Pervasive, conserved secondary structure in highly charged protein regions
Fig 3
eIF3A, an essential eukaryotic translation initiation factor, contains a conserved, highly charged helix that varies in length but not in secondary structure.
a Alignment of the eIF3A highly charged region (orthologs from all distantly-related species with predicted proteomes in AlphaFold) with negatively charged residues colored red, positively charged residues colored blue, and gaps and all other amino acids in white. Although the highly charged nature of the region is conserved, the sequence itself is variable. b Representative image of the cryoEM structure of yeast eIF3A [42] with the highly charged region (resolved as a helix) shown in purple, and a reference helix shown in black. c Alignment of eIF3A (same as in a) colored by the secondary structure predicted by AlphaFold; S. cerevisiae sequence is highlighted in red. Note that the highly charged region is predicted to be helical in every species represented. d Despite strong secondary structure conservation, the length of the highly charged helix varies significantly more than a reference helix from the same protein.