Figure 4. Flexible fitting by MDFF focusing on RF1 conformation and interactions.
(A)–(C) Comparison of E. coli RF1 conformations after MDFF. (A) RF1 in RC-RF1. (B) RF1 (and RF3) in RC-RF1•RF3. (C) Superimposition of RF1 from (A) and (B). Arrow in (C) denotes the conformational change of domain 1. (D) In the RC-RF1 complex, RF1 interacts through helices α2 and α3 with the P-rich 310-helix in the L11-NTD. (E) In the RC-RF1•RF3 complex α3 (RF1) interacts with the 310-helix (L11-NTD), while α2 (RF1) interacts with RF3. α2 and α3 denote helices α2 and α3 in domain 1 of RF1; P-rich 310 denotes the P-rich 310 helix in L11-NTD. Root mean square deviation and cross correlation coefficient plots for our MD flexible fitting are presented in Figure 4—figure supplement 1.
Figure 4—figure supplement 1. RMSD and CCC values for MD flexible fitting.
(A) Root mean square deviation (RMSD) over the course of MD flexible fitting between model in current frame and initial model in the three systems. (B) Cross-correlation coefficients (CCC) over the course of MD flexible fitting between models and density maps. Red lines indicate the time points at which frames (models) were selected for presentation in this study.