Physics – Condensed Matter – Soft Condensed Matter
Scientific paper
2002-04-02
In H.A.Lim and C.A.Cantor (eds.), Proc. Bioinformatics and Genome Research, p. 445 (World Scientific, 1994)
Physics
Condensed Matter
Soft Condensed Matter
14 pages, 7 figures
Scientific paper
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. The proposed structure demonstrates that in the genetic code there is a balance between conservatism and innovation. Comparing aligned positions in homologous protein sequences two different behaviors are found: a) There are sites in which the different amino acids present may be explained by one or two "attractor nodes" (coding for the dominating amino acid(s)) and their one-bit neighbors in the codon hypercube, and b) There are sites in which the amino acids present correspond to codons located in closed paths in the hypercube. The structure of the code facilitates evolution: the variation found at the variable positions of proteins do not corresponds to random jumps at the codon level, but to well defined regions of the hypercube.
Jimenez-Montano Miguel A.
la Mora-Basanez Carlos R. de
Poeschel Thorsten
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