2010 rcas annual report

2010 RCAS Annual Report

Jung-Hsin LinDivision of Mechanics, Research Center for Applied Sciences

Academia Sinica

Dynamics of the molecular motor F0 under electric fields and its interactions with membrane

Lin et al. Biophys. J., 98, 1009-1017 (2010) Featured Article

Nature 402: 263-268 (1999)

PDB ID: 1c17

Surface electrostatic potential of F0

top view bottom view

F0 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(F1-facing side)

periplasm

• All Asp61 residues except the one at the c1 subunit are always protonated.

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)

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 8th 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 8th ns.

RMSD=3.521 Å

Superposition of MD snapshot with the NMR model

Projecting the MD trajectories on to the essential subspace

Rastogi-Girvin model Locked state, Ez=0 V/nm

Unlocked state, Ez=0 V/nm Unlocked state, Ez=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 c1, viewed from the top.

Twisting motion at the absence of electric field

1-23

24-36

51-64

65-79

Correlation map from the simulation of the locked state

(D)

0

5

10

15

20

25

-0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1-1pearson 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 +Ez

＊ MD with -Ez

SCD profiles averaged over all the lipids

SCD profiles of different lipid shells

--- pure bilayer

△ zero-field MD

○ MD with +Ez

＊ MD with -Ez

The lateral diffusion coefficient of pure POPC512 bilayer is : )

scm( 105.58

27-

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

Lateral diffusion coefficient profiles

• 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.

Conclusion: