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Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints

Figure 3

Monomers and genetic code for construction of model proteins.

A) The set of vector monomers, named according to compass direction and length (i.e., Nem indicating a northeast vector of medium length). To ensure that vector addition produces different results with different vector combinations, small vectors are of length 1, medium vectors of length e1/2 (≈1.65), and long vectors of length e (≈2.72). B) A standard genetic code for specifying the monomers with nucleotide triplets. Like the natural code [15] this code incorporates several features that reduce the impact of point mutations. These include extensive use of third-position degeneracy, strong correlation of second position with a key physical property (direction), and underrepresentation of vectors that would be most disruptive as substitutes (long vectors).

Figure 3