Zhang Wengang, Liu Yonglan, Jang Hyunbum, Nussinov Ruth
Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States.
Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States.
JACS Au. 2024 May 14;4(5):1911-1927. doi: 10.1021/jacsau.4c00138. eCollection 2024 May 27.
Cyclin-dependent kinases (CDKs), particularly CDK4 and CDK2, are crucial for cell cycle progression from the Gap 1 (G1) to the Synthesis (S) phase by phosphorylating targets such as the Retinoblastoma Protein (Rb). CDK4, paired with cyclin-D, operates in the long G1 phase, while CDK2 with cyclin-E, manages the brief G1-to-S transition, enabling DNA replication. Aberrant CDK signaling leads to uncontrolled cell proliferation, which is a hallmark of cancer. Exactly how they accomplish their catalytic phosphorylation actions with distinct efficiencies poses the fundamental, albeit overlooked question. Here we combined available experimental data and modeling of the active complexes to establish their conformational functional landscapes to explain how the two cyclin/CDK complexes differentially populate their catalytically competent states for cell cycle progression. Our premise is that CDK could be more important for cell cycle progression than the cyclin-CDK biochemical binding specificity and that efficiency is likely the prime determinant of cell cycle progression. We observe that CDK4 is more dynamic than CDK2 in the ATP binding site, the regulatory spine, and the interaction with its cyclin partner. The N-terminus of cyclin-D acts as an allosteric regulator of the activation loop and the ATP-binding site in CDK4. Integrated with a suite of experimental data, we suggest that the CDK4 complex is less capable of remaining in the active catalytically competent conformation, and may have a lower catalytic efficiency than CDK2, befitting their cell cycle time scales, and point to critical residues and motifs that drive their differences. Our mechanistic landscape may apply broadly to kinases, and we propose two drug design strategies: (i) allosteric Inhibition by conformational stabilization for targeting allosteric CDK4 regulation by cyclin-D, and (ii) dynamic entropy-optimized targeting which leverages the dynamic, entropic aspects of CDK4 to optimize drug binding efficacy.
细胞周期蛋白依赖性激酶（CDKs），特别是CDK4和CDK2，通过磷酸化诸如视网膜母细胞瘤蛋白（Rb）等靶标，对于细胞周期从G1期向S期的进展至关重要。CDK4与细胞周期蛋白D配对，在较长的G1期发挥作用，而CDK2与细胞周期蛋白E一起，负责短暂的G1期到S期的转换，从而启动DNA复制。CDK信号异常会导致细胞增殖失控，这是癌症的一个标志。它们究竟如何以不同的效率完成催化磷酸化作用，这提出了一个基本但被忽视的问题。在这里，我们结合现有的实验数据和活性复合物的模型，建立它们的构象功能图谱，以解释这两种细胞周期蛋白/CDK复合物如何以不同的方式进入其对细胞周期进展具有催化活性的状态。我们的前提是，对于细胞周期进展而言，CDK可能比细胞周期蛋白-CDK的生化结合特异性更为重要，并且效率可能是细胞周期进展的主要决定因素。我们观察到，在ATP结合位点、调节脊柱以及与细胞周期蛋白伴侣的相互作用方面，CDK4比CDK2更具动态性。细胞周期蛋白D的N末端作为CDK4中激活环和ATP结合位点的变构调节剂。结合一系列实验数据，我们认为CDK4复合物较难保持在具有催化活性的构象中，并且其催化效率可能低于CDK2，这与它们在细胞周期中的时间尺度相符，并指出了驱动它们差异的关键残基和基序。我们的机制图谱可能广泛适用于激酶，并且我们提出了两种药物设计策略：（i）通过构象稳定进行变构抑制，以靶向细胞周期蛋白D对CDK4的变构调节；（ii）动态熵优化靶向，利用CDK4的动态、熵的方面来优化药物结合效果。
