Matsuoka Masanari, Fujita Aoi, Kawai Yosuke, Kikuchi Takeshi
Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
Biomolecules. 2014 Feb 27;4(1):268-88. doi: 10.3390/biom4010268.
A protein in the globin-like fold contains six alpha-helices, A, B, E, F, G and H. Among them, the E-to-H helix unit (E, F, G and H helices) forms a compact structure. In this study, we searched similar structures to the E-to-H helix of leghomoglobin in the whole protein structure space using the Dali program. Several similar structures were found in other helical folds, such as KaiA/RbsU domain and Type III secretion system domain. These observations suggest that the E-to-H helix unit may be a common subunit in the whole protein 3D structure space. In addition, the common conserved hydrophobic residues were found among the similar structures to the E-to-H helix unit. Hydrophobic interactions between the conserved residues may stabilize the 3D structures of the unit. We also predicted the possible compact regions of the units using the average distance method.
一种具有类珠蛋白折叠的蛋白质包含六个α螺旋，即A、B、E、F、G和H螺旋。其中，E到H螺旋单元（E、F、G和H螺旋）形成一个紧密结构。在本研究中，我们使用Dali程序在整个蛋白质结构空间中搜索与来航鸡血红蛋白E到H螺旋相似的结构。在其他螺旋折叠中发现了几个相似结构，如KaiA/RbsU结构域和III型分泌系统结构域。这些观察结果表明，E到H螺旋单元可能是整个蛋白质三维结构空间中的一个常见亚基。此外，在与E到H螺旋单元相似的结构中发现了常见的保守疏水残基。保守残基之间的疏水相互作用可能稳定该单元的三维结构。我们还使用平均距离法预测了这些单元可能的紧密区域。
