Fig. 1: Molecular dynamics (MD) and circular dichroism (CD) of Gdrd confirm a partially ordered alpha helical structure.

a Representative backbone ensemble of the modeled Gdrd structure composed of ten frames sampled every 20 ns from each of three 200-ns MD replicates (shown as green, blue, and red ribbons, respectively). The central helix and a portion of the N-terminal helix remain stably folded across all three simulations despite considerable flexibility in the rest of the protein structure, indicative of a partially ordered structure. b Plot of C_α root-mean-square fluctuation (RMSF) versus residue position (averaged over three MD replicates) further demonstrates that the central helix of Gdrd, shaded, is the most conformationally rigid structure in the protein (C_α RMSF = 2–4 Å). c Mapping the RMSF values to a representative Gdrd MD structure for each of the three simulations shows similar regions of conformational flexibility for each replicate. d CD spectrum of Gdrd demonstrates characteristics typical of helical proteins. A helix minimum at 222 nm that is weaker than the helix minimum at 208 nm is characteristic of a flexible or distorted helix as was observed in the MD simulation⁹⁰.