Takase Yasumichi, Yamazaki Yoichi, Hayashi Yugo, Toma-Fukai Sachiko, Kamikubo Hironari
Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan.
Biophys Physicobiol. 2021 Feb 18;18:50-59. doi: 10.2142/biophysico.bppb-v18.006. eCollection 2021.
Previously, the structure elements of dihydrofolate reductase (DHFR) were determined using comprehen-sive Ala-insertion mutation analysis, which is assumed to be a kind of protein "building blocks." It is hypo-thesized that our comprehension of the structure elements could lead to understanding how an amino acid sequence dictates its tertiary structure. However, the comprehensive Ala-insertion mutation analysis is a time- and cost-consuming process and only a set of the DHFR structure elements have been reported so far. Therefore, developing a computational method to predict structure elements is an urgent necessity. We focused on intramolecular residue-residue contacts to predict the structure elements. We introduced a simple and effective parameter: the overlapped contact volume (CV) among the residues and calculated the CV along the DHFR sequence using the crystal structure. Our results indicate that the CV profile can recapitulate its precipitate ratio profile, which was used to define the structure elements in the Ala-insertion mutation analysis. The CV profile allowed us to predict structure elements like the experimentally determined structure elements. The strong correlation between the CV and precipitate ratio profiles indicates the importance of the intramolecular residue-residue contact in maintaining the tertiary structure. Additionally, the CVs between the structure elements are considerably more than those between a structure element and a linker or two linkers, indicating that the structure elements play a funda-mental role in increasing the intramolecular adhesion. Thus, we propose that the structure elements can be considered a type of "building blocks" that maintain and dictate the tertiary structures of proteins.
此前，利用全面的丙氨酸插入突变分析确定了二氢叶酸还原酶（DHFR）的结构元件，该分析被认为是一种蛋白质“构建模块”。据推测，我们对结构元件的理解可能有助于理解氨基酸序列如何决定其三级结构。然而，全面的丙氨酸插入突变分析是一个耗时且成本高昂的过程，到目前为止仅报道了一组DHFR结构元件。因此，开发一种预测结构元件的计算方法迫在眉睫。我们专注于分子内残基 - 残基接触来预测结构元件。我们引入了一个简单有效的参数：残基间的重叠接触体积（CV），并使用晶体结构沿DHFR序列计算CV。我们的结果表明，CV图谱可以概括其沉淀率图谱，该图谱用于在丙氨酸插入突变分析中定义结构元件。CV图谱使我们能够像通过实验确定的结构元件那样预测结构元件。CV与沉淀率图谱之间的强相关性表明分子内残基 - 残基接触在维持三级结构中的重要性。此外，结构元件之间的CV明显大于结构元件与连接子或两个连接子之间的CV，这表明结构元件在增加分子内粘附力方面起着重要作用。因此，我们提出结构元件可被视为维持和决定蛋白质三级结构的一种“构建模块”。
