Figure 1. MDFF Fittings of Four Example Proteins Starting from their Closed Conformations.

(A) Root-mean-squared-deviation (RMSD; C_α) as a function of simulation time (ns) during MDFF fitting of each protein into five maps of different resolutions (5Å (8.5 Å for GroEL), 18Å, 20Å, 22 Å, and 24 Å). Top panels for each protein show the RMSD from the initial closed-state crystal structures and bottom panels show the RMSD from the final open-state crystal structures. Different colors for traces indicate four independent MDFF runs for each map. For the case of GroEL chaperonin, RMSD only from the starting structure is reported for the 8.5 Å map resolution MDFF fitting due to the absence of structural information on the target open-state conformation. The RMSD from the target open-state conformation in 18 Å to 24 Å maps of GroEL were computed by using as a basis the structure with the highest correlation-coefficient obtained from the MDFF fitting in 8.5 Å map. The numbers in italics on bottom RMSD panels for each protein represent the final average RMSD with respect to known target crystal structures. (B) Cartoon representations of two different views of the overlay of final conformations generated via MDFF fitting of each protein at each map resolution is shown. Out of four independent runs for each map resolution, only the structure with the highest correlation-coefficient is rendered. Black cartoons correspond to the known target crystal conformations which are used as a basis to judge the quality of all fitting simulations, while colored cartoons correspond to the fitting with the highest correlation-coefficient for each map of each protein. See also Figures S1 (the final conformations for each of the four runs at all map resolutions), S2, and S3, and Table S1 (correlation-coefficients).

Vashisth, Skiniotis, and Brooks, 2012