Sreerama N, Venyaminov S Y, Woody R W
Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523, USA.
Protein Sci. 1999 Feb;8(2):370-80. doi: 10.1110/ps.8.2.370.
A simple approach to estimate the number of alpha-helical and beta-strand segments from protein circular dichroism spectra is described. The alpha-helix and beta-sheet conformations in globular protein structures, assigned by DSSP and STRIDE algorithms, were divided into regular and distorted fractions by considering a certain number of terminal residues in a given alpha-helix or beta-strand segment to be distorted. The resulting secondary structure fractions for 29 reference proteins were used in the analyses of circular dichroism spectra by the SELCON method. From the performance indices of the analyses, we determined that, on an average, four residues per alpha-helix and two residues per beta-strand may be considered distorted in proteins. The number of alpha-helical and beta-strand segments and their average length in a given protein were estimated from the fraction of distorted alpha-helix and beta-strand conformations determined from the analysis of circular dichroism spectra. The statistical test for the reference protein set shows the high reliability of such a classification of protein secondary structure. The method was used to analyze the circular dichroism spectra of four additional proteins and the predicted structural characteristics agree with the crystal structure data.
本文描述了一种从蛋白质圆二色光谱估计α-螺旋和β-链段数量的简单方法。通过DSSP和STRIDE算法确定的球状蛋白质结构中的α-螺旋和β-折叠构象，通过将给定α-螺旋或β-链段中的一定数量的末端残基视为扭曲，分为规则部分和扭曲部分。所得的29种参考蛋白质的二级结构分数用于通过SELCON方法分析圆二色光谱。根据分析的性能指标，我们确定，在蛋白质中，平均每个α-螺旋有四个残基、每个β-链有两个残基可能被视为扭曲。根据从圆二色光谱分析确定的扭曲α-螺旋和β-链构象分数，估计给定蛋白质中α-螺旋和β-链段的数量及其平均长度。对参考蛋白质集的统计检验表明，这种蛋白质二级结构分类具有很高的可靠性。该方法用于分析另外四种蛋白质的圆二色光谱，预测的结构特征与晶体结构数据一致。
