1. 2010 RCAS Annual Report Jung-Hsin Lin Division of Mechanics, Research Center for Applied Sciences Academia Sinica Dynamics of the molecular motor F 0 under electric fields and its interactions with membrane Lin et al. Biophys. J., 98, 1009-1017 (2010) Featured Article

2. Nature 402: 263-268 (1999) PDB ID: 1c17

3. Surface electrostatic potential of F 0 top viewbottom view F 0 is not a symmetric protein complex

4. Simulation procedure The NMR structure of the a-c complex (1c17) was embedded into the POPC bilayer. The lipids overlapping with the protein complex were removed. Different numbers of lipid molecules were placed inside the c- ring, and energy minimization was performed only for these lipids. Protein was retrained for the whole-system energy minimization, and the subsequent 1-ns molecular dynamics simulation. The case with smallest RMSD was continued for further MD simulation. After the RMSD of the a-c complex has reached the plateau, either changed the protonation state of cAsp61 or applied electric fields of ±0.03 V/nm to the system.

5. 8 ns Snapshot cytoplasm (F 1 -facing side) periplasm

6. All Asp61 residues except the one at the c 1 subunit are always protonated. Simulation details F 0 (a1c12) 451 POPC lipids 25,247 SPC water molecules 16 Cl - ions Totally 109,378 atoms 315 K Particle mesh Ewald (PME) Cut off = 12 Å Electric field (±0.03 V/nm) Time step = 2 fs Protein force field: Gromos96 (ffgmx) Lipid force field: (Berger ‘97)

7. Side view Top view Bottom view The cavity of the c-ring filled with lipids

8. Gray: Rastogi-Girvin model; Yellow & Pink: Simulation of the locked state at the 8 th ns. RMSD=3.208 Å Superposition of MD snapshot with the NMR model

9. Gray: Rastogi-Girvin model; Yellow & Pink: Simulation of the unlocked state at the 8 th ns. RMSD=3.521 Å Superposition of MD snapshot with the NMR model

10. Projecting the MD trajectories on to the essential subspace

11. Rastogi-Girvin modelLocked state, E z =0 V/nm Unlocked state, E z =0 V/nmUnlocked state, E z =0.03 V/nm

12. Porcupine plots of three MD simulations in the unlocked state based on the PCA-1 eigenvector projected on the membrane plane for the two segments of the N- (A, C, E) and C-terminal (B, D, F) helices of c 1, viewed from the top. Twisting motion at the absence of electric field 1-23 24-36 51-64 65-79

13. Correlation map from the simulation of the locked state

14. (D) 0 5 10 15 20 25 -0.8-0.6-0.4-0.200.20.40.60.81 pearson coefficient (E) Correlation map from the simulation of the unlocked state

15. Interaction energies between the a-subunit and the c-ring

16. --- pure bilayer △ zero-field MD ○ MD with +E z ＊ MD with -E z S CD profiles averaged over all the lipids

18. S CD profiles of different lipid shells --- pure bilayer △ zero-field MD ○ MD with +E z ＊ MD with -E z

19. The lateral diffusion coefficient of pure POPC512 bilayer is : index : 0 : total lipids 3 : second shell 1 : inside the C-ring 4 : third shell 6: far away from F 0 2 : first shell 5 : fourth shell Lateral diffusion coefficient profiles

20. The essential dynamics analysis can clearly discriminate the motions of F 0 under electric fields, which is consistent with the known behavior of this motor at the macroscopic time scale. The N-terminal helix of the c1 subunit underwent a twisted motion, which may be a necessary intermediate step progressing toward larger conformational transitions. The correlated motions among the residues at the a-c interface were substantially reduced at the presence of electric fields. Lipids in the first shell have a very ordered structure which may lubricate the F 0 motor to rotate easily in the membrane environment. Conclusion: