Department of Biotechnology, Chemistry and Pharmacy, University of Siena, I-53100 Siena, Italy.
Comput Biol Chem. 2013 Apr;43:29-34. doi: 10.1016/j.compbiolchem.2012.12.007. Epub 2012 Dec 31.
Defining the amino acid composition of protein cores is fundamental for understanding protein folding, as different architectures might achieve structural stability only in the presence of specific amino acid networks. Quantitative characterization of protein cores in relation to the corresponding structures and dynamics is needed to increase the reliability of protein engineering procedures. Unambiguous criteria based on atom depth considerations were established to assign amino acid residues to protein cores and, hence, for classifying inner and outer molecular moieties. These criteria were summarized in a new tool named ProCoCoA, Protein Core Composition Analyzer. An user-friendly web interface was developed, available at the URL: http://www.sbl.unisi.it/prococoa. An accurate estimate of protein core composition for six protein architectures selected from the CATH database of solved structures has been carried out, and the obtained results indicate the presence of specific patterns of amino acid core composition in different protein folds.
确定蛋白质核心的氨基酸组成对于理解蛋白质折叠至关重要，因为不同的结构可能只有在存在特定的氨基酸网络的情况下才能实现结构稳定性。为了提高蛋白质工程程序的可靠性，需要定量描述与相应结构和动力学相关的蛋白质核心。基于原子深度考虑的明确标准被建立起来，用于将氨基酸残基分配到蛋白质核心中，从而对内部和外部分子部分进行分类。这些标准被总结在一个名为 ProCoCoA 的新工具中，即蛋白质核心组成分析器。开发了一个用户友好的网络界面，可在以下网址获得：http://www.sbl.unisi.it/prococoa。对从已解决结构的 CATH 数据库中选择的六种蛋白质结构的蛋白质核心组成进行了准确估计，所得结果表明不同蛋白质折叠中存在特定的氨基酸核心组成模式。
