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, (2010) Featured Article

Nature 402: (1999) PDB ID: 1c17

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

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.

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

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)

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

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

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

Projecting the MD trajectories on to the essential subspace

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

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

Correlation map from the simulation of the locked state

(D) pearson coefficient (E) Correlation map from the simulation of the unlocked state

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

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

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

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

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: