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Updated: Jun 6, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Role of everlasting triplet expansions in protein evolution
Zohar Koren1, Edward N Trifonov
1Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel.
Abstract:
Analysis of occurrence of simple amino acid repeats in large ensemble of prokaryotic and eukaryotic sequences reveals that nearly all amino acids found in the repeats belong to those which have in their codon repertoires aggressively expanding triplets, all of three known pathologically expanding classes GCU (GCU, CUG, UGC, AGC, GCA, CAG), GCC (GCC, CCG, CGC, GGC, GCG, CGG), and AAG (AAG, AGA, GAA, CTT, TTC, TCT). This is observed especially clear in the first exons of proteins of higher eukaryotes. The data are interpreted as manifestation of everlasting triplet expansions, which, presumably, started from the very origin of the triplet code. The spontaneous expansions continued to occur all the way during evolution, leaving their footprints in the protein-coding sequences as still visible simple amino acid repeats, as preferred triplets encoding the repeats, and as preferred codons in the codon usage tables.
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