Figure 5
From: Uptake dynamics in the Lactose permease (LacY) membrane protein transporter
Free energy landscape associated with the periplasmic pathway. The free energies with respect to six reference positions of the TDG molecule in the simulated periplasmic pathway in (A) 2- and (B) 1-dimensions (blue). The arrows mark the two free energy minima. Standard errors correspond to variation in-between the free energy profiles resulting from the six parallel simulations. The average minimum TDG-Phe 27 distance is also shown (red). (C) The average minimum distances between TDG (oxygen atoms) and Phe 27 and binding residues Arg 144, Asn 272, Glu 126, and Glu 269 are shown with respect to the pathway (reference structures S = 1–6).
