FAMILY SPECIFIC ANALYSIS OF BETA BULGES & BETA TWIST IN BETA SANDWICH PROTEINS

蛋白质的折叠结构在不同的 层次：一级结构、二级结构、三级结构 和四元结构。Beta-Sheet由几条线和 必须列为三级结构元素。自然发现 测试版不是平坦的，而是表现得更强或更弱 左手旋转(沿横跨股线的轴线查看 表)。此外，氢键图案中的不规则性， 所谓的“贝塔膨胀”并不少见。今天有足够的时间 具有几个确定的3D结构的蛋白质家族，使 描述扭度的几何参数分析和 同源蛋白家族中的β-突起(即 通过共同的祖先在进化上有血缘关系)。数据库中的 已知的“Beta-夹层”结构是从现有的 三维结构(布鲁克海文数据库)。我们目前正在分析和 编译各种几何参数(例如，链间和 链内角)来描述β片材的扭曲特性和 在三明治数据库结构中出现Beta-凸起。我们会 首先使用数据来检验来自于 一种规则的薄片(即具有恒定的平均扭曲参数) 同源蛋白质对及其进化距离。通过 几何数据与相应倍数的相关性 序列比对，这项研究的结果应该可以让我 开发新的启发式算法来改进蛋白质结构预测 氨基酸序列数据。例如，许多常见的 在预测β链二级结构时遇到了困难 结构产生于对贝塔扭曲的了解不足和 板材结构中的β-凸起。计算机图形学实验室 资源提供了计算和可视化 在概述的项目中测量的几何参数 以及进一步分析它们之间的相关性的方法 参数和主序列数据。

The folded structure of a protein is described at different levels: primary structure, secondary structure, tertiary structure and quaternary structure. Beta-Sheets are made of several strands and must be listed as tertiary structural elements. Naturally found beta-sheets are not flat, but rather display stronger or weaker left-handed rotation (viewed along an axis lying across the strands in the sheet). Further, irregularities in the hydrogen-bonding pattern, so-called "beta-bulges", are not uncommon. There are today enough protein families with several determined 3D-structures to enable an analysis of geometrical parameters describing the twist and beta-bulges within families of homologous proteins (i.e. evolutionarily related through a common ancestor). A database of known "beta-sandwich" structures has been derived from the available 3D- structures (Brookhaven Data Base). We are currently analyzing and compiling various geometrical parameters (e.g. inter-strand and intra-strand angles) to describe the beta-sheet twist properties and occurring beta-bulges in the sandwich database structures. We will use the data first to examine the relation between the distortion from a regular sheet (i.e. with constant, average twist parameters) of pairs of homologous proteins and their evolutionary distance. By correlation of the geometrical data with the corresponding mu ltiple sequence alignments, the results of this study should allow me to develop new heuristics to improve protein structure prediction from amino acid sequence data. For example, many of the commonly encountered difficulties with predicting beta-strand secondary structure arise from insufficient knowledge about the beta-twist and beta-bulges in the sheet structures. The Computer Graphics Laboratory resources provide the means for computing and visualizing the geometrical parameters that are surveyed in the project outlined above, and further the means to analyze the correlation of these parameters with primary sequence data.