- Protein crystallography
- Protein purification
- Programs for crystallography
- X-ray detectors
- Amino Acids
Description of peptides
Like proteins, peptides are large biological molecules with molecular weight up to 10 kDa. Peptides are made of amino acid linked into linear chain with overall length is up to 100 amino acids. Nowadays, many scientists descripe peptides as a polypeptide chains with up to 50 amino acids. It is difficult to unambiguously classify peptides and proteins, especially for long peptides and small proteins. One of the most reasonable classification is based on the structural flexibility. According to this classification peptides are flexible polypeptide chains without one preferable conformation, whereas proteins maintain some preferable conformation, at least for the core residues. According to this classification, 51 amino acid insulin is a protein with the core structure fixed by three disulphide bridges.
Peptide classification by function of peptides
Peptides are involved into many processes in the living organisms and it is possible to classify them on the basis of their function. As usually this classification is not perfect because some of the peptides can belongs to different groups simultaneously, for example, oxytocin can be considered as a hormone (transmitting signal between cells) and also oxytocin can be classified as neuropeptide because ther function as neurotransmitter in the brain.
Hormones. Hormones are involved into carrying signals between cells. Classical examples of hormones are: bradykinins, gastrins, oxytocins etc.
Neuropeptides. Neuropeptides found in neural tissues. usually these peptides are produced in the brain and involved into regulatory and signalling processes. Classical examples of neuropeptides are: endorphins, vasopressin, atrial-natriuretic peptide etc.
Alkaloids. Alkaloids are peptides, usually from plants, fungi and some animals like shellfish. Alkaloids involved into defend of one organism from consuming by other organisms. Classical examples of peptide alkaloid are: ergotamine, pandamine, dynorphin A-(1-8)-octapeptide, N beta-(D-Leu-D-Arg-D-Arg-D-Leu-D-Phe)-naltrexamine, etc.
Antibiotics. Antibiotics are inhibits the grows of micro organisms, usually bacterial cells and locationally fungi and protozoa. Classical examples of peptide antibiotics are: tyrothricinm bacitracin, gramicidin, valinomicin etc.
Toxins. Toxin is the poison substance. Peptide toxins are the most poison substances. Examples of peptide toxins are: palutoxins, agatoxins, curtatoxins etc.
Regulation peptides. The group of regulation peptides is not well defined because almost any peptides can regulate some processes in organisms, but this group is used to classify peptides which are not clearly belongs to other groups. examples of regulatory peptides are: anserine, carnosine, etc.
Peptide classification by synthesis
Sometimes peptides can be classified by their synthesis type.
Ribosomal peptides. Ribosomal peptides (almost all known peptides) are synthesized by translation of mRNA on ribosomes. Usually they subjected to further postranslational modification, wich can involve even recemization of L-amino acids to D-amino acids.
Nonribosomal peptides. Nonribosomal peptides (glutathione cyclopeptides etc.), are synthesized during enzymatic catalysis
Peptones. Peptones are peptides derived from digestion processes.
Peptide synthesis is a chemical process of coupling of the carboxyl group of one amino acid to the amino group of another amino acid. Usually chemical techniques are used to synthesize peptides of up to 30-40 amino acids length. The fist peptide synthesis was carries out by T. Curtius 1882 via reaction between benzyl cloride and silver salt of glycine. During this process Curtius produce crystals of N-benzyl-glycile-glycine. The first pure di-peptide (Gly-Gly) was synthesized by E. Fischer in 1901.
In 1932, Bergmann from Fisher's lab discover carbobenzoxy group C6H5CH2OCO which is very convenient as a protective group for peptide synthesis. In 1950-1960 the first biological peptides, like oxytocin, vasopressin, insulin and others were synthesized.
Types of peptide synthesis
Peptide synthesis process can be classified on the basis of used techniques and type of the final product.
Liquid-phase peptide synthesis. Liquid-phase, or classical peptide synthesis can be devided into two classes - step-by-step peptide synthesis with subsequent adding of one amino acid at ones from C-terminal to N-terminal and block-synthesis with coupling of polypeptide fragments. Liquid-phase peptide synthesis is used in large-scale peptide production for industry.
Solid-phase peptide synthesis. Solid-phase peptide synthesis is a process during which the polypeptide chain is covalently bound via linker to the porous insoluble beds particles. Each cycle of this solid-phase peptide synthesis can be described in few steps - deprotection of N-terminal group, coupling with N-protected amino acid. The standard repetitious steps allows to use robotic equipment for this type of synthesis. Solid-phase peptide synthesis is perfect for researche laboratories and small quantities of production.
Homo-polymerisation. Homo-polymerisation is used to synthesize homo-polymeric chains of amino acids.
Enzymatic peptide synthesis. Enzymatic peptide synthesis is based on enzymes which are able to formate peptide bond. Unfortunately this technique is very complicated and there is no remarkable results was achieved yet.
Partial peptide synthesis. In partial peptide synthesis technique the natural peptides and proteins are used as a source of peptide fragments.
Cyclopeptide synthesis. Cyclopeptide synthesis is the cyclization of linear peptides.
Non-standard peptide synthesis. Non-standard peptide synthesis is used to produce peptides with non-standard peptide bonds, for example ester-bonds etc.