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Figure 3 | BMC Bioinformatics

Figure 3

From: Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2

Figure 3

Fluctuation and Structural Changes Detected in the Activation Cycle of CDK2. Deviation of fluctuation changes (Z diff ) between different CDK2 conformers: (A) apo and ATP bound structure, (B) ATP bound and cyclin binding, (C) phosphorylated and unphosphorylated T160, and (D) fully activated CDK2 and substrate bound conformer. Structural and fluctuation changes are plotted separately against the residue index of CDK2 only. Different fluctuation changes are observed for the kinase when comparing large amplitude modes (solid lines) and experimental temperature factors (dashed lines) between conformers. Significant changes are identified based on the threshold of 1.5 standard deviations from the mean fluctuation centered at zero (red lines). Structural changes are measured by RMSD between Cα atoms. At top, black bars mark regions of particular interest: (a) N-terminal lobe, (b) PSTAIRE Helix, (c) T-Loop, (d) G-Loop, (e) residues 34–47 important for phosphoryl transfer as well as substrate binding, and finally (f) the CDK insert that is an important binding site for other regulatory proteins.

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