背景:肌萎缩侧索硬化症(ALS)是一种严重的神经退行性疾病,影响大脑和脊髓中的神经细胞,由超氧化物歧化酶1(SOD1)酶的突变引起。ALS相关突变会导致错误折叠,二聚化不稳定性,并增加了聚集体的形成。潜在的变构机制,然而,就其基本原子结构的细节而言,仍然晦涩难懂。因此,这种知识上的差距限制了新型SOD1抑制剂的开发以及对远端位点疾病相关突变如何影响酶活性的理解.
方法:我们将基于微秒尺度的无偏分子动力学(MD)模拟与网络分析相结合,以阐明SOD1Apo(未金属化形式)中的局部和全局构象变化和变构通讯,霍洛,Apo_CallA(突变体和未金属化形式),和Holo_CallA(突变形式)系统。为了鉴定参与SOD1信号传导和变构通讯的热点残基,我们表现出网络中心性,社区网络,和路径分析。
结果:结构分析表明,未金属化的SOD1系统和半胱氨酸突变在催化位点显示出很大的结构变化,影响结构稳定性。间和内H键分析确定了几个重要的残基对于保持界面稳定性至关重要,结构稳定性,和酶催化。动态运动分析表明,在Holo系统中,原子位移更加平衡,运动高度相关。使用距离和二面体概率分布分析阐明了在Apo和Holo系统中二硫键形成和R143构型中观察到的结构差异的基本原理。
结论:我们的研究强调了将广泛的MD模拟与网络分析相结合以揭示蛋白质变形性特征的效率。
Amyotrophic lateral sclerosis (ALS) is a serious neurodegenerative disorder affecting nerve cells in the brain and spinal cord that is caused by mutations in the superoxide dismutase 1 (SOD1) enzyme. ALS-related mutations cause misfolding, dimerisation instability, and increased formation of aggregates. The underlying allosteric mechanisms, however, remain obscure as far as details of their fundamental atomistic structure are concerned. Hence, this gap in knowledge limits the development of novel SOD1 inhibitors and the understanding of how disease-associated mutations in distal sites affect enzyme activity.
We combined microsecond-scale based unbiased molecular dynamics (MD) simulation with network analysis to elucidate the local and global conformational changes and allosteric communications in SOD1 Apo (unmetallated form), Holo, Apo_CallA (mutant and unmetallated form), and Holo_CallA (mutant form) systems. To identify hotspot residues involved in SOD1 signalling and allosteric communications, we performed network centrality, community network, and path analyses.
Structural analyses showed that unmetallated SOD1 systems and cysteine mutations displayed large structural variations in the catalytic sites, affecting structural stability. Inter- and intra H-bond analyses identified several important residues crucial for maintaining interfacial stability, structural stability, and enzyme catalysis. Dynamic motion analysis demonstrated more balanced atomic displacement and highly correlated motions in the Holo system. The rationale for structural disparity observed in the disulfide bond formation and R143 configuration in Apo and Holo systems were elucidated using distance and dihedral probability distribution analyses.
Our study highlights the efficiency of combining extensive MD simulations with network analyses to unravel the features of protein allostery.