How subunit coupling produces the {gamma}-subunit rotary motion in F1-ATPase -- Pu and Karplus 105 (4): 1192 Data Supplement - HTML Page - index.htslp -- Proceedings of the National Academy of Sciences

Pu and Karplus 1010.1073/pnas.0708746105

Supporting Information

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SI Figure 5
SI Figure 6
SI Figure 7
SI Figure 8
SI Figure 9
SI Figure 10
SI Movie 1
SI Movie 2
SI Movie 3
SI Text

SI Figure 5

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.

SI Figure 6

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.

SI Figure 7

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.

SI Figure 8

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.

SI Figure 9

Fig. 9. The time series of the distance between b_EL391-gM25 (blue curve) and that of the b_E:L391-g:M25 (red curve) for a representative trajectory of the 85° rotation simulation. See SI Text (Distance of b_E:L391-g:M25 and b_E:L391-g:K237 During the 85° Rotation) for detailed discussion.

SI Figure 10

Fig. 10. g-Angles of 10 simulations using a different set of elastic constants for the PNM: k^a3b3 = 5.0 kcal/mol/Å² and k^g = 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.

SI Movie 1

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, b_E; orange, b_HO; tan, b_TP; gray, g.

SI Movie 2

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.

SI Movie 3

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 (b_E:I390-L391 and g:20-25) identified from the simulation is highlighted by spheres (b, yellow; g, red).