Structural elucidation of transmembrane domain zero (TMD0) of EcdL: A multidrug resistance-associated protein (MRP) family of ATP-binding cassette transporter protein revealed by atomistic simulation

Abstract

ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known. We hypothesized that the transportation of echonocandinB is mediated via EcdL protein. Henceforth, it is pertinent to know the topological arrangement of TMD0, with other domains of protein and its possible role in transportation of echinocandinB. Absence of effective template for TMD0 domain lead us to model by I-TASSER, further structure has been refined by multiple template modelling using homologous templates of remaining domains (TMD1, NBD1, TMD2, NBD2). The modelled structure has been validated for packing, folding and stereochemical properties. MD simulation for 0.1 μs has been carried out in the biphasic environment for refinement of modelled protein. Non-redundant structures have been excavated by clustering of MD trajectory. The structural alignment of modelled structure has shown Z-score -37.9; 31.6, 31.5 with RMSD; 2.4, 4.2, 4.8 with ABC transporters; PDB ID 4F4C, 4M1 M, 4M2T, respectively, reflecting the correctness of structure. EchinocandinB has been docked to the modelled as well as to the clustered structures, which reveals interaction of echinocandinB with TMD0 and other TM helices in the translocation path build of TMDs.

The impact of ATP-binding cassette transporters on metabolic diseases

“…Typically, ABC transporters consist of a combination of two TMDs and two cytoplasmic nucleotide-binding domains (NBDs). TMDs are variable in sequence and mechanism while NBDs are highly conserved and have characteristic amino acid motifs such as Walker A and Walker B [ 3 , 24 , 25 ]. Walker A and Walker B are key identifiers of ABC proteins [ 6 ].…”

“…Walker A and Walker B are key identifiers of ABC proteins [ 6 ]. TMDs and NBDs interact with each other closely to transport substances and hydrolyze ATP, respectively [ 24 ].…”

“…Two TMDs are intertwined with 4–6 transmembrane α-helices to form a cavity that is involved in substrate binding, recognition, transportation and making contacts with NBDs [ 4 , 16 , 24 ]. TMDs need to undergo conformational changes, and the degree of opening is diverse during transportation but has no close relationship with the size of the substance [ 1 ].…”

Gibbs Free Energy Calculation of Mutation in PncA and RpsA Associated With Pyrazinamide Resistance

“…To explore the dynamic properties behind mutations, molecular dynamic (MD) simulations have been widely performed, and have been especially useful in unveiling the mechanism of drug failure behind mutation (Carter Childers and Daggett, 2017;Dong et al, 2018;Hashemzadeh et al, 2019;Kaushik et al, 2019). MD simulation studies of ligand-protein interactions are a widely applied approach for explaining the mechanisms of drug resistance behind mutations (Aggarwal et al, 2017;Carter Childers and Daggett, 2017;Bera et al, 2018;Liu et al, 2018;Pandey et al, 2018;Ishima et al, 2019). During in vivo analysis, the crystal structure is analyzed for drug resistance.…”

Identification of new benzamide inhibitor againstα-subunit of tryptophan synthase fromMycobacterium tuberculosisthrough structure-based virtual screening, anti-tuberculosis activity and molecular dynamics simulations

“…These efflux pumps reduces the effect of antibiotics by effecting their transport across cell membrane through various multi-drug-resistant (MDR) transporters (Kesherwani, Michael Gromiha, Fukui, & Velmurugan, 2017). Multi-drug-resistant transporters comprises five families including ATP-binding cassette, major facilitator, resistance-nodulation-cell division, Multidrug and Toxic compound extrusion and small multi-drug resistance family (SMR) family (Bera et al, 2017;Verma, Maurya, et al, 2017). Different in silico studies have been reported previously on these MDR transporter families to identify novel lead compounds for antibiotic discovery (Kesherwani et al, 2017).…”