Figure 1
Molecular dynamics modelling of the FCM-ybbR peptide. (a) Secondary structure and primary sequence of the FCMybbR peptide design. The motifs of interest are underlined and color coded. (b) Modelled structure of FCMybbR obtained using PEP-FOLD and the linear structure obtained at the end of ASMD simulation. (c) Four systems were considered for MD simulations, System 1—with no fluorophores attached, System 2—with FlAsH attached, System 3—with CoA-AF647 attached, and System 4—with both fluorophores attached (Supplementary Movies S1–4). Colored beacons represent FlAsH (green) and CoA-AF647 (red). (d–g) Computed radius of gyration (RG) from 300 ns simulations for (d) FCMybbR, (e) FlAsH-FCMybbR, (f) FCMybbR-Co-AF647, and (g) FlAsH-FCMybbR-CoA-Alexa647. Conformational snapshots of the peptide in (d–g) correspond to those observed after 0, 75, 150, 225, and 300 ns, respectively.
