A SELF-CONSISTENT METHOD FOR THE ANALYSIS OF PROTEIN SECONDARY STRUCTURE FROM CIRCULAR-DICHROISM
A SELF-CONSISTENT METHOD FOR THE ANALYSIS OF PROTEIN SECONDARY STRUCTURE FROM CIRCULAR-DICHROISM
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DOI：
10.1006/abio.1993.1079
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发表时间：
1993-02-15
影响因子：
2.9
通讯作者：
WOODY, RW
中科院分区：
文献类型：
--
作者：
SREERAMA, N;WOODY, RW
本文提出了一种从蛋白质圆二色光谱中估算二级结构含量的自洽方法。在该方法中，待分析蛋白质的光谱被包括在基集中，并且对未知结构进行初始猜测作为第一近似。使用奇异值分解算法求解得到的矩阵方程，并用解代替初始猜测。重复该过程，直到达到自洽性。变量选择和局部线性化方法的最佳功能被纳入这个过程中。我们应用这种方法来检查CD数据中的不一致性，比较CD数据不同范围和分辨率的预测，并在二级结构预测的背景下比较X射线结构分析中二级结构的不同归属。使用均方根差和相关系数对结果进行比较。所获得的结果与以前的分析一样好或更好。对于大多数的蛋白质考虑的自洽的解决方案得到不同的初始猜测是相似的。我们发现Kabsch和Sander蛋白质晶体结构分析是最适合我们的预测方法。
A self-consistent procedure for estimating the secondary structure content from circular dichroism spectra of proteins is presented. In this method the spectrum of the protein to be analyzed is included in the basis set and an initial guess is made for the unknown structure as a first approximation. The resulting matrix equation is solved using the singular value decomposition algorithm and the initial guess is replaced by the solution. The process is repeated until self-consistency is attained. The best features of the variable selection and the locally linearized methods are incorporated in this procedure. We have applied this method to examine the inconsistencies in the CD data, to compare the predictions with different ranges and resolutions of the CD data, and to compare different assignments of secondary structures from X-ray structure analyses in the context of secondary structure predictions. The results are compared using the root mean square differences and correlation coefficients. The results obtained are as good as or better than the previous analyses. For most of the proteins considered the self-consistent solutions obtained with different initial guesses were similar. We find the Kabsch and Sander protein crystal structure analysis to be most suitable for our prediction method.