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. 2021 Jun 29;6(27):17609–17620. doi: 10.1021/acsomega.1c02159

Figure 3.

Figure 3

PCA of pocket conformation using MD trajectories of apo-TNKS2, TNKS2–XAV complex, and TNKS2–OLA complex. For the PCA, the first 250 ns of the MD trajectory of apo-TNKS2 and 800 ns trajectories of the TNKS2–XAV complex and the TNKS2–OLA complex were used. The left panel shows the MD trajectories projected onto the plane of the first two components (PC1 and PC2). The contribution ratios of PC1 and PC2 were 44 and 7%, respectively. The black circles represent the projections of the representative conformations of the ligand binding pocket. (A–F) were determined based on the PC1 value histogram shown in Figure 5, and these correspond to conformations of (A–F) of Figure 6. The black circles of 3KR7, 3KR8, and 3U9Y correspond to the ligand-binding pockets of X-ray crystallographic structures of apo-TNKS2, the TNKS2–XAV complex, and the TNKS2–OLA complex. The right panel shows the motions corresponding to the two eigenvectors, respectively. The red regions indicate the position of the 21 amino acid residues used for PCA (see the Methods section). The blue and green arrows represent the motions of PC1 and PC2, respectively.