Romanowski M, Song P S
Department of Chemistry, University of Nebraska, Lincoln 68588-0304.
J Protein Chem. 1992 Apr;11(2):139-55. doi: 10.1007/BF01025219.
A method of semiempirical identification of structural domains is proposed. The procedure is based on the comparison of amino acid sequences in groups of homologous proteins. This approach was tested using 32 known protein sequences from different cytochrome b5, cytochrome c, lysozyme, hemoglobin, and myoglobin proteins. The method presented was able to identify all structural domains of these reference proteins. A consensus secondary structure provided information on structural content of these domains predicting correctly 21 of 23 (91%) of alpha-helices. We applied this method to six homologous phytochrome sequences from Avena, Arabadopsis, Cucurbita, Maize, Oryza, and Pisum. Some of the identified domains can be assigned to the known tertiary structure categories. For example, an alpha/beta domain is localized in the region known to stabilize the phytochrome chromophore in the red light absorbing form (Pr). One alpha-helical and one alpha/beta domains are localized in regions important for the chromophore stabilization in the far-red absorbing form (Pfr). From an analysis of noncovalent interaction patterns in another domain it is proposed that a phytochrome dimer contact involves two segments localized between residues 730 and 821 (using numbering of aligned sequences). Also, a possible antiparallel beta-sheet structure of this region has been suggested. According to this model, the long axis of the interacting structures is perpendicular to a twofold symmetry axis of the phytochrome dimer.
提出了一种半经验性的结构域鉴定方法。该程序基于同源蛋白质组中氨基酸序列的比较。使用来自不同细胞色素b5、细胞色素c、溶菌酶、血红蛋白和肌红蛋白蛋白质的32个已知蛋白质序列对该方法进行了测试。所提出的方法能够鉴定这些参考蛋白质的所有结构域。共有二级结构提供了有关这些结构域结构内容的信息，正确预测了23个α螺旋中的21个（91%）。我们将此方法应用于来自燕麦、拟南芥、南瓜、玉米、水稻和豌豆的六个同源植物色素序列。一些鉴定出的结构域可归为已知的三级结构类别。例如，一个α/β结构域位于已知能稳定红光吸收形式（Pr）的植物色素发色团的区域。一个α螺旋结构域和一个α/β结构域位于对远红光吸收形式（Pfr）的发色团稳定很重要的区域。通过对另一个结构域中非共价相互作用模式的分析，有人提出植物色素二聚体接触涉及位于残基730和821之间的两个片段（使用比对序列的编号）。此外，还提出了该区域可能的反平行β折叠结构。根据该模型，相互作用结构的长轴垂直于植物色素二聚体的二重对称轴。
