Shokhen Michael, Albeck Amnon, Borisov Veronika, Israel Yonat, Levy Nina S, Levy Andrew P
Department of Chemistry, Bar Ilan University, Ramat Gan, Israel.
Technion Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel.
Curr Res Struct Biol. 2024 Oct 3;8:100158. doi: 10.1016/j.crstbi.2024.100158. eCollection 2024.
Mutations in the IQSEC2 gene result in severe intellectual disability, epilepsy and autism. The primary function of IQSEC2 is to serve as a guanine exchange factor (GEF) controlling the activation of ARF6 which in turn mediates membrane trafficking and synaptic connections between neurons. As IQSEC2 is a large intrinsically disordered protein little is known of the structure of the protein and how this influences its function. Understanding this structure and function relationship is critical for the development of novel therapies to treat IQSEC2 disease. We therefore sought to identify IQSEC2 conformers in unfolded and folded states and analyze how conformers differ when binding to ARF6 and thereby influence GEF catalysis. We simulated the folding process of IQSEC2 by accelerated molecular dynamics (aMD). Following the ensemble method of Gibbs, we proposed that the number of microstates in the ensemble replicating a protein macroscopic system is the total number of MD snapshots sampled on the production MD trajectory. We divided the entire range of reaction coordinate into a series of consecutive, non-overlapping bins. Thermal fluctuations of biomolecules in local equilibrium states are Gaussian in form. To predict the free energy and entropy of different conformational states using statistical thermodynamics, the density of states was estimated taking into account how many MD snapshots constitute each conformational state. IQSEC2 dimers derived from the most stable folded and unfolded conformers of IQSEC2 were generated by protein-protein docking and then used to construct IQSEC2-ARF6 encounter complexes. We suggest that IQSEC2 folding and dimerization are two competing processes that may be used by nature to regulate the process of GDP exchange on ARF6 catalyzed by IQSEC2.
IQSEC2基因突变会导致严重智力残疾、癫痫和自闭症。IQSEC2的主要功能是作为鸟嘌呤核苷酸交换因子（GEF），控制ARF6的激活，而ARF6进而介导神经元之间的膜运输和突触连接。由于IQSEC2是一种大型内在无序蛋白，人们对其结构以及结构如何影响其功能知之甚少。了解这种结构与功能的关系对于开发治疗IQSEC2疾病的新疗法至关重要。因此，我们试图识别IQSEC2在未折叠和折叠状态下的构象异构体，并分析与ARF6结合时构象异构体如何不同，从而影响GEF催化作用。我们通过加速分子动力学（aMD）模拟了IQSEC2的折叠过程。按照吉布斯系综方法，我们提出，在系综中复制蛋白质宏观系统的微观状态数是在生产MD轨迹上采样的MD快照总数。我们将反应坐标的整个范围划分为一系列连续的、不重叠的区间。处于局部平衡状态的生物分子的热涨落呈高斯形式。为了使用统计热力学预测不同构象状态的自由能和熵，考虑到构成每个构象状态的MD快照数量来估计状态密度。通过蛋白质-蛋白质对接生成源自IQSEC2最稳定折叠和未折叠构象异构体的IQSEC2二聚体，然后用于构建IQSEC2-ARF6相遇复合物。我们认为，IQSEC2的折叠和二聚化是两个相互竞争的过程，自然界可能利用它们来调节IQSEC2催化的ARF6上GDP交换过程。
