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. 2006 Oct 6;92(1):23–33. doi: 10.1529/biophysj.106.084715

FIGURE 1.

FIGURE 1

(A) Side view of part of the LH1 ring seen from the membrane plane in van der Waals representation. Protein atoms are shown in blue, BChl atoms in green, and Car atoms in orange. A channel through the LH1 ring is clearly visible. (B) Side view of one of the initial systems used to explore the ubiquinone diffusion through the LH1 ring. The protein subunits are shown in blue, ubiquinone atoms in red, BChl atoms in green, and Car atoms in orange. The ubiquinone headgroup is on the left side (outside) of the LH1 ring. The lipid environment is superimposed in the background. (C and D) Top view of the two initial systems used to find a suitable pathway for ubiquinone diffusion through the LH1 ring. Only protein (white and gray), ubiquinone (orange), and chlorophyll/carotenoid atoms (green/yellow) are shown for clarity. In the Forward system, the ubiquinone headgroup is on the inside of the LH1 ring (blue). In the Backward system, the headgroup is on the outside of the LH1 ring (red). The system's x axis lies parallel to the connecting line between the center of the LH1 ring and the channel opening. SMD simulations were performed on both initial systems, where the ubiquinone was pulled out of the LH1 ring. The focus in these simulations lies on the headgroup of the ubiquinone, which is more voluminous than the rest of the molecule and will therefore have the largest effect on the resulting PMF. The moving constraint was attached to the last carbon atom of the last isoprenoid unit of the ubiquinone tail. This was done to perturb the movement of the headgroup of the ubiquinone as little as possible to find an unbiased pathway. In the SMD simulations for reconstructing the potential of mean force along the pathway (see text), the moving constraint was attached to the center of gravity of the ubiquinone headgroup, which was chosen as the reaction coordinate. (E) Side view onto a cross section of the channel region of the LH1 ring shown in surface representation. The channel region is highlighted (yellow box). Hydrophobic regions are colored in white, polar regions in green, and charged amino acids in red and blue. The lipid environment is shown in licorice representation. The hydrophobic region of the channel is visible. Lipid tails partly occupy the entrance of the channel on both sides, as seen in equilibration runs of the LH1 ring.