce blood pressure,  although the evidence is mixed.

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 tetrapeptide has four amino acids.
 * A pentapeptide has five amino acids.
 * An octapeptide has eight amino acids (e.g., angiotensin II).
 * A nonapeptide has nine amino acids (e.g., oxytocin).
 * A decapeptide has ten amino acids (e.g., gonadotropin-releasing hormone & angiotensin I).
 * A neuropeptide is a peptide that is active in association with neural tissue.
 * 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.