1
|
Martins-Gomes C, Silva AM. Natural Products as a Tool to Modulate the Activity and Expression of Multidrug Resistance Proteins of Intestinal Barrier. J Xenobiot 2023; 13:172-192. [PMID: 37092502 PMCID: PMC10123636 DOI: 10.3390/jox13020014] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
The role of intestinal barrier homeostasis in an individual’s general well-being has been widely addressed by the scientific community. Colorectal cancer is among the illnesses that most affect this biological barrier. While chemotherapy is the first choice to treat this type of cancer, multidrug resistance (MDR) is the major setback against the commonly used drugs, with the ATP-binding cassette transporters (ABC transporters) being the major players. The role of P-glycoprotein (P-gp), multidrug resistance protein 1 (MRP1), or breast cancer resistance protein (ABCG2) in the efflux of chemotherapeutic drugs is well described in cancer cells, highlighting these proteins as interesting druggable targets to reverse MDR, decrease drug dosage, and consequently undesired toxicity. Natural products, especially phytochemicals, have a wide diversity of chemical structures, and some particular classes, such as phenolic acids, flavonoids, or pentacyclic triterpenoids, have been reported as inhibitors of P-gp, MRP1, and ABCG2, being able to sensitize cancer cells to chemotherapy drugs. Nevertheless, ABC transporters play a vital role in the cell’s defense against xenobiotics, and some phytochemicals have also been shown to induce the transporters’ activity. A balance must be obtained between xenobiotic efflux in non-tumor cells and bioaccumulation of chemotherapy drugs in cancer cells, in which ABC transporters are essential and natural products play a pivotal role that must be further analyzed. This review summarizes the knowledge concerning the nomenclature and function of ABC-transporters, emphasizing their role in the intestinal barrier cells. In addition, it also focuses on the role of natural products commonly found in food products, e.g., phytochemicals, as modulators of ABC-transporter activity and expression, which are promising nutraceutical molecules to formulate new drug combinations to overcome multidrug resistance.
Collapse
|
2
|
Grigoreva TA, Vorona SV, Novikova DS, Tribulovich VG. Analysis of P-Glycoprotein Transport Cycle Reveals a New Way to Identify Efflux Inhibitors. ACS OMEGA 2022; 7:42835-42844. [PMID: 36467933 PMCID: PMC9713869 DOI: 10.1021/acsomega.2c04768] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
P-glycoprotein (P-gp) is found to be of considerable interest for the design of drugs capable of treating chemoresistant tumors. This transporter is an interesting target for which an efficient approach has not yet been developed in terms of computer simulation. In this work, we use a combination of docking, molecular dynamics, and metadynamics to fully explore the states that occur during the capture of a ligand and subsequent efflux by P-gp. The proposed approach allowed us to substantiate a number of experimentally established facts, as well as to develop a new criterion for identifying potential P-gp inhibitors.
Collapse
|
3
|
Ramzan R, Virk MS, Chen F. The ABCT31 Transporter Regulates the Export System of Phenylacetic Acid as a Side-Chain Precursor of Penicillin G in Monascus ruber M7. Front Microbiol 2022; 13:915721. [PMID: 35966689 PMCID: PMC9370074 DOI: 10.3389/fmicb.2022.915721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The biosynthesis of penicillin G (PG) is compartmentalized, and the transportation of the end and intermediate products, and substrates (precursors) such as L-cysteine (L-Cys), L-valine (L-Val) and phenylacetic acid (PAA) requires traversing membrane barriers. However, the transportation system of PAA as a side chain of PG are unclear yet. To discover ABC transporters (ABCTs) involved in the transportation of PAA, the expression levels of 38 ABCT genes in the genome of Monascus ruber M7, culturing with and without PAA, were examined, and found that one abct gene, namely abct31, was considerably up-regulated with PAA, indicating that abct31 may be relative with PAA transportation. Furthermore the disruption of abct31 was carried out, and the effects of two PG substrate's amino acids (L-Cys and L-Val), PAA and some other weak acids on the morphologies and production of secondary metabolites (SMs) of Δabct31 and M. ruber M7, were performed through feeding experiments. The results revealed that L-Cys, L-Val and PAA substantially impacted the morphologies and SMs production of Δabct31 and M. ruber M7. The UPLC-MS/MS analysis findings demonstrated that Δabct31 did not interrupt the synthesis of PG in M. ruber M7. According to the results, it suggests that abct31 is involved in the resistance and detoxification of the weak acids, including the PAA in M. ruber M7.
