Stetz Gabrielle, Verkhivker Gennady M
Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America.
Chapman University School of Pharmacy, Irvine, California, United States of America.
PLoS One. 2015 Nov 30;10(11):e0143752. doi: 10.1371/journal.pone.0143752. eCollection 2015.
Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.
热休克蛋白70（Hsp70）和热休克蛋白110（Hsp110）伴侣蛋白在调节涉及蛋白质折叠和稳定的细胞过程中发挥着重要作用，而这些过程对于信号网络的完整性至关重要。尽管近年来的实验研究对Hsp70和Hsp110伴侣蛋白变构调节机制的许多方面进行了广泛研究并取得了显著进展，但基于动力学的信号传播和能量学的原子水平图景仍未得到解决。在这项工作中，我们将伴侣蛋白结构的分子动力学模拟和蛋白质稳定性分析与残基相互作用网络的网络建模相结合，以表征变构机制的分子决定因素。我们已经表明，Hsp70和Hsp110伴侣蛋白的变构机制可能主要由核苷酸诱导的结构域间区域和底物结合结构域中局部构象集合的重新分布所决定。使用自由能计算分析了肽底物与Hsp70结构结合的构象动力学和能量学，揭示了控制调节位点之间负协同性的变构热点。结果表明，协同相互作用可能促进Hsp70中的群体转移机制，其中功能残基组织在一个广泛而强大的变构网络中，该网络可以连接核苷酸结合位点和底物结合区域。Hsp110结构中较小的变构网络可能引发在没有全局结构变化的情况下发生的熵驱动变构。我们发现，具有高网络中心性的全局介导残基可能组织在稳定的局部群落中，这些群落对于结构稳定性和有效的变构通信不可或缺。变构相互作用的以网络为中心的分析还表明，功能残基的中心性可能与其对不同伴侣蛋白功能中突变的敏感性相关。这项研究通过展示分子模拟和以网络为中心的建模的整合如何解释伴侣蛋白变构调节的热力学和机制方面，协调了广泛的结构和功能实验。
