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. 2020 Oct 14;119(10):2010–2018. doi: 10.1016/j.bpj.2020.06.040

Figure 3.

Figure 3

Key interactions governing binding and release of Y88. Shown are selected free-energy profile reconstructions from multiple-walker, multiple-replica, parallel-bias simulation (Table S1, Ref. D) showing (A) the cooperative binding of F87 and Y88 to the Cdk2 binding site, the stabilization of the bound state through key polar interactions between (B) the side chain of Cdk2 K33 and the backbone of p27 and (C) a hydrogen bond from Y88 itself. Shown are representations of (D) F87 and Y88 in the active site of Cdk2 and (E) Cdk2 K33 and the backbone carbonyl oxygen atoms of p27 F87 and R90. (F) The free-energy profile of CV capturing contacts between Cdk2 and Y88/Y74, respectively, show that Y74 stays bound in these simulations. Black dots in (A)–(C) and (F) represent conformations from the unbiased MD simulation starting from the X-ray structure (Table S1, Ref. B). To see this figure in color, go online.