Fig. 2: An N-terminal conformational change generates a high-affinity binding site.
From: Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion
a Movement of a single benzene within the unrestrained wild-type protein, corresponding to the simulation shown in Supplementary Fig. 2a. The benzene becomes confined to the P-pocket after the protein undergoes a conformational rearrangement to state II, after about 60 ns. The surface of the plug domain (yellow) is shown to emphasise the difference in conformation. b Benzene is mobile with the N-terminus of the protein restrained in state I (left panel), whereas restraining the N-terminus in state II rapidly confines the benzene to the P-pocket. c Benzene freely diffuses through the protein in simulations of the N-terminal deletion mutant. All simulations show benzene molecules from 250 equally spaced frames, according to the colour scheme indicated (0 ns, red; 250 or 500 ns, violet).
