Fig. 3. Interprotein structure factor and its correction to obtain single-protein dynamics.

(A) Experimental interprotein structure factor, S(q) = I(q)/F(q). To obtain S(q) on an absolute scale, I(q) was multiplied by a constant to match the values of F(q) at q > 1 Å⁻¹ (inset), because the interprotein scattering at high q is much smaller than at low q (32). (B) Comparison of ζ_{coh_exp}(q,Δt) with ζ_{coh_MD}(q,Δt) corrected by experimental S(q). (C) Comparison of MD-derived S(q)_MD with the ratio between the single-protein ζ_{coh_MD}(q) and the overall value, ζ_{coh_MD8}(q). ζ_{coh_MD}(q) is the average over the values calculated from each of the eight protein molecules in the simulation box, whereas ζ_{coh_MD8}(q) is estimated by taking the eight protein molecules as a whole solution. S(q)_MD arises from the interprotein packing in the MD box. (D) Comparison of ζ_{coh_MD}(q,Δt) before and after removing the global motion of the protein molecule. Removal of the global motion was performed by fitting the MD trajectory of each protein molecule to its structure in the first frame.