Figure 3.

Superposition of three structures of wild-type GFP generated by molecular dynamics simulations. The dotted structure is a configuration from a previous MD simulation of GFP with a cis chromophore after 300 ps of equilibration (39). This structure was used to model a trans chromophore by rotation around τ by 180° (gray structure); 465 ps of simulation were performed starting from this configuration (32), and the structure in black is an average structure over the last 80 ps. Cis and trans configuration of the chromophore overlap well, but the trans chromophore is less well coordinated by surrounding protein residues.