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Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking

Glucosinolate transporters (GTRs) are part of the nitrate/peptide transporter (NPF) family, members of which also transport specialized secondary metabolites as substrates. Glucosinolates are defense compounds derived from amino acids. We selected 4-methylthiobutyl (4MTB) and indol-3-ylmethyl (I3M)...

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Autores principales: Peña-Varas, Carlos, Kanstrup, Christa, Vergara-Jaque, Ariela, González-Avendaño, Mariela, Crocoll, Christoph, Mirza, Osman, Dreyer, Ingo, Nour-Eldin, Hussam, Ramírez, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8836200/
https://www.ncbi.nlm.nih.gov/pubmed/35163519
http://dx.doi.org/10.3390/ijms23031595
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author Peña-Varas, Carlos
Kanstrup, Christa
Vergara-Jaque, Ariela
González-Avendaño, Mariela
Crocoll, Christoph
Mirza, Osman
Dreyer, Ingo
Nour-Eldin, Hussam
Ramírez, David
author_facet Peña-Varas, Carlos
Kanstrup, Christa
Vergara-Jaque, Ariela
González-Avendaño, Mariela
Crocoll, Christoph
Mirza, Osman
Dreyer, Ingo
Nour-Eldin, Hussam
Ramírez, David
author_sort Peña-Varas, Carlos
collection PubMed
description Glucosinolate transporters (GTRs) are part of the nitrate/peptide transporter (NPF) family, members of which also transport specialized secondary metabolites as substrates. Glucosinolates are defense compounds derived from amino acids. We selected 4-methylthiobutyl (4MTB) and indol-3-ylmethyl (I3M) glucosinolates to study how GTR1 from Arabidopsis thaliana transports these substrates in computational simulation approaches. The designed pipeline reported here includes massive docking of 4MTB and I3M in an ensemble of GTR1 conformations (in both inward and outward conformations) extracted from molecular dynamics simulations, followed by clustered and substrate–protein interactions profiling. The identified key residues were mutated, and their role in substrate transport was tested. We were able to identify key residues that integrate a major binding site of these substrates, which is critical for transport activity. In silico approaches employed here represent a breakthrough in the plant transportomics field, as the identification of key residues usually takes a long time if performed from a purely wet-lab experimental perspective. The inclusion of structural bioinformatics in the analyses of plant transporters significantly speeds up the knowledge-gaining process and optimizes valuable time and resources.
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spelling pubmed-88362002022-02-12 Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking Peña-Varas, Carlos Kanstrup, Christa Vergara-Jaque, Ariela González-Avendaño, Mariela Crocoll, Christoph Mirza, Osman Dreyer, Ingo Nour-Eldin, Hussam Ramírez, David Int J Mol Sci Article Glucosinolate transporters (GTRs) are part of the nitrate/peptide transporter (NPF) family, members of which also transport specialized secondary metabolites as substrates. Glucosinolates are defense compounds derived from amino acids. We selected 4-methylthiobutyl (4MTB) and indol-3-ylmethyl (I3M) glucosinolates to study how GTR1 from Arabidopsis thaliana transports these substrates in computational simulation approaches. The designed pipeline reported here includes massive docking of 4MTB and I3M in an ensemble of GTR1 conformations (in both inward and outward conformations) extracted from molecular dynamics simulations, followed by clustered and substrate–protein interactions profiling. The identified key residues were mutated, and their role in substrate transport was tested. We were able to identify key residues that integrate a major binding site of these substrates, which is critical for transport activity. In silico approaches employed here represent a breakthrough in the plant transportomics field, as the identification of key residues usually takes a long time if performed from a purely wet-lab experimental perspective. The inclusion of structural bioinformatics in the analyses of plant transporters significantly speeds up the knowledge-gaining process and optimizes valuable time and resources. MDPI 2022-01-29 /pmc/articles/PMC8836200/ /pubmed/35163519 http://dx.doi.org/10.3390/ijms23031595 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
Peña-Varas, Carlos
Kanstrup, Christa
Vergara-Jaque, Ariela
González-Avendaño, Mariela
Crocoll, Christoph
Mirza, Osman
Dreyer, Ingo
Nour-Eldin, Hussam
Ramírez, David
Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking
title Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking
title_full Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking
title_fullStr Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking
title_full_unstemmed Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking
title_short Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking
title_sort structural insights into the substrate transport mechanisms in gtr transporters through ensemble docking
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8836200/
https://www.ncbi.nlm.nih.gov/pubmed/35163519
http://dx.doi.org/10.3390/ijms23031595
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