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Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate

BtuCD–BtuF from Escherichia coli is a binding protein-dependent adenosine triphosphate (ATP)-binding cassette (ABC) transporter system that uses the energy of ATP hydrolysis to transmit vitamin B12 across cellular membranes. Experimental studies have showed that during the transport cycle, the trans...

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Autores principales: Su, Ji-Guo, Zhang, Xiao, Zhao, Shu-Xin, Li, Xing-Yuan, Hou, Yan-Xue, Wu, Yi-Dong, Zhu, Jian-Zhuo, An, Hai-Long
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581229/
https://www.ncbi.nlm.nih.gov/pubmed/26247943
http://dx.doi.org/10.3390/ijms160817933
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author Su, Ji-Guo
Zhang, Xiao
Zhao, Shu-Xin
Li, Xing-Yuan
Hou, Yan-Xue
Wu, Yi-Dong
Zhu, Jian-Zhuo
An, Hai-Long
author_facet Su, Ji-Guo
Zhang, Xiao
Zhao, Shu-Xin
Li, Xing-Yuan
Hou, Yan-Xue
Wu, Yi-Dong
Zhu, Jian-Zhuo
An, Hai-Long
author_sort Su, Ji-Guo
collection PubMed
description BtuCD–BtuF from Escherichia coli is a binding protein-dependent adenosine triphosphate (ATP)-binding cassette (ABC) transporter system that uses the energy of ATP hydrolysis to transmit vitamin B12 across cellular membranes. Experimental studies have showed that during the transport cycle, the transporter undergoes conformational transitions between the “inward-facing” and “outward-facing” states, which results in the open–closed motions of the cytoplasmic gate of the transport channel. The opening–closing of the channel gate play critical roles for the function of the transporter, which enables the substrate vitamin B12 to be translocated into the cell. In the present work, the extent of opening of the cytoplasmic gate was chosen as a function-related internal coordinate. Then the mean-square fluctuation of the internal coordinate, as well as the cross-correlation between the displacement of the internal coordinate and the movement of each residue in the protein, were calculated based on the normal mode analysis of the elastic network model to analyze the function-related motions encoded in the structure of the system. In addition, the key residues important for the functional motions of the transporter were predicted by using a perturbation method. In order to facilitate the calculations, the internal coordinate was introduced as one of the axes of the coordinate space and the conventional Cartesian coordinate space was transformed into the internal/Cartesian space with linear approximation. All the calculations were carried out in this internal/Cartesian space. Our method can successfully identify the functional motions and key residues for the transporter BtuCD–BtuF, which are well consistent with the experimental observations.
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spelling pubmed-45812292015-09-28 Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate Su, Ji-Guo Zhang, Xiao Zhao, Shu-Xin Li, Xing-Yuan Hou, Yan-Xue Wu, Yi-Dong Zhu, Jian-Zhuo An, Hai-Long Int J Mol Sci Article BtuCD–BtuF from Escherichia coli is a binding protein-dependent adenosine triphosphate (ATP)-binding cassette (ABC) transporter system that uses the energy of ATP hydrolysis to transmit vitamin B12 across cellular membranes. Experimental studies have showed that during the transport cycle, the transporter undergoes conformational transitions between the “inward-facing” and “outward-facing” states, which results in the open–closed motions of the cytoplasmic gate of the transport channel. The opening–closing of the channel gate play critical roles for the function of the transporter, which enables the substrate vitamin B12 to be translocated into the cell. In the present work, the extent of opening of the cytoplasmic gate was chosen as a function-related internal coordinate. Then the mean-square fluctuation of the internal coordinate, as well as the cross-correlation between the displacement of the internal coordinate and the movement of each residue in the protein, were calculated based on the normal mode analysis of the elastic network model to analyze the function-related motions encoded in the structure of the system. In addition, the key residues important for the functional motions of the transporter were predicted by using a perturbation method. In order to facilitate the calculations, the internal coordinate was introduced as one of the axes of the coordinate space and the conventional Cartesian coordinate space was transformed into the internal/Cartesian space with linear approximation. All the calculations were carried out in this internal/Cartesian space. Our method can successfully identify the functional motions and key residues for the transporter BtuCD–BtuF, which are well consistent with the experimental observations. MDPI 2015-08-04 /pmc/articles/PMC4581229/ /pubmed/26247943 http://dx.doi.org/10.3390/ijms160817933 Text en © 2015 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/4.0/).
spellingShingle Article
Su, Ji-Guo
Zhang, Xiao
Zhao, Shu-Xin
Li, Xing-Yuan
Hou, Yan-Xue
Wu, Yi-Dong
Zhu, Jian-Zhuo
An, Hai-Long
Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate
title Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate
title_full Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate
title_fullStr Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate
title_full_unstemmed Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate
title_short Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD–BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate
title_sort conformational motions and functionally key residues for vitamin b12 transporter btucd–btuf revealed by elastic network model with a function-related internal coordinate
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581229/
https://www.ncbi.nlm.nih.gov/pubmed/26247943
http://dx.doi.org/10.3390/ijms160817933
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