The volume changes of unfolding of dsDNA
The volume changes of unfolding of dsDNA
复制标题
双链DNA展开时的体积变化
DOI：
10.1016/j.bpj.2022.08.005
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发表时间：
2022
影响因子：
3.4
通讯作者：
Marky, Luis A.
中科院分区：
文献类型：
--
作者：
Makhatadze, George I.;Chen, Calvin R.;Khutsishvili, Irine;Marky, Luis A.
高静水压对生物大分子的稳定性有着深远的影响。该效应的大小和方向（稳定或不稳定）由系统的体积变化ΔV定义。正体积变化将稳定起始原生状态，而负体积变化将导致最终未折叠状态的稳定。对于DNA双螺旋，实验数据表明，当dsDNA的热稳定性低于50°C时，静水压力的增加将导致不稳定;即，螺旋到螺旋转变具有负ΔV。与此相反，具有高于50°C的热稳定性的dsDNA序列显示正Δ V值，并且通过静水压力稳定。为了深入了解dsDNA对作为温度函数的静水压力的响应中的这种转换，首先，我们使用压力扰动量热法对10种不同dsDNA序列的Δ V进行实验测量，进一步验证了这种趋势。我们还开发了一种计算方案来计算dsDNA解折叠的预期体积变化，该方案以实验组的50个Δ V值为基准，除了我们的数据外，还包括文献中的值。计算结果与实验值吻合较好。计算和实验之间的这种一致性为计算协议提供了可信度，并为观察到的Δ V的温度依赖性提供了分子水平的合理性，其可以追溯到水合作用。本文还讨论了A/T和G/C碱基对Δ V值的差异。
High hydrostatic pressure can have profound effects on the stability of biomacromolecules. The magnitude and direction (stabilizing or destabilizing) of this effect is defined by the volume changes in the system, ΔV. Positive volume changes will stabilize the starting native state, whereas negative volume changes will lead to the stabilization of the final unfolded state. For the DNA double helix, experimental data suggested that when the thermostability of dsDNA is below 50°C, increase in hydrostatic pressure will lead to destabilization; i.e., helix-to-coil transition has negative ΔV. In contrast, the dsDNA sequences with the thermostability above 50°C showed positive ΔVvalues and were stabilized by hydrostatic pressure. In order to get insight into this switch in the response of dsDNA to hydrostatic pressure as a function of temperature, first we further validated this trend using experimental measurements of ΔVfor 10 different dsDNA sequences using pressure perturbation calorimetry. We also developed a computational protocol to calculate the expected volume changes of dsDNA unfolding, which was benchmarked against the experimental set of 50 ΔVvalues that included, in addition to our data, the values from the literature. Computation predicts well the experimental values of ΔV. Such agreement between computation and experiment lends credibility to the computation protocol and provides molecular level rational for the observed temperature dependence of ΔVthat can be traced to the hydration. Difference in the ΔVvalue for A/T versus G/C basepairs is also discussed.