Shen Chi, Menon Rajiv, Das Dipanwita, Bansal Nidhi, Nahar Neha, Guduru Neelima, Jaegle Stephen, Peckham Joan, Reshetnyak Yana K
Department of Computer Sciences and Statistics, University of Rhode Island, Kingston, Rhode Island 02881, USA.
Proteins. 2008 Jun;71(4):1744-54. doi: 10.1002/prot.21857.
Protein fluorescence is a powerful tool for studying protein structure and dynamics if we have a means to interpret the spectral data in terms of protein structural properties. Our previous research successfully provided this support through the development of individual software modules implementing the algorithms for fluorescence and structural analyses. Now we have integrated the developed software modules, introduced a new program for the assignment of tryptophan residues to spectral-structural classes, and created a web-based toolkit PFAST: protein fluorescence and structural toolkit: http://pfast.phys.uri.edu/. PFAST contains three modules: (1) FCAT is a fluorescence-correlation analysis tool, which decomposes protein fluorescence spectra to reveal the spectral components of individual tryptophan residues or groups of tryptophan residues located close to each other, and assigns spectral components to one of five previously established spectral-structural classes. (2) SCAT is a structural-correlation analysis tool for the calculation of the structural parameters of the environment of tryptophan residues from the atomic structures of the proteins from the Protein Data Bank (PDB), and for the assignment of tryptophan residues to one of five spectral-structural classes. (3) The last module is a PFAST database that contains protein fluorescence and structural data obtained from results of the FCAT and SCAT analyses.
如果我们有办法根据蛋白质结构特性来解释光谱数据，那么蛋白质荧光就是研究蛋白质结构和动力学的有力工具。我们之前的研究通过开发实现荧光和结构分析算法的各个软件模块成功提供了这种支持。现在，我们已经整合了开发的软件模块，引入了一个将色氨酸残基分配到光谱 - 结构类别的新程序，并创建了一个基于网络的工具包PFAST：蛋白质荧光和结构工具包：http://pfast.phys.uri.edu/。PFAST包含三个模块：（1）FCAT是一个荧光相关分析工具，它分解蛋白质荧光光谱以揭示单个色氨酸残基或彼此靠近的色氨酸残基组的光谱成分，并将光谱成分分配到先前建立的五个光谱 - 结构类别之一。（2）SCAT是一个结构相关分析工具，用于根据蛋白质数据银行（PDB）中蛋白质的原子结构计算色氨酸残基环境的结构参数，并将色氨酸残基分配到五个光谱 - 结构类别之一。（3）最后一个模块是PFAST数据库，它包含从FCAT和SCAT分析结果中获得的蛋白质荧光和结构数据。