Collapse
Affiliation(s)
- Rabia Ramzan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- Department of Food Science and Technology, Government College Women University, Faisalabad, Pakistan
| | - Muhammad Safiullah Virk
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Fusheng Chen
| |
Collapse
|
4
|
Pérez Carrillo VH, Rose-Sperling D, Tran MA, Wiedemann C, Hellmich UA. Backbone NMR assignment of the nucleotide binding domain of the Bacillus subtilis ABC multidrug transporter BmrA in the post-hydrolysis state. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:81-86. [PMID: 34988902 PMCID: PMC9068644 DOI: 10.1007/s12104-021-10063-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 05/11/2023]
Abstract
ATP binding cassette (ABC) proteins are present in all phyla of life and form one of the largest protein families. The Bacillus subtilis ABC transporter BmrA is a functional homodimer that can extrude many different harmful compounds out of the cell. Each BmrA monomer is composed of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). While the TMDs of ABC transporters are sequentially diverse, the highly conserved NBDs harbor distinctive conserved motifs that enable nucleotide binding and hydrolysis, interdomain communication and that mark a protein as a member of the ABC superfamily. In the catalytic cycle of an ABC transporter, the NBDs function as the molecular motor that fuels substrate translocation across the membrane via the TMDs and are thus pivotal for the entire transport process. For a better understanding of the structural and dynamic consequences of nucleotide interactions within the NBD at atomic resolution, we determined the 1H, 13C and 15N backbone chemical shift assignments of the 259 amino acid wildtype BmrA-NBD in its post-hydrolytic, ADP-bound state.
Collapse
Affiliation(s)
- Victor Hugo Pérez Carrillo
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Dania Rose-Sperling
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Mai Anh Tran
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Christoph Wiedemann
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, 07743, Jena, Germany.
| |
Collapse
|
5
|
Mandal SK, Kanaujia SP. Structural and thermodynamic insights into a novel Mg 2+-citrate-binding protein from the ABC transporter superfamily. Acta Crystallogr D Struct Biol 2021; 77:1516-1534. [PMID: 34866608 DOI: 10.1107/s2059798321010457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/08/2021] [Indexed: 11/11/2022] Open
Abstract
More than one third of proteins require metal ions to accomplish their functions, making them obligatory for the growth and survival of microorganisms in varying environmental niches. In prokaryotes, besides their involvement in various cellular and physiological processes, metal ions stimulate the uptake of citrate molecules. Citrate is a source of carbon and energy and is reported to be transported by secondary transporters. In Gram-positive bacteria, citrate molecules are transported in complex with divalent metal ions, whereas in Gram-negative bacteria they are translocated by Na+/citrate symporters. In this study, the presence of a novel divalent-metal-ion-complexed citrate-uptake system that belongs to the primary active ABC transporter superfamily is reported. For uptake, the metal-ion-complexed citrate molecules are sequestered by substrate-binding proteins (SBPs) and transferred to transmembrane domains for their transport. This study reports crystal structures of an Mg2+-citrate-binding protein (MctA) from the Gram-negative thermophilic bacterium Thermus thermophilus HB8 in both apo and holo forms in the resolution range 1.63-2.50 Å. Despite binding various divalent metal ions, MctA possesses the coordination geometry to bind its physiological metal ion, Mg2+. The results also suggest an extended subclassification of cluster D SBPs, which are known to bind and transport divalent-metal-ion-complexed citrate molecules. Comparative assessment of the open and closed conformations of the wild-type and mutant MctA proteins suggests a gating mechanism of ligand entry following an `asymmetric domain movement' of the N-terminal domain for substrate binding.
