Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.
Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.
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蛋白质二级结构分配重新审视：对不同分配方法的详细分析。
DOI：
10.1186/1472-6807-5-17
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发表时间：
2005-09-15
影响因子：
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通讯作者：
Gibrat, Jean-Francois
中科院分区：
文献类型：
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作者：
Martin, Juliette;Letellier, Guillaume;Marin, Antoine;Taly, Jean-Francois;de Brevern, Alexandre G;Gibrat, Jean-Francois
现在有许多方法可用于根据二级结构的不同特性从原子坐标自动分配周期性二级结构。一般来说，这些方法对蛋白质结构中大多数螺旋和链核心片段的位置表现出广泛的共识。然而，区段的末端通常是不明确的，并且难以明确地决定必须包括区段边缘处的哪些残基。此外，还有一个“模糊区”，其中二级结构片段显着偏离鲍林和科里的理想化模型。对于这些片段，我们必须确定观察到的结构变化是否仅仅是扭曲，或者它们是否构成二级结构的断裂。为了解决这些问题，我们开发了一种二级结构分配方法，称为KAKSI。在4个数据集（具有不同分辨率范围的X射线结构、NMR结构）上，将KAKSI所做的结构图与DSSP、STRIDE、XTLSSTR、PSEA和SECSTR给出的结构图以及PDB文件中发现的二级结构图进行了比较。KAKSI分配与STRIDE和PSEA分配的详细比较显示，在片段之间一一对应的情况下，KAKSI分配比STRIDE稍长的螺旋和链。然而，当STRIDE和PSEA指定较长的扭结螺旋时，KAKSI也倾向于倾向于指定几个短螺旋。KAKSI指定的螺旋具有与PDB中描述的几何特征接近的几何特征。它们比其他方法指定的螺旋线更线性。对于链，也观察到同样的长片段分裂趋势，尽管不那么系统化。我们提出了一些二级结构分配的情况下，说明这种行为。我们的方法提供了有价值的任务，有利于二级结构片段的规则性。
A number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure. To address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures). A detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior. Our method provides valuable assignments which favor the regularity of secondary structure segments.