The cardinal principle of like attracting like generates many ubiquitous oligopeptides shared by divergent proteins.
Actual protein amino acid sequences are very different from random assemblages of 20 varieties of amino acids. The separate survey of 20 unrelated proteins in two steps that included eight of the 18 discussed in this paper, revealed that at the level of 5000 total residues, one out of every 32 tetrapeptides appeared in two or more identical copies, whereas at the level of 10,000 total residues, the frequency was elevated to one out of every 29. It would thus appear that only 60,000 or so, out of the possible 160,000 (20(4)) varieties of tetrapeptides, are regularly used by all proteins. These shall be defined as ubiquitous tetrapeptides. Those tetrapeptides occasionally found to be stray which did not belong to the above group of 60,000 must have been generated by new mutations. Thus, they are expected to return to the group by subsequent mutations. The above ubiquity is due to the cardinal principle of protein construction which is like attracting like. On the average, 28% of each residue is devoted to the formation of homodipeptides such as Leu-Leu, Asn-Asn and Trp-Trp. Consequently, homo-oligopeptides, pentapeptidic and longer, are readily found in two or more proteins unrelated to each other. The next in line among the ubiquitous oligopeptides are those made of similar residues. They usually contain palindromic cores such as Leu-Val-Leu, Ala-Gly-Ala and Lys-Arg-Lys.(ABSTRACT TRUNCATED AT 250 WORDS)
Ohno
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Beckman Research Institute of the City of Hope, Duarte, California 91010-0269.
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis / Q000737:chemistry; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D004563:Electrochemistry; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000235:genetics*; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D017386:Sequence Homology, Amino Acid
D000596:Amino Acids; D001426:Bacterial Proteins; D009842:Oligopeptides; D011506:Proteins