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Peptides are the family of short molecules formed from the linking, in a defined order, of various α-amino acids. The link between one amino acid residue and the next is an amide bond and is sometimes referred to as 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 flaws.
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 Native chemical ligation has given access to even longer proteins, so this convention seems to be outdated.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. Because of the arbitrary nature of this definition, there is considerable movement within the scientific community to ascribe the more-specific definition that “a peptide is an amino acid molecule without secondary structure; on gaining defined structure, it is a protein.” Thus the same molecule can be either a peptide or a protein depending on its environment, though there are peptides that cannot be proteins.
1. Peptide classes
Here are the major classes of peptides, according to how they are produced:
1.1. 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 lower organisms produce peptides as antibiotics, such as microcin J25. Since they are translated, the amino acid residues involved are restricted to those utilized by the ribosome, and posttranslational modifications thereof, such as phosphorylation, hydroxylation, sulfonation, disulfide formation, etc. In general, they are linear, although lariat structures are common. More exotic manipulations do occur, however, such as racemization (as in platypus venom) or usage of nonribosmal peptide modules (see below) (as in bistratamide a).
1.2. Nonribosomal peptides
Nonribosomal peptides are synthesized using a modular enzyme complex (which functions much like a conveyor belt on a factory). Nonribosomal peptides are confined primarily to unicellular organisms, plants, and fungi. All of these complexes are 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. In general, these peptides are cyclic (often with highly-complex cyclic structures), although linear nonribosomal peptides are common. Since the system is modular and closely related to the machinery for building fatty acids and polyketides, hybrid compounds are often found. Oxazoles, thiazoles, and their reduced counterparts often indicate that the compound was synthesized in this fashion.
1.3. Peptones
Peptones are derived from animal meat digested by proteolases. The resulting material is used as a source of proteins in nutrient media for growing bacteria and fungi.
1.4. Peptide Fragments
Refer to fragments of proteins which 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 which have been degraded by natural effects.
2. 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 antibodies in animals without the need to purify the protein of interest. One can simply make antigenic peptides of sections of the protein of interest. These will suffice in making 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.
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.
3. Well-known peptide families
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 signaling functions.
3.1. The Tachykinin peptides
• Substance P
• Kassinin
• Neurokinin A
• Eledoisin
• Neurokinin B
3.2. 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
3.3. Pancreatic polypeptide-related peptides
• NPY
• PYY Peptide YY
• APP Avian pancreatic polypeptide
• HPP Human pancreatic polypeptide
3.4. Calcitonin peptides
• Calcitonin
• Amylin
• AGG01
