Multi-state design of flexible proteins predicts sequences optimal for conformational change
Fig 4
Comparison of exchangeability rates.
(A) Average amino acid exchangeability of PSI-BLAST, RECON MSD, and SSD sequence profiles. Single-letter amino acid codes were used for both x and y axes, with the x axis representing the original amino acid and the y axis representing the average mutation frequency the original amino acid to the indicated mutation. (B) Comparison of exchangeability rates between profiles, excluding rates of native sequence conservation rates. The y axis represents the mean frequency a native amino acid is replaced with a specific, non-native amino acid, which we term as amino acid exchangeability. (C) Difference of mean amino acid-specific exchangeability observed in a PSI-BLAST profile compared to a design profile. The x axis represents each type of amino acid present in the native sequence. The y axis represents the difference in average exchangeability frequency of each amino acid type, or rather, the average frequency a native amino acid type is replaced with any other non-native amino acid. A positive value indicates the native amino acid is less likely to be exchanged for a non-native amino acid during design, whereas a negative value indicates the native amino acid is more likely to be exchanged, as compared to a PSI-BLAST profile.