Multi-state design of flexible proteins predicts sequences optimal for conformational change
Fig 5
Comparison of mutation profiles predicted by protein design to mutation profiles observed within calmodulin and influenza type A HA2 multiple sequence alignments.
(A) Comparison of root mean square deviation of mutation frequencies derived from calmodulin natural homologues to mutation profiles predicted by RECON MSD or SSD. Calmodulin natural homologue mutation preferences were derived from the multiple sequence alignment of calmodulin homologues. The root mean square deviation (RMSD) here represents the mean standard deviation of an individual residue’s mutation profile, consisting as the mean sum of squared differences of all twenty amino acid frequencies as determined by the multiple sequence alignment of calmodulin homologue sequences in relation to either RECON MSD or SSD residue profile. (B) Residue profile standard deviations between calmodulin multiple sequence alignment profiles and design profiles mapped onto the unbound conformation of calmodulin (PDB ID 1CLL). Here, RMSD represents the mean sum of squared differences of all twenty amino acid frequencies of each residue between homologue and design profiles. Residues whose sequence profiles were predicted to have identical mutation profiles as that within the corresponding position with the multiple sequence alignment are colored in white. The greater the dissimilarity between the homologue mutation profile and design profile, the greater the saturation in red, with complete saturation indicating an RMSD of 1.0. Residues within all four of the conserved EF-hand motifs are labeled, with the bidentate ligand at position 12 critical for Ca2+ binding labeled in boldface. (C) Comparison of root mean square deviation of mutation frequencies derived from influenza type A sequence alignments to mutation profiles predicted by RECON MSD or SSD. RMSD is calculated in a similar fashion as in Panel A. (D) Residue profile standard deviations between HA2 multiple sequence alignment profiles and design profiles mapped onto the pre-fusion conformation of the HA2 trimer (PDB ID 2HMG). RMSD is calculated and labeled the same as in Panel B, but only one HA2 monomer is labeled with RMSD values of the influenza A IVR residue profiles in relation to RECON MSD or SSD profiles. The N- and C-terminal residues of loop regions that undergo large local conformational rearrangements in the post-fusion form are labeled. This includes the B loop that rearranges into an alpha helix and the S5 domain, which stabilizes the alpha helical form of the B loop. Residues within the CR8020 broadly neutralizing epitope [32], including N146 and E150, are also labeled.