From amino acid landscape to protein landscape: Analysis of genetic codes in terms of fitness landscape

Assigning the values of a certain physicochemical property for individual a mino acids to the corresponding codons, we can make an amino acid property "landscape" on a four valued three dimensional sequence: space from a genet ic code table. Eleven property landscapes made from the standard genetic co de (SGC) were analyzed. The evaluation of correlation for each landscape is done by theta value, which represents the ratio of the mean slope (as an a dditive term) to the degree of roughness (as a nonadditive term). The theta -values for hydropathy indices, polarity, specific heat, and beta-sheet pro pensity were considerably large with respect to SGC. This implies that the additivity of the contribution from each letter holds for these properties. To clarify the meaning of the so-called mutational robustness of SGC, we n ext examined correlations between the amino acid property and the actual "s ite fitnesses" of a protein. The site fit nesses were derived from a set of binding preference scores of amino acid residues at every site in MHC clas s I molecule binding peptides (Udaka et al. in press). We found that the SG C's theta value for an amino acid property is correlated with the significa nce of the property in the protein function. Adaptive walk simulation on fi tness (= affinity) landscapes in a base sequence space for these model pept ides confirmed better evolvability due to the introduction of SGC.