Pu and Karplus 1010.1073/pnas.0708746105 |
Fig. 5. Superpositions of the g-subunit of the Ka structure (red) and the Me structure (blue), based on Ca atoms. (a) Superposition of the entire g-subunit. (b) Superposition of the g-subunit taking into consideration potential amino acid insertions. The small kink found on the C-terminal helix in the Ka structure is indicated as black arrows. See SI Text (Internal Structural Difference of the g-Subunit in the Ka and Me Structures) for additional details.
Fig. 6. A superimposition of two b-subunits (see labels) of the Me [blue ribbon; Protein Data Bank (PDB) entry 1H8E] and the Ka (red ribbon; PDB entry 2HLD) crown structures as a ribbon diagram; the g-subunit from the Ka structure is shown as light gray spheres. The g-subunit corresponds to the conformation and orientation in the Ka crystal structure.
Fig. 7. g-Angle during a simulation using the crown structure of Abrahams et al. [Abrahams JP, Leslie AGW, Lutter R, Walker JE (1994) Nature 370:621-628] reported in 1994 (Ab, PDB entry 1BMF) for ATP binding. See SI Text (Control Simulations Using Ab as the Starting Crown Structure) for discussion.
Fig. 8. Typical calculated torque profile (in units of pN nm) as a function of time during an 85° substep rotation. See SI Text (A Typical Torque Profile During the 85° Rotation) for discussion.
Fig. 9. The time series of the distance between bEL391-gM25 (blue curve) and that of the bE:L391-g:M25 (red curve) for a representative trajectory of the 85° rotation simulation. See SI Text (Distance of bE:L391-g:M25 and bE:L391-g:K237 During the 85° Rotation) for detailed discussion.
Fig. 10. g-Angles of 10 simulations using a different set of elastic constants for the PNM: ka3b3 = 5.0 kcal/mol/Å2 and kg = 5.0 kcal/mol/Å2, where all other parameters and the simulation protocols remain unchanged, as described in the text. See SI Text [Details of the Plastic Network Model (PNM) Used in the Simulations] for discussion.
Movie 1. A trajectory of the simulations based on the coarse-grained model developed in the article. A 360° rotation cycle of the g-stalk is shown based on an actual simulation of a 120° rotation, where the frames between 120° and 360° were obtained from the corresponding frames in the first 120° rotation by a procedure described in Ma et al. [Ma J, Flynn TC, Cui Q, Leslie AGW, Walker JE, Karplus M (2002) Structure 10:921-931]. Only b(ribbon) and g (sphere) subunits are shown: yellow, bE; orange, bHO; tan, bTP; gray, g.
Movie 2. A side view of the same trajectory as in SI Movie 1. See the legend of SI Movie 1 for the color scheme.
Movie 3. A bottom view of the same trajectory (viewed toward the membrane) in the neighborhood of a torque generation configuration (also see Fig. 4) in a repeated "rocking" mode. See the legend of SI Movie 1 for the color scheme. The b/g mechanical coupling interaction (bE:I390-L391 and g:20-25) identified from the simulation is highlighted by spheres (b, yellow; g, red).