Figure 3: Molecular dynamics trends for the holo-Fdc1 at 350 K simulation.
From: Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding
(a) Collision cross section (calculated using the ‘Exact Hard Sphere’ method) versus time. The EHSSCCSHe for minimized structures is depicted using the green dots; (b) backbone radius of gyration versus time; (c) solvent accessible surface area (SASA) versus time; and (d) secondary structure content versus time. Snapshots of: (e) the initial structure at 0 ns; (f) the smallest found structure by EHSSCCSHe ; and (g) the final structure in the trajectory. The protein structure coloured by the secondary structure features: α-helix (orange), β-strand (purple) and coil (grey). Protein images made using UCSF Chimera33. Data for holo-Fdc1UbiX at 300 K is available in the Supplementary Fig. 2.
