A free energy calculation study on the thermal stability and denatured state structure of RNaseHII

蛋白质的热稳定性取决于天然状态和变性状态的自由能之间的微妙平衡。许多蛋白质的天然状态的结构已经在高分辨率下获得。然而，变性状态的结构还没有得到任何蛋白质，尽管它们在澄清蛋白质的稳定性机制的重要性。在这项研究中，我们得到了可靠的模型结构RNaseHII在变性状态下的高温分子动力学模拟。模型结构成功地给出了几乎相同的稳定性自由能的实验值为所有的Ile和Leu突变体。采用分子动力学模拟的自由能微扰法计算了突变体的稳定自由能。本研究中使用的软件，COSMOS 90的MD模拟，PERTURB的氨基酸取代，和FENE的自由能估计，作者开发的。

The thermal stability of proteins is determined by the delicate balance between the free energy of the native state and that of the denatured state. Structures of the native state have been obtained at high resolutions for many proteins. However, structures of the denatured state have not yet obtained for any proteins in spite of their importance in clarifying the stability mechanisms of proteins. In this study, we obtained reliable model structures of RNaseHII in the denatured state from high temperature MD simulations. The model structures successfully gave almost the same stability free energy as experimental values for all Ile and Leu mutants. The stability free energies of the mutants were calculated by the free energy perturbation method based on MD simulations. The software used in this study, COSMOS90 for MD simulations, PERTURB for amino-acid substitutions, and FENE for free energy estimations, were developed by the author.