Developing a method for predicting protein structure based on physical chemistry of liquid

开发基于液体物理化学的蛋白质结构预测方法

• 批准号: 20700267
• 负责人: HARANO Yuichi
• 金额: $ 2.75万
• 依托单位: Osaka University (2009-2011)Tokyo Institute of Technology (2008)
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Young Scientists (B)
• 财政年份: 2008
• 资助国家: 日本
• 起止时间: 2008 至 2011
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20700267/
• 关键词: タンパク質; 立体構造予測; 溶液化学; 溶媒和エントロピー; 蛋白質; 立体構造; 構造予測; 水和熱力学; エントロピー; 液体論

We predicted protein structure using our recently developed free energy function for describing protein stability, which was focused on solvation thermodynamics. The function is combined with the current most reliable sampling methods, i. e., fragment assembly(FA) and comparative modeling(CM). The prediction was tested using 11 small proteins for which high-resolution crystal structures were available. Fairly accurate models with average Cαroot mean square deviation(RMSD)~ 2. 0 A were successfully obtained for all cases. The exhaustive sampling by coarse-grained normal mode analysis around the native structures reveals that our function has a linear correlation with RMSDs<3. 0A. These results suggest that the function is quite reliable for the protein structure prediction while the sampling method remains one of the its major limiting factors in it.

我们用我们最近开发的描述蛋白质稳定性的自由能函数来预测蛋白质结构，这主要集中在溶剂化热力学上。该功能结合了目前最可靠的采样方法，即片段组装（FA）和比较建模（CM）。这一预测用11种小蛋白质进行了测试，这些小蛋白质具有高分辨率的晶体结构。模型精度较高，平均c α均方根偏差（RMSD）~ 2。所有病例均成功获得0 A。通过对原生结构进行粗粒度正态分析的穷举抽样，我们的函数与rmsd <3呈线性相关。0。这些结果表明，该函数对蛋白质结构的预测是相当可靠的，而采样方法仍然是其主要限制因素之一。

项目成果

Theoretical studies for biomolecular behavior in a liquid state from the viewpoint of molecular crowding

从分子拥挤的角度对液态生物分子行为进行理论研究

• 发表时间: 2010
• 作者: T. Yoshidome;Y. Harano;& M. Kinoshita;原野雄一;原野雄一
• 通讯作者: 原野雄一

Pressure effects on structures formed by entropically driven self-assembly: illustration for denaturation of proteins.

压力对由熵驱动的自组装形成的结构的影响：蛋白质变性的图示。

• DOI: 10.1103/physreve.79.011912
• 发表时间: 2009
• 期刊: Physical review. E, Statistical, nonlinear, and soft matter physics
• 作者: Takashi Yoshidome;Y. Harano;M. Kinoshita
• 通讯作者: M. Kinoshita

Development of predicting the native structure of a protein focusing on water entropy

以水熵为重点的蛋白质天然结构预测的进展

• 发表时间: 2010
• 作者: T. Yoshidome;Y. Harano;& M. Kinoshita;原野雄一;原野雄一;原野雄一
• 通讯作者: 原野雄一

Molecular mechanism of pressure denaturation of proteins

• DOI: 10.1063/1.2991176
• 发表时间: 2008-10-14
• 期刊: JOURNAL OF CHEMICAL PHYSICS
• 影响因子: 4.4
• 作者: Harano, Yuichi;Yoshidome, Takashi;Kinoshita, Masahiro
• 通讯作者: Kinoshita, Masahiro

Theoretical studies for biomolecular behavior in a liquid state from the viewpoint of molecular crowding.

从分子拥挤的角度对液态生物分子行为进行理论研究。

• 发表时间: 2010
• 作者: T. Yoshidome;Y. Harano;& M. Kinoshita;原野雄一
• 通讯作者: 原野雄一