Fig. 3: Calculated potentials of mean force (PMF) for the isomerization of the C12–C13 = C14–C15 dihedral of retinal in DA (blue) and LA (red) AR3. | Nature Communications

Fig. 3: Calculated potentials of mean force (PMF) for the isomerization of the C12–C13 = C14–C15 dihedral of retinal in DA (blue) and LA (red) AR3.

From: Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization

Fig. 3

The PMF was computed by sampling the retinal isomerization from all-trans to 13-cis and vice versa. Each point on the curve is generated from two independent 0.5 ns QM(SCC-DFTB)/MM MD trajectories, initiated from two separated equilibrated starting structures. The protein backbone was fixed in place; however, all other atoms (including those in the chromophore and amino acid sidechains) were allowed to move.

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