A reference database for circular dichroism spectroscopy covering fold and secondary structure space
A reference database for circular dichroism spectroscopy covering fold and secondary structure space
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DOI：
10.1093/bioinformatics/btl327
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发表时间：
2006-08-15
期刊：
影响因子：
5.8
通讯作者：
Wallace, B. A.
中科院分区：
文献类型：
--
作者：
Lees, Jonathan G.;Miles, Andrew J.;Wallace, B. A.
圆二色谱（CD）光谱是一种用于研究溶液中蛋白质二级结构的长期建立的技术。CD数据的实证分析依赖于由晶体结构已确定的蛋白质的远紫外CD光谱组成的参考数据集的可用性。本文报告了一个新的参考数据集的创建，该数据集有效地涵盖了二级结构和折叠空间，并使用同步辐射圆二色性（SRCD）中可用的更高信息量与现有的参考数据集相比，光谱可以更准确地预测二级结构。它还研究了波长范围，结构冗余和不同的二级结构分类方法对分析准确性的影响。此外，它描述了一种新的使用层次聚类分析，以确定蛋白质的相关性的基础上，光谱特性。该数据库是适用于传统的CD和SRCD光谱分析的蛋白质。因此，通过结合新的生物信息学和生物物理学方法，已经产生了一个数据库，作为结构分子生物学的工具，应该具有广泛的适用性。
Motivation: Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined.This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology.