Multi-state design of flexible proteins predicts sequences optimal for conformational change
Fig 3
Design native sequence recovery and mutation profile variability comparisons to PSI-BLAST profiles.
(A) Comparison of total native sequence recovery of relaxed and unminimized RECON MSD and SSD designs to PSI-BLAST sequence profiles generated using the native sequence. For this figure and all subsequent boxplots, shaded regions of each box plot denote values within the first and third quartiles (interquartile range, or IQR), with the median indicated as a solid line and whiskers representing values ± 1.5 × IQR. Outliers are represented as dots. Asterisks indicate the significance of difference of means of each design in comparison to the PSI-BLAST profile, with a z-test p-value < 0.01 represented by one asterisk, and a p-value < 0.00001 by three asterisks. The p-value provided in this figure and all subsequent figures represents a two-sided, 95% confidence interval. (B) Mutation frequency root mean square deviations of designs in comparison to a PSI-BLAST profile. The y-axis values represent the root mean square deviation (RMSD) of mutation profiles for each designed residue in relation to a PSI-BLAST profile, represented as: where aaj represents the frequency of an amino acid observed at position i for each of all twenty amino acids (j), and y is the sum of all i differences for all amino acids within a protein of length n residues. A y-value of 0 would indicate that the design profile is identical to the PSI-BLAST profile, and an increase in y-value indicates the root mean square deviation of the sequence profile for each residue is more dissimilar to a PSI-BLAST profile.