Johnson W C
Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-7305, USA.
Proteins. 1999 May 15;35(3):307-12.
We have developed an algorithm to analyze the circular dichroism of proteins for secondary structure. Its hallmark is tremendous flexibility in creating the basis set, and it also combines the ideas of many previous workers. We also present a new basis set containing the CD spectra of 22 proteins with secondary structures from high quality X-ray diffraction data. High flexibility is obtained by doing the analysis with a variable selection basis set of only eight proteins. Many variable selection basis sets fail to give a good analysis, but good analyses can be selected without any a priori knowledge by using the following criteria: (1) the sum of secondary structures should be close to 1.0, (2) no fraction of secondary structure should be less than -0.03, (3) the reconstructed CD spectrum should fit the original CD spectrum with only a small error, and (4) the fraction of alpha-helix should be similar to that obtained using all the proteins in the basis set. This algorithm gives a root mean square error for the predicted secondary structure for the proteins in the basis set of 3.3% for alpha-helix, 2.6% for 3(10)-helix, 4.2% for beta-strand, 4.2% for beta-turn, 2.7% for poly(L-proline) II type 3(1)-helix, and 5.1% for other structures when compared with the X-ray structure.
我们开发了一种用于分析蛋白质圆二色性以确定二级结构的算法。其特点是在创建基集时具有极大的灵活性，并且它还融合了许多前人的思路。我们还展示了一个新的基集，其中包含22种具有二级结构的蛋白质的圆二色光谱，这些二级结构来自高质量的X射线衍射数据。通过使用仅由八种蛋白质组成的可变选择基集进行分析可获得高灵活性。许多可变选择基集无法给出良好的分析结果，但通过使用以下标准可以在没有任何先验知识的情况下选择出良好的分析结果：（1）二级结构的总和应接近1.0；（2）二级结构的任何部分都不应小于-0.03；（3）重建的圆二色光谱应与原始圆二色光谱拟合，误差很小；（4）α-螺旋的比例应与使用基集中所有蛋白质获得的比例相似。与X射线结构相比，该算法对基集中蛋白质预测二级结构的均方根误差为：α-螺旋为3.3%，3(10)-螺旋为2.6%，β-链为4.2%，β-转角为4.2%，聚（L-脯氨酸）II型3(1)-螺旋为2.7%，其他结构为5.1%。
