title: Similar structures to the E-to-H helix unit in the globin-like fold are found in other helical folds.
abstract: 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.
authors: Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan. cb006060@ed.ritsumei.ac.jp.
authors: Masanari
authors: M
authors: Matsuoka
authors: Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan. cb05066@is.ritsumei.ac.jp.
authors: Aoi
authors: A
authors: Fujita
authors: Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan. ykawai@sk.ritsumei.ac.jp.
authors: Yosuke
authors: Y
authors: Kawai
authors: Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan. tkikuchi@sk.ritsumei.ac.jp.
authors: Takeshi
authors: T
authors: Kikuchi
mesh_terms: D005914:Globins / Q000737:chemistry; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007874:Leghemoglobin / Q000737:chemistry*; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013025:Glycine max / Q000737:chemistry*
chemical_list: D007874:Leghemoglobin; D005914:Globins