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Biomolecules 2014, 4(1), 268-288; doi:10.3390/biom4010268

Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds

Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
Japan Society for the Promotion of Science (JSPS), Ichibancho, Chiyoda-ku, Tokyo 102-8471, Japan
Present address: Division of Biomedical Information Analysis, Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8575, Japan
Author to whom correspondence should be addressed.
Received: 6 December 2013 / Revised: 11 February 2014 / Accepted: 13 February 2014 / Published: 27 February 2014
(This article belongs to the Special Issue Protein Folding and Misfolding)
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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. View Full-Text
Keywords: Globin-like fold; super-fold; keyword; dali search; average distance map Globin-like fold; super-fold; keyword; dali search; average distance map

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This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Matsuoka, M.; Fujita, A.; Kawai, Y.; Kikuchi, T. Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds. Biomolecules 2014, 4, 268-288.

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