2010 RCAS Annual Report

1. 2010 RCAS Annual Report Dynamics of the molecular motor F0 under electric fields and its interactions with membrane Jung-Hsin Lin Division of Mechanics, Research Center for Applied Sciences Academia Sinica Lin et al.Biophys. J.,98, 1009-1017 (2010) Featured Article

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

3. F0 is not a symmetric protein complex top view bottom view Surface electrostatic potential of F0

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. cytoplasm (F1-facing side) periplasm Snapshot 8 ns

6. Simulation details • F0 (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) • All Asp61 residues except the one at the c1 subunit are always protonated.

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

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

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

10. Projecting the MD trajectories on to the essential subspace

11. Rastogi-Girvin model Locked state, Ez=0 V/nm Unlocked state, Ez=0 V/nm Unlocked state, Ez=0.03 V/nm

12. Twisting motion at the absence of electric field 1-23 51-64 65-79 24-36 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 c1, viewed from the top.

13. Correlation map from the simulation of the locked state

14. (D) 25 (E) 20 15 10 5 0 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1 pearson coefficient Correlation map from the simulation of the unlocked state

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

16. SCD profiles averaged over all the lipids ---pure bilayer △ zero-field MD ○ MD with +Ez ＊MD with -Ez

18. SCD profiles of different lipid shells ---pure bilayer △ zero-field MD ○ MD with +Ez ＊MD with -Ez

19. The lateral diffusion coefficient of pure POPC512 bilayer is : Lateral diffusion coefficient profiles index : 0 : total lipids 3 : second shell 1 : inside the C-ring 4 : third shell 6: far away from F0 2 : first shell 5 : fourth shell

20. Conclusion: • The essential dynamics analysis can clearly discriminate the motions of F0 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 F0 motor to rotate easily in the membrane environment.