Computational Molecular Biophysics Laboratory, Bioinformatics Center, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur 613401, Tamil Nadu, India.
Computational Molecular Biophysics Laboratory, Bioinformatics Center, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur 613401, Tamil Nadu, India.
Comput Biol Chem. 2023 Aug;105:107883. doi: 10.1016/j.compbiolchem.2023.107883. Epub 2023 May 18.
Osmolytes play an important role in cellular physiology by modulating the properties of proteins, including their molecular specificity. EcoRI is a model restriction enzyme whose specificity to DNA is altered in the presence of osmolytes. Here, we investigate the effect of two different osmolytes, glycerol and DMSO, on the dynamics and hydration of the EcoRI enzyme using molecular dynamics simulations. Our results show that the osmolytes, alter the essential dynamics of EcoRI. Particularly, we observe that the dynamics of the arm region of EcoRI which is involved in DNA binding is significantly altered. In addition, conformational free energy analyses reveals that the osmolytes bring about a change in the landscape similar to that of EcoRI bound to cognate DNA. We further observe that the hydration of the enzyme for each of the osmolyte is different, indicating that the mechanism of action of each of these osmolytes could be different. Further analyses of interfacial water dynamics using rotational autocorrelation function reveals that while the protein surface contributes to a slower tumbling motion of water, osmolytes, additionally contribute to the slowing of the angular motion of the water molecules. Entropy analysis also corroborates with this finding. We also find that the slowed rotational motion of interfacial waters in the presence of osmolytes contributes to a slowed relaxation of the hydrogen bonds between the interfacial waters and the functionally important residues in the protein. Taken together, our results show that osmolytes alter the dynamics of the protein by altering the dynamics of water. This altered dynamics, mediated by the changes in the water dynamics and hydrogen bonds with functionally important residues, may contribute to the altered specificity of EcoRI in the presence of osmolytes.
渗透剂在调节蛋白质的性质方面发挥着重要作用，包括其分子特异性。EcoRI 是一种模型限制酶，其对 DNA 的特异性在渗透剂存在下发生改变。在这里，我们使用分子动力学模拟研究了两种不同的渗透剂，甘油和 DMSO，对 EcoRI 酶的动力学和水合作用的影响。我们的结果表明，渗透剂改变了 EcoRI 的基本动力学。特别是，我们观察到涉及 DNA 结合的 EcoRI 臂区域的动力学发生了显著改变。此外，构象自由能分析表明，渗透剂带来了类似于与同源 DNA 结合的 EcoRI 的类似变化。我们还观察到，对于每种渗透剂，酶的水合作用不同，这表明这些渗透剂的作用机制可能不同。使用旋转自相关函数进一步分析界面水动力学表明，尽管蛋白质表面有助于水的翻滚运动变慢，但渗透剂还会导致水分子的角运动变慢。熵分析也证实了这一发现。我们还发现，在渗透剂存在下界面水的旋转运动减慢导致界面水与蛋白质中功能重要残基之间的氢键松弛减慢。总之，我们的结果表明，渗透剂通过改变水的动力学来改变蛋白质的动力学。这种由与功能重要残基的水动力学和氢键变化介导的改变的动力学可能导致 EcoRI 在渗透剂存在下特异性的改变。
