Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis
Fig 3
Analysis of the mobility of a simulation of the Ligand Binding Domain Thyroid Hormone Receptor-β, in which the structure diverges with time [19].
(A) The standard Cα RMSD indicates an unfolding process in a high temperature simulation (black). The RMSD of an equilibrium room-temperature simulation is also shown (red). (B) The alignment between the first and last conformations of the unfolding simulation with variable ϕ indicates that there is a persistent subset of about 30% of backbone atoms that can be aligned to 2Å. (C) The 30% least mobile atoms display structural deviations of about 2Å relative to the initial structure (RMSDL), while the remaining structure diverges (RMSDH). (D) Superposition of the unfolding simulation frames using standard Cα alignment. (E) Superposition using MDLovoFit for 30% of Cα atoms (blue) highlights the existence of a well preserved structural core. The 70% most mobile atoms are shown in red. (F) Structure colored according to the RMSF of each residue relative to the initial structure after alignment.