Collapse
Affiliation(s)
- Suraj Kumar Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| |
Collapse
|
6
|
Structural dynamics of ABC transporters: molecular simulation studies. Biochem Soc Trans 2021; 49:405-414. [PMID: 33634827 DOI: 10.1042/bst20200710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/31/2022]
Abstract
The biological activities of living organisms involve various inputs and outputs. The ATP-driven substances (biomolecules) responsible for these kinds of activities through membrane (i.e. uptake and efflux of substrates) include ATP-binding cassette (ABC) transporters, some of which play important roles in multidrug resistance. The basic architecture of ABC transporters comprises transmembrane domains (TMDs) and nucleotide-binding domains (NBDs). The functional dynamics (substrate transport) of ABC transporters are realized by concerted motions, such as NBD dimerization, mechanical transmission via coupling helices (CHs), and the translocation of substrates through TMDs, which are induced by the binding and/or hydrolysis of ATP molecules and substrates. In this mini-review, we briefly discuss recent progresses in the structural dynamics as revealed by molecular simulation studies at all-atom (AA), coarse-grained (CG), and quantum mechanics/molecular mechanics (QM/MM) levels.
Collapse
|
7
|
Abstract
Drug transporters are integral membrane proteins that play a critical role in drug disposition by affecting absorption, distribution, and excretion. They translocate drugs, as well as endogenous molecules and toxins, across membranes using ATP hydrolysis, or ion/concentration gradients. In general, drug transporters are expressed ubiquitously, but they function in drug disposition by being concentrated in tissues such as the intestine, the kidneys, the liver, and the brain. Based on their primary sequence and their mechanism, transporters can be divided into the ATP-binding cassette (ABC), solute-linked carrier (SLC), and the solute carrier organic anion (SLCO) superfamilies. Many X-ray crystallography and cryo-electron microscopy (cryo-EM) structures have been solved in the ABC and SLC transporter superfamilies or of their bacterial homologs. The structures have provided valuable insight into the structural basis of transport. This chapter will provide particular focus on the promiscuous drug transporters because of their effect on drug disposition and the challenges associated with them.
Collapse
Affiliation(s)
- Arthur G Roberts
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, Athens, GA, USA.
| |
Collapse
|
8
|
Seelig A. P-Glycoprotein: One Mechanism, Many Tasks and the Consequences for Pharmacotherapy of Cancers. Front Oncol 2020; 10:576559. [PMID: 33194688 PMCID: PMC7649427 DOI: 10.3389/fonc.2020.576559] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/31/2020] [Indexed: 12/31/2022] Open
Abstract
P-glycoprotein or multidrug resistance protein (MDR1) is an adenosine triphosphate (ATP) binding cassette transporter (ABCB1) intensely investigated because it is an obstacle to successful pharmacotherapy of cancers. P-glycoprotein prevents cellular uptake of a large number of structurally and functionally diverse compounds, including most cancer therapeutics and in this way causes multidrug resistance (MDR). To overcome MDR, and thus improve cancer treatment, an understanding of P-glycoprotein inhibition at the molecular level is required. With this goal in mind, we propose rules that predict whether a compound is a modulator, substrate, inhibitor, or inducer of P-glycoprotein. This new set of rules is derived from a quantitative analysis of the drug binding and transport properties of P-glycoprotein. We further discuss the role of P-glycoprotein in immune surveillance and cell metabolism. Finally, the predictive power of the proposed rules is demonstrated with a set of FDA approved drugs which have been repurposed for cancer therapy.
