TY - JOUR

T1 - Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking

AU - Peña‐Varas, Carlos

AU - Kanstrup, Christa

AU - Vergara‐jaque, Ariela

AU - González‐avendaño, Mariela

AU - Crocoll, Christoph

AU - Mirza, Osman

AU - Dreyer, Ingo

AU - Nour‐eldin, Hussam

AU - Ramírez, David

N1 - Funding Information: This research was funded by the Fondo Nacional de Desarrollo Cient?fico y Tecnol?gico? Chile (FONDECYT), grant number 11180604, by CONICYT Programa de Cooperaci?n Internacional grant Numbers REDES190074 and REDES190025, by ANID ACT210012, by CONICYT?FOND? EQUIP grant number EQM160063, and by the Danish National Research Foundation grant number DNRF99. Funding Information: grant Numbers REDES190074 and REDES190025, by ANID ACT210012, by CONICYT‐FOND‐ EQUIP grant number EQM160063, and by the Danish National Research Foundation grant number DNRF99. Funding Information: Funding: This research was funded by the Fondo Nacional de Desarrollo Científico y Tecnológico‐ Chile (FONDECYT), grant number 11180604, by CONICYT Programa de Cooperación Internacional Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - Ensemble docking

KW - Glucosinolates

KW - GTRs

KW - Membrane protein modeling

KW - Phytocompounds transport mechanism

U2 - 10.3390/ijms23031595

DO - 10.3390/ijms23031595

M3 - Journal article

C2 - 35163519

AN - SCOPUS:85123522795

VL - 23

JO - International Journal of Molecular Sciences (CD-ROM)

JF - International Journal of Molecular Sciences (CD-ROM)

SN - 1424-6783

IS - 3

M1 - 1595

ER -