School of Biomedical Engineering, Guangdong Medical University, Dongguan 523808, China.
School of Chemistry and Molecular Engineering, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, East China Normal University, Shanghai 200062, China.
Phys Chem Chem Phys. 2022 Mar 30;24(13):7653-7665. doi: 10.1039/d2cp00274d.
As the hub of major signaling pathways, Ras proteins are implicated in 19% of tumor-caused cancers due to perturbations in their conformational and/or catalytic properties. Despite numerous studies, the functions of the conformational substates for the most important isoform, KRas, remain elusive. In this work, we perform an extensive simulation analysis on the conformational landscape of KRas in its various chemical states during the GTP hydrolysis cycle: the reactant state KRasGTP·Mg, the intermediate state KRasGDP·Pi·Mg and the product state KRasGDP·Mg. The results from enhanced sampling simulations reveal that State 1 of KRasGTP·Mg has multiple stable substates in solution, one of which might account for interacting with GEFs. State 2 of KRasGTP·Mg features two substates "Tyr32" and "Tyr32", which are poised to interact with effectors and GAPs, respectively. For the intermediate state KRasGDP·Pi·Mg, Gln61 and Pi are found to assume a broad set of conformations, which might account for the weak oncogenic effect of Gln61 mutations in KRas in contrast to the situation in HRas and NRas. Finally, the product state KRasGDP·Mg has more than two stable substates in solution, pointing to a conformation-selection mechanism for complexation with GEFs. Based on these results, some specific inhibition strategies for targeting the binding sites of the high-energy substates of KRas during GTP hydrolysis are discussed.
作为主要信号通路的枢纽，Ras 蛋白由于其构象和/或催化特性的扰动，与 19%的肿瘤引起的癌症有关。尽管进行了大量研究，但对于最重要的同工型 KRas 的构象亚基的功能仍然难以捉摸。在这项工作中，我们对 KRas 在其 GTP 水解循环中的各种化学状态下的构象景观进行了广泛的模拟分析：反应物状态 KRasGTP·Mg、中间状态 KRasGDP·Pi·Mg 和产物状态 KRasGDP·Mg。增强采样模拟的结果表明，KRasGTP·Mg 的状态 1 在溶液中有多个稳定的亚基，其中一个可能与 GEFs 相互作用。KRasGTP·Mg 的状态 2 具有两个亚基“Tyr32”和“Tyr32”，分别准备与效应物和 GAP 相互作用。对于中间状态 KRasGDP·Pi·Mg，发现 Gln61 和 Pi 假定了一组广泛的构象，这可能解释了与 HRas 和 NRas 相比，KRas 中 Gln61 突变的弱致癌效应。最后，产物状态 KRasGDP·Mg 在溶液中有两个以上的稳定亚基，表明与 GEF 复合物形成的构象选择机制。基于这些结果，讨论了一些针对 KRas 在 GTP 水解过程中高能亚基结合位点的特定抑制策略。
