Failure sequences/truncated peptides

Fig. 15. The schematic description of truncated and failure sequences in the Merrifield peptide synthesis characterizing the product composition...

Formation of error-peptides Weygand and Obermeier (1968) and Bayer et aL (1970a) have divided the error-peptides (peptides other than those desired) into two classes (a) truncated sequences and (b) failure sequences. When a peptide chain on the resin fails to grow beyond a certain length, it is termed a truncated sequence. In a failure sequence, one or more amino acids may be missing from the desired peptide sequences. 

The formation of truncated sequences has been attributed to steric factors and alkylation of chain ends by residual chloromethyl groups. The most common situation, however, is one in which the growth of the peptide chain in some of the sites may stop prematurely due to the limiting size of the cavity in the polymer. To overcome this problem, low cross-linked resins with low functionalization have been employed. Truncated sequences do not pose a problem either, when pellicular resins are used. It is difficult to assign a proper explanation for the formation of failure sequences other than to propose a statistical failure of some amino acids being incorporated into certain peptide chains. The formation of failure sequences can only be minimized by choosing proper, i.e., different, sets of experimental conditions for coupling different amino acids. 

A major drawback in the Merrifield (1963) method has been the unchecked synthesis of the peptide chain, since it can be cleaved from the resin only at the end of the sequence of reactions. This has frequently resulted in failure sequences and truncated sequences, as well as doubling of sequences because of interpolymer acylation reactions. In the polymeric active ester method, the peptide formed remains in solution. Thus it can be isolated, purified, and its purity checked before use in the subsequent coupling reaction. Therefore, it appears that the use of polymeric esters may provide a suitable and time-saving method for the synthesis of medium-sized, protected peptides, i.e., those containing... 

Frank and Hagenmaier suggested an alternative to both solid- and liquid-phase peptide synthesis by creating the solid-liquid-phase method in order to overcome the problem of failure and truncated sequences [105, 106], To this end, poly(ethylene glycol) monoalkyl ethers were used as carboxy protecting poups. The principle of this method is depicted in Scheme 2. 

Fig. 5-11. Isocratic purification of the crude synthetic peptide, ACP (65-74), from its truncated failure sequences using the polystyrene reversed phase matrix, PLRP-S 100 A (Polymer Laboratories). Column dimensions, 150mmx4.6mm ID and the eluent was acetonitrile/water (20 80 v/v) containing 0.1% TFA. (A) Shows the separation of approximately 5 pg of peptide, (B) shows the separation of approximately 1 mg of peptide.

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