Bulheller Benjamin M, Rodger Alison, Hirst Jonathan D
School of Chemistry, University of Nottingham, University Park, Nottingham, UK NG7 2RD.
Phys Chem Chem Phys. 2007 May 7;9(17):2020-35. doi: 10.1039/b615870f. Epub 2007 Feb 20.
Circular dichroism (CD) is an important technique in the structural characterisation of proteins, and especially for secondary structure determination. The CD of proteins can be calculated from first principles using the so-called matrix method, with an accuracy which is almost quantitative for helical proteins. Thus, for proteins of unknown structure, CD calculations and experimental data can be used in conjunction to aid structure analysis. Linear dichroism (LD) can be calculated using analogous methodology and has been used to establish the relative orientations of subunits in proteins and protein orientation in an environment such as a membrane. However, simple analysis of LD data is not possible, due to overlapping transitions. So coupling the calculations and experiment is an important strategy. In this paper, the use of LD for the determination of protein orientation and how these data can be interpreted with the aid of calculations, are discussed. We review methods for the calculation of CD spectra, focusing on semiempirical and ab initio parameter sets used in the matrix method. Lastly, a new web interface for online CD and LD calculation is presented.
圆二色性（CD）是蛋白质结构表征中的一项重要技术，尤其对于二级结构的测定。蛋白质的CD可以使用所谓的矩阵法从第一原理计算得出，对于螺旋状蛋白质而言，其准确性几乎是定量的。因此，对于未知结构的蛋白质，CD计算和实验数据可以结合使用，以辅助结构分析。线性二色性（LD）可以使用类似的方法进行计算，并已用于确定蛋白质中亚基的相对取向以及蛋白质在诸如膜等环境中的取向。然而，由于跃迁重叠，对LD数据进行简单分析是不可能的。因此，将计算与实验相结合是一项重要策略。本文讨论了LD在确定蛋白质取向方面的应用以及如何借助计算来解释这些数据。我们回顾了CD光谱的计算方法，重点关注矩阵法中使用的半经验和从头算参数集。最后，介绍了一个用于在线CD和LD计算的新网络界面。
