Mapping the Structural and Dynamical Features of Kinesin Motor Domains
Figure 2
Results of PCA on the kinesin motor domain.
(A) Conformer plot: projection of all kinesin X-ray structures onto the principal planes defined by the two most significant PCs (PC1 and PC2). Structures are colored by ligand bound, triphosphate (red), diphosphate (green), and Eg5 inhibitor (pink). Structures are also labeled with their RCSB PDB code where space permits (see Table S1 for full details). Colored dashed ovals represent the major groupings obtained from hierarchical clustering of the projected structures in the PC1 to PC5 planes (see cluster dendrogram in Figure S1B). Insert: eigenvalue spectrum detailing results obtained from diagonalization of the atomic displacement correlation matrix of Ca atom coordinates. The magnitude of each eigenvalue is expressed as the percentage of the total variance (mean-square fluctuation) captured by the corresponding eigenvector. Labels beside each point indicate the cumulative sum of the total variance accounted for in all preceding eigenvectors. (B) Kinesin motor domain structures colored according to their clustering in PC-space (i.e ovals in panel A). Red = ATP-like, Pink = Eg5 inhibitor-bound, green = ADP-like.