Collapse
Affiliation(s)
- Anna Seelig
- Biozentrum, University of Basel, Basel, Switzerland
| |
Collapse
|
9
|
Göddeke H, Schäfer LV. Capturing Substrate Translocation in an ABC Exporter at the Atomic Level. J Am Chem Soc 2020; 142:12791-12801. [PMID: 32578427 DOI: 10.1021/jacs.0c05502] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
ATP-binding cassette (ABC) transporters chemomechanically couple ATP binding and hydrolysis to large-scale conformational changes, ultimately leading to substrate translocation across biological membranes. Despite recent progress in the structure determination of substrate-bound ABC exporters, the inherently dynamic mechanism of substrate transport remains unclear at the atomic level. In this work, we capture substrate translocation in the heterodimeric ABC exporter TM287/288 from the hyperthermophilic bacterium Thermotoga maritima using all-atom molecular dynamics (MD) simulations. Unguided multimicrosecond simulations at 375 K show how the drugs daunorubicin and verapamil, which were initially docked into the ABC transporter, get translocated through the exporter by following its large-scale alternating access conformational transitions between an inward-facing (IF) and an outward-facing (OF) conformation. Triggered by the affinity difference due to differential solvation of the binding cavity in the IF and OF conformations, the substrates unbind from the OF transporter and partition into the lipid bilayer. While daunorubicin is stably inserted into the outer leaflet of the bilayer, verapamil dynamically flip flops between the bilayer leaflets, possibly rendering its net transport futile.
Collapse
Affiliation(s)
- Hendrik Göddeke
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| |
Collapse
|
10
|
Morsy MA, El-Sheikh AAK, Ibrahim ARN, Venugopala KN, Kandeel M. In silico and in vitro identification of secoisolariciresinol as a re-sensitizer of P-glycoprotein-dependent doxorubicin-resistance NCI/ADR-RES cancer cells. PeerJ 2020; 8:e9163. [PMID: 32566390 PMCID: PMC7293189 DOI: 10.7717/peerj.9163] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/18/2020] [Indexed: 12/27/2022] Open
Abstract
P-glycoprotein (P-gp) is one of the highly expressed cancer cell efflux transporters that cause the failure of chemotherapy. To reverse P-gp induced multidrug resistance, we employed a flaxseed-derived lignan; secoisolariciresinol (SECO) that acts as an inhibitor of breast cancer resistance protein; another efflux transporter that shares some substrate/inhibitor specificity with P-gp. Molecular dynamics (MD) simulation identified SECO as a possible P-gp inhibitor. Comparing root mean square deviation (RMSD) of P-gp bound with SECO with that bound to its standard inhibitor verapamil showed that fluctuations in RMSD were lower in P-gp bound to SECO demonstrating higher stability of the complex of P-gp with SECO. In addition, the superimposition of P-gp structures after MD simulation showed that the nucleotide-binding domains of P-gp bound to SECO undertook a more central closer position compared with that bound to verapamil. Using rhodamine efflux assay on NCI/ADR-RES cancer cells, SECO was confirmed as a P-gp inhibitor, where cells treated with 25 or 50 µM of SECO showed significantly higher fluorescence intensity compared to control. Using MTT assay, SECO alone showed dose-dependent cytotoxicity, where 25 or 50 µM of SECO caused significantly less NCI/ADR-RES cellular viability compared to control. Furthermore, when 50 µM of SECO was added to doxorubicin (DOX), an anticancer drug, SECO significantly enhanced DOX-induced cytotoxicity compared to DOX alone. The combination index calculated by CompuSyn software indicated synergism between DOX and SECO. Our results suggest SECO as a novel P-gp inhibitor that can re-sensitize cancer cells during DOX chemotherapy.
