Figure 3

Predicting the structural differences between wildtype and yellow mutant cut proteins. (a) The cut protein sequence includes 3 cut domains (grey boxes) and a homeobox domain (light grey circle). Coiled-coil regions (MARCOIL probability > 90) are indicated by red squares. MARCOIL probability list per residue for the wildtype (bottom) and yellow mutant (top) sequence (residues 30–63, labelled above) are highlighted from white to red in color scale from 0 to 100. MARCOIL probability plots for the N-terminal sequence (residues 1–80) of (b) wildtype and (c) Yellow mutant variant. (d/e) The cut coiled-coil (predicted from residues 20–55) is depicted in cartoon tube from the N-terminus (left) to the C-terminus (right), with residues in stick and colored according to atom type: carbon (white), nitrogen (blue) and oxygen (red); the wildtype sequence (d) can form helix stabilizing backbone hydrogen bonds (black dots) surrounding Ala38. Hydrogen bonds form between the Ala38 backbone nitrogen (and the i-1 Arg residue backbone nitrogen) and the i-4 Trp residue backbone carbonyl (green dots). The Ala38Pro mutation removes the ability to form a hydrogen bond between the backbone nitrogen and the i-4 carbonyl (colored green) in the yellow mutant variant (e) which destabilizes the helical propensity and can kink the coil.