By P. Karlson (Auth.)
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The atoms of the peptide bonds, is designated as secondary structure. In globular proteins, however, it is the functional groups of the side chains that effect the particular kind of folding. These situations, represented diagrammatically in Fig. IV-1, will be discussed briefly here. Hydrogen Bonds. The most important secondary valence forces that maintain the conformation of the protein molecule are hydrogen bonds. 8 A . This secondary valence b o n d is symbolized by a dotted line, CO- Ή — N .
Earlier it had been supposed that the arrangement of amino acids in the chains would be subject to certain periodicities. N o n e of these hypotheses hold, however. If any rules can be derived from the available data, it may be that acidic amino acids tend to group themselves together, and the basic and aromatic acids d o the same. Often the same amino acid appears several times in a row. The question may be turned around: Are all possibilities of the amino acid sequence realized? A simple consideration will show that this is utterly impossible.
We will frequently use these conventions, since they are used widely in describing sequences of amino acids. 2. D e t e r m i n a t i o n of A m i n o Acid Sequence in Peptides It is essential to be able to ascertain the sequence of amino acids in naturally occur ring peptides as well as in peptides obtained from the fragmentation of proteins (cf. Chapter IV,2). The Edman degradation has been particularly useful for this purpose. S C H 6 Phenylthiohydantoin 5 H C -NH 5 6 2. DETERMINATION OF A M I N O A C I D SEQUENCE IN PEPTIDES 37 The amino g r o u p of the peptide undergoes reaction at p H 8-9 with phenylisothiocyanate.
