Department of Chemistry, University of the Pacific, Stockton, California 95211, USA.
Proteins. 2009 Aug 1;76(2):418-38. doi: 10.1002/prot.22357.
The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in three-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77 proteins to determine all secondary structural units via specific kappa(s) and tau(s) patterns. A total of 533 alpha-helices and 644 beta-strands were recognized by APSA, whereas DSSP gives 536 and 651 units, respectively. Kinks and distortions were quantified and the boundaries (entry and exit) of secondary structures were classified. Similarity between proteins can be easily quantified using APSA, as was demonstrated for the roll architecture of proteins ubiquitin and spinach ferridoxin. A twenty-by-twenty comparison of all alpha domains showed that the curvature-torsion patterns generated by APSA provide an accurate and meaningful similarity measurement for secondary, super secondary, and tertiary protein structure. APSA is shown to accurately reflect the conformation of the backbone effectively reducing three-dimensional structure information to two-dimensional representations that are easy to interpret and understand.
自动蛋白质结构分析 (APSA) 方法将蛋白质骨架描述为三维空间中的平滑线，并通过曲率 κ 和扭转 τ 作为弧长 s 的函数来描述其特征。该方法应用于 77 种蛋白质，通过特定的 κ(s) 和 τ(s) 模式确定所有二级结构单元。APSA 识别出 533 个α-螺旋和 644 个β-折叠，而 DSSP 分别给出 536 和 651 个单元。该方法还对扭曲和变形进行了量化，并对二级结构的边界（进入和退出）进行了分类。APSA 可轻松定量比较蛋白质之间的相似性，这在蛋白质泛素和菠菜铁氧还蛋白的滚装结构中得到了证明。对所有α结构域进行的二十乘二十比较表明，APSA 生成的曲率-扭转模式为二级、超二级和三级蛋白质结构提供了准确且有意义的相似性度量。APSA 能够准确反映骨架的构象，有效地将三维结构信息简化为易于解释和理解的二维表示。
