Fig. 3
From: Structural basis for the homotypic fusion of chlamydial inclusions by the SNARE-like protein IncA
Molecular dynamics simulations show that IncA87–246 monomer is stable. a Root-mean-square fluctuation (RMSF) analysis of the three simulations performed: IncA87–246 (green line), IncA87–237 (blue line), and IncA87–246(G144A) (orange line). Prior to calculating RMSF, each of the three trajectories was aligned by minimizing the root-mean-square deviation (RMSD) of backbone atoms between the equilibrated structure and every subsequent frame. b Three snapshots (t = 0 µs, t = 2.1 µs, t = 3.8 µs) of the observed conformational change during the IncA87–237 simulation. The two regions of interest, Hclamp and HA(94–100), are colored in cyan. c Bar plot of the number of hydrogen bonds occurring between the Hclamp and HA(94–100) over the course of all three simulations. Hydrogen bonds were identified using a contact-analysis between hydrogen, oxygen, and nitrogen atoms within a cutoff of 3.2 Å
