Oligopeptide

J. Kostrowicki and H.A. Scheraga, Application of the diffusion equation method for global optimization to oligopeptides, J. Phys. Chem. 96 (1992), 7442-7449. M. Levitt, A simplified representation of protein confomations for rapid simulation of protein folding, J. Mol. Biol. 104 (1976), 59-107. 

The following short descriptions of the steps involved in the synthesis of a tripeptide will demonstrate the complexity of the problem amino acid units. In the later parts of this section we shall describe actual syntheses of well defined oligopeptides by linear elongation reactions and of less well defined polypeptides by fragment condensation. 

In more recent publications the analytical standards have been raised considerably (HPLC, H-NMR, CD R.F. Nutt, 1980), and one may predict that in the near future it will be possible to characterize fully synthetic oligopeptides of moderate size. 

First the protected oligopeptide is coupled with polymer-bound nitrophenol by DCC. N"-Deblocking leads then to simultaneous cycliiation and detachment of the product from the polymer (M. Fridkin, 1965). Recent work indicates that high dilution in liquid-phase cycli-zation is only necessary, if the cyclization reaction is sterically hindered. Working at low temperatures and moderate dilution with moderately activated acid derivatives is the method of choice for the formation of macrocyclic lactams (R.F. Nutt, 1980). 

Short chains of amino acid residues are known as di-, tri-, tetrapeptide, and so on, but as the number of residues increases the general names oligopeptide and polypeptide are used. When the number of chains grow to hundreds, the name protein is used. There is no definite point at which the name polypeptide is dropped for protein. Twenty common amino acids appear regularly in peptides and proteins of all species. Each has a distinctive side chain (R in Figure 45.3) varying in size, charge, and chemical reactivity. 

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