Graduate School of Energy Science, Kyoto University , Uji, Kyoto 611-0011, Japan.
J Phys Chem B. 2012 Jul 12;116(27):7776-86. doi: 10.1021/jp301541z. Epub 2012 Jun 29.
We show how to characterize the native-structure models of a protein using our free-energy function F which is based on hydration thermodynamics. Ubiquitin is adopted as an example protein. We consider models determined by the X-ray crystallography and two types of NMR model sets. A model set of type 1 comprises candidate models for a fixed native structure, and that of type 2 forms an ensemble of structures representing the structural variability of the native state. In general, the X-ray models give lower F than the NMR models. There is a trend that, as a model deviates more from the model with the lowest F among the X-ray models, its F becomes higher. Model sets of type 1 and those of type 2, respectively, exhibit two different characteristics with respect to the correlation between the deviation and F. It is argued that the total amount of constraints such as NOEs effectively taken into account in constructing the NMR models can be examined by analyzing the behavior of F. We investigate structural characteristics of the models in terms of the energetic and entropic components of F which are relevant to intramolecular hydrogen bonding and to backbone and side-chain packing, respectively.
我们展示了如何使用基于水热力学术语的自由能函数 F 来描述蛋白质的天然结构模型。我们采用泛素作为示例蛋白。我们考虑了由 X 射线晶体学和两种类型的 NMR 模型集确定的模型。第一类模型集包含固定天然结构的候选模型，第二类模型集则形成了代表天然状态结构可变性的结构集合。一般来说，X 射线模型的 F 值比 NMR 模型低。存在一种趋势，即随着模型与 X 射线模型中 F 值最低的模型的偏差增大，其 F 值变得更高。第一类和第二类模型集分别表现出与偏差和 F 值之间相关性相关的两个不同特征。有人认为，通过分析 F 的行为，可以检验在构建 NMR 模型时有效考虑的 NOE 等约束的总量。我们研究了模型的结构特征，涉及到 F 的能量和熵分量，分别与分子内氢键以及主链和侧链包装有关。
