Abstract：
The ATP-dependent phosphorylation activity of cyclin-dependent kinase 1 (CDK1), an essential enzyme for cell cycle progression, is regulated by interactions with Cyclin-B, substrate, and Cks proteins. We have recently shown that active site acetylation in CDK1 abrogated binding to Cyclin-B which posits an intriguing long-range communication between the catalytic site and the protein-protein interaction (PPI) interface. Now, we demonstrate a general allosteric link between the CDK1 active site and all three of its PPI interfaces through atomistic molecular dynamics (MD) simulations. Specifically, we examined ATP binding free energies to CDK1 in native nonacetylated (K33wt) and acetylated (K33Ac) forms as well as the acetyl-mimic K33Q and the acetyl-null K33R mutant forms, which are accessible in vitro. In agreement with experiments, ATP binding is stronger in K33wt relative to the other three perturbed states. Free energy decomposition reveals, in addition to expected local changes, significant and selective nonlocal entropic responses to ATP binding/perturbation of K33 from the αC $$ \\alpha C $$ -helix, activation loop (A-loop), and αG $$ \\alpha G $$ - α $$ \\alpha $$ H segments in CDK1 which interface with Cyclin-B, substrate, and Cks proteins, respectively. Statistical analysis reveals that while entropic responses of protein segments to active site perturbations are on average correlated with their dynamical changes, such correlations are lost in about 9%-48% of the dataset depending on the segment. Besides proving the bi-directional communication between the active site and the CDK1:Cyclin-B interface, our study uncovers a hitherto unknown mode of ATP binding regulation by multiple PPI interfaces in CDK1.
摘要：
细胞周期蛋白依赖性激酶1（CDK1）的ATP依赖性磷酸化活性，细胞周期进程中必不可少的酶，受与细胞周期蛋白B的相互作用调节，基材,和Cks蛋白。我们最近表明，CDK1中的活性位点乙酰化消除了与Cyclin-B的结合，这使得催化位点与蛋白质-蛋白质相互作用（PPI）界面之间的远距离交流变得有趣。现在,我们通过原子分子动力学（MD）模拟证明了CDK1活性位点及其所有三个PPI界面之间的一般变构联系。具体来说,我们检查了天然非乙酰化（K33wt）和乙酰化（K33Ac）形式以及模拟乙酰基K33Q和无乙酰基K33R突变体形式的ATP结合自由能对CDK1的影响。在体外是可以接近的。与实验一致，相对于其他三种扰动状态,K33wt中的ATP结合更强。自由能分解揭示，除了预期的局部变化，来自αC$$\\αC$$$-螺旋对K33的ATP结合/扰动的显着和选择性非局部熵响应，激活循环（A循环），和CDK1中与Cyclin-B接口的αG$$\\alphaG$$-α$$H段，基材,和Cks蛋白质，分别。统计分析表明，虽然蛋白质片段对活性位点扰动的熵响应平均与它们的动态变化相关，这种相关性在大约9%-48%的数据集中丢失，这取决于片段。除了证明活动站点和CDK1：Cyclin-B接口之间的双向通信之外，我们的研究揭示了CDK1中多个PPI界面对ATP结合调节的一种迄今未知的模式.
