Benrezkallah D, Dauchez M, Krallafa A M
a LCPM Laboratory, Faculty of Sciences, Chemistry Department , University of Oran , Oran , Algeria.
b SirMa CNRS UMR 7369 MEDyC , University of Reims Champagne Ardenne , Reims , France.
J Biomol Struct Dyn. 2015;33(11):2511-21. doi: 10.1080/07391102.2014.1002007. Epub 2015 Feb 3.
The effects of salt on the stability of globular proteins have been known for a long time. In the present investigations, we shall focus on the effect of the salt ions upon the structure and the activity of the endonuclease I enzyme. In the present work, we shall focus on the relationship between ion position and the structural features of the Vibrio salmonicida (VsEndA) enzyme. We will concentrate on major questions such as: how can salt ions affect the molecular structure? What is the activity of the enzyme and which specific regions are directly involved? For that purpose, we will study the behaviour of the VsEndA over different salt concentrations using molecular dynamics (MD) simulations. We report the results of MD simulations of the endonuclease I enzyme at five different salt concentrations. Analysis of trajectories in terms of the root mean square fluctuation (RMSF), radial distribution function, contact numbers and hydrogen bonding lifetimes, indicate distinct differences when changing the concentration of NaCl. Results are found to be in good agreement with experimental data, where we have noted an optimum salt concentration for activity equal to 425 mM. Under this salt concentration, the VsEndA exhibits two more flexible loop regions, compared to the other salt concentrations. When analysing the RMSF of these two specific regions, three residues were selected for their higher mobility. We find a correlation between the structural properties studied here such as the radial distribution function, the contact numbers and the hydrogen bonding lifetimes, and the structural flexibility of only two polar residues. Finally, in the light of the present work, the molecular basis of the salt adaptation of VsEndA enzyme has been explored by mean of explicit solvent and salt treatment. Our results reveal that modulation of the sodium/chloride ions interaction with some specific loop regions of the protein is the strategy followed by this type of psychrophilic enzyme to enhance catalytic activity at the physiological conditions.
盐对球状蛋白质稳定性的影响早已为人所知。在本研究中，我们将聚焦于盐离子对核酸内切酶I的结构和活性的影响。在本工作中，我们将关注离子位置与杀鲑气单胞菌（VsEndA）酶的结构特征之间的关系。我们将集中探讨一些主要问题，例如：盐离子如何影响分子结构？酶的活性如何，哪些特定区域直接参与其中？为此，我们将使用分子动力学（MD）模拟研究VsEndA在不同盐浓度下的行为。我们报告了核酸内切酶I在五种不同盐浓度下的MD模拟结果。根据均方根波动（RMSF）、径向分布函数、接触数和氢键寿命对轨迹进行分析，结果表明改变NaCl浓度时存在明显差异。结果与实验数据高度吻合，我们注意到活性的最佳盐浓度为425 mM。在此盐浓度下，与其他盐浓度相比，VsEndA表现出另外两个更灵活的环区域。在分析这两个特定区域的RMSF时，选择了三个具有较高流动性的残基。我们发现这里研究的结构特性，如径向分布函数、接触数和氢键寿命，与仅两个极性残基的结构灵活性之间存在相关性。最后，根据本工作，通过明确的溶剂和盐处理方法探索了VsEndA酶盐适应性的分子基础。我们的结果表明，调节钠/氯离子与蛋白质某些特定环区域的相互作用是这类嗜冷酶在生理条件下提高催化活性所采用的策略。
