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Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation
The major facilitator superfamily (MFS) is the largest secondary transporter family and is responsible for transporting a broad range of substrates across the biomembrane. These proteins are involved in a series of conformational changes during substrate transport. To decipher the transport mechanis...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9266783/ https://www.ncbi.nlm.nih.gov/pubmed/35806248 http://dx.doi.org/10.3390/ijms23137235 |
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author | Xiao, Qingjie Xu, Mengxue Wang, Weiwei Wu, Tingting Zhang, Weizhe Qin, Wenming Sun, Bo |
author_facet | Xiao, Qingjie Xu, Mengxue Wang, Weiwei Wu, Tingting Zhang, Weizhe Qin, Wenming Sun, Bo |
author_sort | Xiao, Qingjie |
collection | PubMed |
description | The major facilitator superfamily (MFS) is the largest secondary transporter family and is responsible for transporting a broad range of substrates across the biomembrane. These proteins are involved in a series of conformational changes during substrate transport. To decipher the transport mechanism, it is necessary to obtain structures of these different conformations. At present, great progress has been made in predicting protein structure based on coevolutionary information. In this study, AlphaFold2 was used to predict different conformational structures for 69 MFS transporters of E. coli after the selective mutation of residues at the interface between the N- and C-terminal domains. The predicted structures for these mutants had small RMSD values when compared to structures obtained using X-ray crystallography, which indicates that AlphaFold2 predicts the structure of MSF transporters with high accuracy. In addition, different conformations of other transporter family proteins have been successfully predicted based on mutation methods. This study provides a structural basis to study the transporting mechanism of the MFS transporters and a method to probe dynamic conformation changes of transporter family proteins when performing their function. |
format | Online Article Text |
id | pubmed-9266783 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-92667832022-07-09 Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation Xiao, Qingjie Xu, Mengxue Wang, Weiwei Wu, Tingting Zhang, Weizhe Qin, Wenming Sun, Bo Int J Mol Sci Article The major facilitator superfamily (MFS) is the largest secondary transporter family and is responsible for transporting a broad range of substrates across the biomembrane. These proteins are involved in a series of conformational changes during substrate transport. To decipher the transport mechanism, it is necessary to obtain structures of these different conformations. At present, great progress has been made in predicting protein structure based on coevolutionary information. In this study, AlphaFold2 was used to predict different conformational structures for 69 MFS transporters of E. coli after the selective mutation of residues at the interface between the N- and C-terminal domains. The predicted structures for these mutants had small RMSD values when compared to structures obtained using X-ray crystallography, which indicates that AlphaFold2 predicts the structure of MSF transporters with high accuracy. In addition, different conformations of other transporter family proteins have been successfully predicted based on mutation methods. This study provides a structural basis to study the transporting mechanism of the MFS transporters and a method to probe dynamic conformation changes of transporter family proteins when performing their function. MDPI 2022-06-29 /pmc/articles/PMC9266783/ /pubmed/35806248 http://dx.doi.org/10.3390/ijms23137235 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Xiao, Qingjie Xu, Mengxue Wang, Weiwei Wu, Tingting Zhang, Weizhe Qin, Wenming Sun, Bo Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation |
title | Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation |
title_full | Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation |
title_fullStr | Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation |
title_full_unstemmed | Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation |
title_short | Utilization of AlphaFold2 to Predict MFS Protein Conformations after Selective Mutation |
title_sort | utilization of alphafold2 to predict mfs protein conformations after selective mutation |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9266783/ https://www.ncbi.nlm.nih.gov/pubmed/35806248 http://dx.doi.org/10.3390/ijms23137235 |
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