Peptide sequence deduction

The mass difference between consecutive ions within a series allows the identity of the consecutive amino acids to be determined (see Table 8.2) and thus deduction of the peptide sequence. Indeed, the 20 common amino acid residues have distinctive elemental compositions and consequently distinctive masses. There is one exception with Leu and He, which are isomers. However, a low-accuracy measurement may be incapable of discriminating between Gin and Lys, which differ by 0.036 u. In addition, there are combinations of amino acid residues that yield the same nominal mass or even the same elemental composition. 

Deduction of peptide sequence from analysis of overlapping sequences of component peptides. 

Figure 11 displays the soft and the hard ionization mass spectra of the decapeptide angiotensin I. Again the soft ionization mass spectrum shows exclusively the molecular ion of this compound. The partial hard ionization mass spectrum shows mass patterns that permit the deduction of the peptide sequence. The main signals are due to the bond breaking around the carbonyl group of the peptide chain. The breakdown pattern of this compound is shown schematically in Figure 12. Only minor fragmentation occurs in the side chain.

Because of their ease of synthesis and their structural similarity to peptides, many laboratories have used peptoids as the basis for combinatorial drug discovery. Peptoids were among the first non-natural compounds used to establish the basic principles and practical methods of combinatorial discovery [17]. Typically, diverse libraries of relatively short peptoids (< 10 residues) are synthesized by the mix-and-split method and then screened for biological activity. Individual active compounds can then be identified by iterative re-synthesis, sequencing of compounds on individual beads, or indirect deduction by the preparation of positional scanning libraries. 

Besides AFl and AF2, 16 other Ascaris FMRFamide-like peptides have been isolated and sequenced (12 sequences are shown in Table 14.2) (194-197 Cowden and Stretton, unpublished). These sequences are unique and not related by post-translational modification or, in most cases, by proteolysis they are also different from FMRFamide-like sequences reported in other organisms, whether obtained from isolated and sequenced peptides, or by deduction from the DNA sequences of genes. It is clear that there is a family of FMRFamide-like peptides in A. suum. They can be divided into several subfamilies related by sequence. Initial experiments on their bioactivity suggest that these may also be functional subfamilies. Measurements of effects on muscle tension, and on input resistance of four types of motoneurons, show that there are at least four classes of biological activity controlled by these peptides AFl and AF2 form one class that causes contraction and the generation of rhythmic activity in muscle (194,197), AF3 and AF4 cause muscle contraction (195), AF5 and AF7 reduce the input resistance of both excitatory and inhibitory motoneurons, and AFl 1 relaxes muscle and increases the input resistance of inhibitory motoneurons (Davis and Stretton, unpublished). 

Chart VIII-8. The complete amino-acid sequences deduced for clupeine Y l, Yll and Z with illustration of several degradations. (Structures of tryptic peptides obtained from whole clupeine from Clupea harengus were also referred to for this deduction. See text) (A = Arg) (Chang, 1969 Chang, Nakahara, and Ando, to be published)... 

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