A new catalog of protein beta-sheets.
A new catalog of protein beta-sheets.
复制标题
蛋白质β-折叠的新目录。
DOI：
--
复制
发表时间：
2005
期刊：
影响因子：
--
通讯作者：
F. Major
中科院分区：
文献类型：
--
作者：
M. Parisien;F. Major
系统的蛋白质折叠研究依赖于蛋白质三维结构注释，即从原子坐标分配氨基酸结构类型。最近已经表征了相邻 β-折叠肽链之间的重要稳定因素，但在开发先前发表的注释方法期间并未考虑这些因素。为了生成准确的 β-折叠结构域目录并涵盖完整的 β-折叠景观，我们开发了一种方法，β-Spider，它根据新发现的稳定因子评估相邻肽链之间的堆积能。在考虑重要的能量因素的同时，我们的方法还最大限度地减少了主观标准的使用，例如其他现有方法中使用的 (phi,psi) 边界和氢键图案集。由于将 β-Spider 应用到一组可用的高分辨率 X 射线晶体结构，我们在此提出了一个新的 β-折叠目录，该目录与最受好评的 DSSP 方法产生的目录有很大不同。该目录包括从未报道过的新氢键图案。
Systematic protein folding studies depend on protein three-dimensional structure annotation, the assignment of amino acid structural types from atomic coordinates. Significant stabilizing factors between adjacent beta-sheet peptide chains have recently been characterized and were not considered during the development of previously published annotation methods. To produce an accurate beta-sheet domain catalog and to encompass the full beta-sheet spectacle, we developed a method, beta-Spider, which evaluates a packing energy between adjacent peptide chains in accordance with the newly discovered stabilizing factors. While considering important energetic factors, our approach also minimizes the use of subjective criteria, such as (phi,psi) boundaries and sets of H-bonding motifs that are used in other existing methods. As a result of the application of beta-Spider to a set of available high-resolution X-ray crystal structures, we present here a new beta-sheet catalog that differs considerably from the one produced by the most acclaimed DSSP method. The catalog includes new H-bonding motifs that were never reported.