Classification and analysis of local structure motifs in protein conformations

为了揭示蛋白质结构的原理，我们确定了常见于不同蛋白质构象的局部结构基序，并对其进行了分析。为此，我们使用了自己开发的方法，其中Delaunay镶嵌应用于蛋白质构象和代码分配给Delaunay四面体，以表征包含它们的局部结构。在这项研究中，我们进行了以下工作。(1)修改了Delaunay码的分配规则，使其能够更好地代表局部结构的特征，并适用于由多条链构建的蛋白质。(2)开发了一种新的算法来检测由多个四面体组成的局部结构基序。(3)应用1：准备构建局部结构数据库。(4)应用二：利用局部结构编码，研究了α-螺旋的位点依赖性和环境依赖性氨基酸出现频率。(5)应用三：我们将疏水核心定义为含有由疏水氨基酸残基占据的具有四个顶点的Delaunay四面体的局部结构。然后对这些结构进行了研究。(6)应用四：利用局部结构编码，该方法可以对具有相同氨基酸序列基序的蛋白质进行更详细的分类。(7)应用五：使用（2）中描述的算法，我们分析了在同源或非同源蛋白质中观察到的相对较大的局部结构的特征。

In order to reveal a principal of protein architectures we identified local structure motifs commonly found in different protein conformations and analyzed them. For this purpose we used the method developed by ourselves, in which Delaunay tessellation is applied to protein conformations and codes are assigned to Delaunay tetrahedrons to characterize the local structures containing them. In this research we carried out the following.(1) The rules to assign the Delaunay codes were modified so that they could represent characteristics of the local structures more properly and be applied to the proteins constructed with more than one chain.(2) A new algorithm was developed to detect a local structural motif consisting of more than one tetrahedron.(3) Application 1 : We prepared to construct local-structure database.(4) Application 2 : Making use of the local-structure codes site-dependent and environment-dependent frequencies of amino acid occurrences were examined for α-helix.(5) Application 3 : We defined a hydrophobic core as the local structure containing a Delaunay tetrahedron with four vertices occupies by the hydrophobic amino acid residues. Then such structures were studied.(6) Application 4 : Using local structure codes, the method was developed to classify proteins with the same amino acid sequence motif with each other in more detail.(7) Application 5 : Using the algorithm described in (2) we analyzed the characteristics of the relatively larger local structures observed in homologous or non-homologous proteins.