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

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 Da...

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Detalles Bibliográficos
Autores principales: Matsuoka, Masanari, Fujita, Aoi, Kawai, Yosuke, Kikuchi, Takeshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030988/
https://www.ncbi.nlm.nih.gov/pubmed/24970216
http://dx.doi.org/10.3390/biom4010268
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author Matsuoka, Masanari
Fujita, Aoi
Kawai, Yosuke
Kikuchi, Takeshi
author_facet Matsuoka, Masanari
Fujita, Aoi
Kawai, Yosuke
Kikuchi, Takeshi
author_sort Matsuoka, Masanari
collection PubMed
description 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.
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spelling pubmed-40309882014-06-24 Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds Matsuoka, Masanari Fujita, Aoi Kawai, Yosuke Kikuchi, Takeshi Biomolecules Article 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. MDPI 2014-02-27 /pmc/articles/PMC4030988/ /pubmed/24970216 http://dx.doi.org/10.3390/biom4010268 Text en © 2014 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Matsuoka, Masanari
Fujita, Aoi
Kawai, Yosuke
Kikuchi, Takeshi
Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds
title Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds
title_full Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds
title_fullStr Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds
title_full_unstemmed Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds
title_short Similar Structures to the E-to-H Helix Unit in the Globin-Like Fold are Found in Other Helical Folds
title_sort similar structures to the e-to-h helix unit in the globin-like fold are found in other helical folds
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030988/
https://www.ncbi.nlm.nih.gov/pubmed/24970216
http://dx.doi.org/10.3390/biom4010268
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