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

蛋白质的热稳定性是由天然态和变性态自由能之间的微妙平衡决定的。许多蛋白质的天然态结构都是以高分辨率获得的。然而，尽管变性状态对阐明蛋白质的稳定机制很重要，但目前还没有得到任何蛋白质的变性状态结构。在本研究中，我们通过高温分子动力学模拟得到了RNaseHII在变性状态下可靠的模型结构。模型结构成功地给出了几乎与所有Ile和Leu突变体的实验值相同的稳定自由能。在分子动力学模拟的基础上，用自由能微扰法计算了突变体的稳定自由能。本研究使用的软件COSMOS90用于分子动力学模拟，微扰用于氨基酸取代，FENE用于自由能估算，这些软件都是作者自行开发的。

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.