Figure 1.

(Top) Free energy profile for glycerol conduction in the GlpF homotetramer obtained from equilibrium ABF simulations totaling 0.12 μs of sampling, via an integration of the force exerted on glycerol along the z-direction of Cartesian space. This potential of mean force corresponds to an average of the individual free energy profiles determined in the four channels forming GlpF. (Inset) Z-dependent diffusion of glycerol in GlpF was derived from additional simulations, wherein the permeant is confined in a harmonic potential. (Bottom) Cross-sectional view of a GlpF monomer. Pore-lining residues are rendered as a smooth surface, whereas a cartoon representation is used to depict the rest of the protein. The residues forming the SF and the water molecules contained in the pore are drawn in a licorice representation. The glycerol molecule located at the SF is highlighted in a space-filling representation. Image rendering was done with VMD (41).