Internal strain regulates the nucleotide binding site of the kinesin leading head

Hyeon and Onuchic. 10.1073/pnas.0610939104.

Supporting Information

Files in this Data Supplement:

SI Text
SI Figure 6
SI Figure 7
SI Figure 8
SI Figure 9

SI Figure 6

Fig. 6. Kinesin structure. (A) Top view when kinesin is bound to tubulin. The helices on the top with respect to the b-sheet are colored in pink. (B) Bottom view. The helices on the bottom with respect to the b-sheet or on the side of the tubulin binding interface are colored in light-blue. The L11 loop, which is not observable in the crystal structure because of disorder, is tentatively drawn with a dashed line. (C) Side view. Note that the neck-linker (b9 and b10) is connecting the a7 neck-helix with the a6 helix in motor domain. (D) View around the nucleotide binding site. The P-loop, switch-1, switch-2, and N4 regions, which are relevant to nucleotide binding, are colored red and include annotation.

SI Figure 7

Fig. 7. Analysis of the kinesin equilibrium dynamics using the Gaussian network model (GNM). (A) The cross-correlation map of the residue fluctuation for the two-headed kinesin structure is shown in Fig. 2C. (B) The amplitudes are color-coded based on its value. The relative difference between the trailing and the leading head with respect to leading head (dij) is plotted on the right. (C) Mean square displacement of residues in the trailing head (red) and the leading head (blue) are plotted on the same plot. A comparison of the amplitudes shows that the leading head fluctuates more than the trailing head. The relative difference between the two plots with respect to the leading head (dii) is plotted on the right.

SI Figure 8

Fig. 8. Analysis of the kinesin equilibrium dynamics using an equilibrium ensemble generated from the simulations under SB-Hamiltonian. The legends for A-C are identical to SI Fig.7.

SI Figure 9

Fig. 9. Results of the strain induced regulation in the kinesin dimer on the MT generated using the self-organized polymer (SOP) potential (Eq. 10). Comparisons between the results obtained with the SOP potential and with the SB potential qualitatively confirm the identical conclusions.