Stetz Gabrielle, Astl Lindy, Verkhivker Gennady M
Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States.
Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States.
J Chem Theory Comput. 2020 Jul 14;16(7):4706-4725. doi: 10.1021/acs.jctc.0c00280. Epub 2020 Jun 14.
Understanding molecular principles underlying chaperone-based modulation of kinase client activity is critically important to dissect functions and activation mechanisms of many oncogenic proteins. The recent experimental studies have suggested that phosphorylation sites in the Hsp90 and Cdc37 proteins can serve as conformational communication switches of chaperone regulation and kinase interactions. However, a mechanism of allosteric coupling between phosphorylation sites in the Hsp90 and Cdc37 during client binding is poorly understood, and the molecular signatures underpinning specific roles of phosphorylation sites in the Hsp90 regulation remain unknown. In this work, we employed a combination of evolutionary analysis, coarse-grained molecular simulations together with perturbation-based network modeling and scanning of the unbound and bound Hsp90 and Cdc37 structures to quantify allosteric effects of phosphorylation sites and identify unique signatures that are characteristic for communication switches of kinase-specific client binding. By using network-based metrics of the dynamic intercommunity bridgeness and community centrality, we characterize specific signatures of phosphorylation switches involved in allosteric regulation. Through perturbation-based analysis of the dynamic residue interaction networks, we show that mutations of kinase-specific phosphorylation switches can induce long-range effects and lead to a global rewiring of the allosteric network and signal transmission in the Hsp90-Cdc37-kinase complex. We determine a specific group of phosphorylation sites in the Hsp90 where mutations may have a strong detrimental effect on allosteric interaction network, providing insight into the mechanism of phosphorylation-induced communication switching. The results demonstrate that kinase-specific phosphorylation switches of communications in the Hsp90 may be partly predisposed for their regulatory role based on preexisting allosteric propensities.
了解基于伴侣蛋白调节激酶客户活性的分子原理对于剖析许多致癌蛋白的功能和激活机制至关重要。最近的实验研究表明，热休克蛋白90（Hsp90）和细胞周期蛋白依赖性激酶37（Cdc37）蛋白中的磷酸化位点可作为伴侣蛋白调节和激酶相互作用的构象通讯开关。然而，在客户蛋白结合过程中，Hsp90和Cdc37中磷酸化位点之间的变构偶联机制尚不清楚，Hsp90调节中磷酸化位点特定作用的分子特征仍然未知。在这项工作中，我们结合了进化分析、粗粒度分子模拟以及基于微扰的网络建模，并扫描未结合和结合状态的Hsp90和Cdc37结构，以量化磷酸化位点的变构效应，并识别激酶特异性客户蛋白结合通讯开关所特有的特征。通过使用基于网络的动态群落桥接度和群落中心性指标，我们表征了参与变构调节的磷酸化开关的特定特征。通过对动态残基相互作用网络的基于微扰的分析，我们表明激酶特异性磷酸化开关的突变可诱导长程效应，并导致Hsp90-Cdc37-激酶复合物中变构网络和信号传递的全局重新布线。我们确定了Hsp90中一组特定的磷酸化位点，其中突变可能对变构相互作用网络产生强烈的有害影响，从而深入了解磷酸化诱导的通讯开关机制。结果表明，Hsp90中激酶特异性通讯磷酸化开关可能部分因其预先存在的变构倾向而具有调节作用。
