Kinoshita Kengo, Nakamura Haruki
Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan.
Protein Sci. 2003 Aug;12(8):1589-95. doi: 10.1110/ps.0368703.
The identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. We have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. Our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database eF-site (electrostatic surface of functional-site in proteins). Using this system, functional sites similar to those of phosphoenoylpyruvate carboxy kinase were detected in several mononucleotide-binding proteins, which have different folds. We also applied our method to a hypothetical protein, MJ0226 from Methanococcus jannaschii, and detected the mononucleotide binding site from the similarity to other proteins having different folds.
在后基因组测序时代，基于蛋白质三维结构来识别其生化功能的需求极为迫切。我们开发了一种新方法，利用分子表面几何形状和表面静电势的相似性信息来识别和预测蛋白质的生化功能。我们的预测系统由基于团搜索算法的相似性搜索方法和分子表面数据库eF-site（蛋白质功能位点的静电表面）组成。使用该系统，在几种具有不同折叠方式的单核苷酸结合蛋白中检测到了与磷酸烯醇丙酮酸羧激酶功能位点相似的功能位点。我们还将我们的方法应用于来自詹氏甲烷球菌的一个假设蛋白MJ0226，并通过与具有不同折叠方式的其他蛋白质的相似性检测到了单核苷酸结合位点。
