Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece.
Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece.
Int J Mol Sci. 2021 May 31;22(11):5931. doi: 10.3390/ijms22115931.
In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.
在当前的工作中，我们通过分子模拟和实验研究了来自四级模体的 4-α-螺旋束的蛋白质折叠和稳定性，该四级模体由四个两亲性α-螺旋以平行或反平行的方式包装而成，是一种常见的模体。重点研究了环区在野生型 Rop（wtRop）和 RM6 蛋白的结构和性质中的作用，通过全原子分子动力学（MD）模拟和实验结果的支持，探索了可能影响它们的关键因素。详细研究了 wtRop 及其无环 RM6 突变体的结构和构象性质，即使在其天然状态下，它们也表现出不同的物理特性。然后，通过所有研究措施探索了这两种蛋白质的热稳定性，结果表明 RM6 比 wtRop 更耐热。与温度相关的偏离主要发生在尾部和环区，指示出最灵活的残基。观察到随着温度的升高氢键减少，并且两种蛋白质中的疏水性接触减少。还呈现了来自圆二色性光谱（CD）的实验数据，突出了温度对 wtRop 和 RM6 结构完整性的影响。本研究的核心目标是在原子水平上探索蛋白质突变如何导致其物理性质（如结构稳定性）发生重大变化。
