Correlation between chemical denaturation and the unfolding energetics of Acanthamoeba actophorin
Correlation between chemical denaturation and the unfolding energetics of Acanthamoeba actophorin
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DOI：
10.1016/j.bpj.2022.11.2941
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发表时间：
2023-07-25
影响因子：
3.4
通讯作者：
Hernandez，Rigoberto
中科院分区：
文献类型：
--
作者：
Thota，Nikhil;Quirk，Stephen;Hernandez，Rigoberto
肌动蛋白丝网络部分地由负责调节单体和丝状肌动蛋白之间的比率的丝切断蛋白家族的作用重塑。最近对来自卡氏变形虫的蛋白质actophorin的研究发现了一系列定点突变，使蛋白质的热稳定性提高了22°C。在这里，我们扩大了这一观察结果表明，突变蛋白质也显着稳定的平衡和动力学化学变性，并采用计算机模拟来解释增加的热或化学稳定性，通过会计原子水平的相互作用。具体来说，平均力（PMF）的势可以从蛋白质解折叠的操纵分子动力学（SMD）模拟中获得。然而，SMD对于大蛋白质可能是低效的，因为它们需要大的溶剂盒，并且计算昂贵，因为它们需要越来越多的SMD轨迹来收敛PMF。自适应转向分子动力学（ASMD）克服了这些限制中的第二个阶段，这使得使用更少的轨迹相比，SMD的PMF收敛的粒子。在ASMD中使用伸缩水方案通过将每个阶段的沃茨的数量减少到仅为在给定阶段内溶剂化结构所需的那些而部分地克服了这些限制中的第一个。在从ASMD获得的PMF中，发现去折叠Acto-2的功比Acto-WT高约120 kCal/mol，并且反映了在化学变性实验中观察到的增加的稳定性。在拉伸过程中的平均氢键数和盐桥数的演变提供了一个机械观点的结构变化的肌动蛋白，因为它是展开的，以及它是如何受到突变的影响与能量通过PMF报告。
The actin filament network is in part remodeled by the action of a family of filament severing proteins that are responsible for modulating the ratio between monomeric and filamentous actin. Recent work on the protein actophorin from the amoebaAcanthamoeba castellaniidentified a series of site-directed mutations that increase the thermal stability of the protein by 22°C. Here, we expand this observation by showing that the mutant protein is also significantly stable to both equilibrium and kinetic chemical denaturation, and employ computer simulations to account for the increase in thermal or chemical stability through an accounting of atomic-level interactions. Specifically, the potential of mean force (PMF) can be obtained from steered molecular dynamics (SMD) simulations in which a protein is unfolded. However, SMD can be inefficient for large proteins as they require large solvent boxes, and computationally expensive as they require increasingly many SMD trajectories to converge the PMF. Adaptive steered molecular dynamics (ASMD) overcomes the second of these limitations by steering the particle in stages, which allows for convergence of the PMF using fewer trajectories compared with SMD. Use of the telescoping water scheme within ASMD partially overcomes the first of these limitations by reducing the number of waters at each stage to only those needed to solvate the structure within a given stage. In the PMFs obtained from ASMD, the work of unfolding Acto-2 was found to be higher than the Acto-WT by approximately 120 kCal/mol and reflects the increased stability seen in the chemical denaturation experiments. The evolution of the average number of hydrogen bonds and number of salt bridges during the pulling process provides a mechanistic view of the structural changes of the actophorin protein as it is unfolded, and how it is affected by the mutation in concert with the energetics reported through the PMF.