Extended Data Fig. 7: Molecular dynamics (MD) trajectories of dyes and/or substrate on AP.
From: Monitoring protein conformational changes using fluorescent nanoantennas
The 100 ns MD simulation of AP with or without a dye (FAM, CAL, Cy3) and with or without the substrate pNPP. We selected the lowest energy pose (see Supplementary Fig. 13) and the next lowest energy pose that does not overlap with it and that has the linker location exposed. Dyes and pNPP are circled for visual clarity. In all cases, we observed that pNPP remains bound at the active sites. For AP with FAM and with or without pNPP, the position of FAM remains unchanged. For AP with CAL and with or without pNPP, the CAL dye does not have a stable position in either case. For AP-Cy3 without pNPP, the Cy3 dye position does not change, but with pNPP bound, the dye position can change, and it even dissociates from the surface. We emphasize that these MD simulations represent a possible signaling mechanism (see main text), and not a definite proposal.