Collapse
Affiliation(s)
- Mohamed A Morsy
- Department of Pharmaceutical Sciences/College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Eastern Region, Saudi Arabia.,Department of Pharmacology/Faculty of Medicine, Minia University, El-Minia, Egypt
| | - Azza A K El-Sheikh
- Department of Pharmacology/Faculty of Medicine, Minia University, El-Minia, Egypt.,Basic Health Sciences Department/Faculty of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ahmed R N Ibrahim
- Department of Clinical Pharmacy/College of Pharmacy, King Khalid University, Abha, Saudi Arabia.,Department of Biochemistry/Faculty of Pharmacy, Minia University, El-Minia, Egypt
| | - Katharigatta N Venugopala
- Department of Pharmaceutical Sciences/College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Eastern Region, Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Mahmoud Kandeel
- Department of Biomedical Sciences/College of Veterinary Medicine, King Faisal University, Al-Ahsa, Eastern Region, Saudi Arabia.,Department of Pharmacology/Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| |
Collapse
|
11
|
Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
|
12
|
Lacabanne D, Orelle C, Lecoq L, Kunert B, Chuilon C, Wiegand T, Ravaud S, Jault JM, Meier BH, Böckmann A. Flexible-to-rigid transition is central for substrate transport in the ABC transporter BmrA from Bacillus subtilis. Commun Biol 2019; 2:149. [PMID: 31044174 PMCID: PMC6488656 DOI: 10.1038/s42003-019-0390-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/15/2019] [Indexed: 01/15/2023] Open
Abstract
ATP-binding-cassette (ABC) transporters are molecular pumps that translocate molecules across the cell membrane by switching between inward-facing and outward-facing states. To obtain a detailed understanding of their mechanism remains a challenge to structural biology, as these proteins are notoriously difficult to study at the molecular level in their active, membrane-inserted form. Here we use solid-state NMR to investigate the multidrug ABC transporter BmrA reconstituted in lipids. We identify the chemical-shift differences between the inward-facing, and outward-facing state induced by ATP:Mg2+:Vi addition. Analysis of an X-loop mutant, for which we show that ATPase and transport activities are uncoupled, reveals an incomplete transition to the outward-facing state upon ATP:Mg2+:Vi addition, notably lacking the decrease in dynamics of a defined set of residues observed in wild-type BmrA. This suggests that this stiffening is required for an efficient transmission of the conformational changes to allow proper transport of substrate by the pump.
Collapse
Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Britta Kunert
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Claire Chuilon
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stéphanie Ravaud
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Beat H. Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| |
Collapse
|
13
|
Immadisetty K, Hettige J, Moradi M. Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter. ACS CENTRAL SCIENCE 2019; 5:43-56. [PMID: 30693324 PMCID: PMC6346382 DOI: 10.1021/acscentsci.8b00480] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 06/09/2023]
Abstract
By undergoing conformational changes, active membrane transporters alternate between an inward-facing (IF) and an outward-facing (OF) state to transport their substrates across cellular membrane. The conformational landscape of membrane transporters, however, could be influenced by their environment, and the dependence of the alternating access mechanism on the lipid composition has not been understood at the molecular level. We have performed an extensive set of microsecond-level all-atom molecular dynamics (MD) simulations on bacterial ATP binding cassette (ABC) exporter Sav1866 in six different phosphocholine (PC) and phosphoethanolamine (PE) lipid membrane environments. This study mainly focuses on the energetically downhill OF-to-IF conformational transition of Sav1866 upon the ATP hydrolysis. We observe that the transporter undergoes large-scale conformational changes in the PE environment, particularly in the POPE lipids, resulting in an IF-occluded conformation, a transition that does not occur when the transporter is embedded in any of the PC lipid bilayers. We propose that the PE lipids facilitate the closing of the protein on the periplasmic side due to their highly polar headgroups that mediate the interaction of the two transmembrane (TM) bundles by a network of lipid-lipid and lipid-protein hydrogen bonds. POPE lipids in particular facilitate the closure of periplasmic gate by promoting a hinge formation in TM helices and an interbundle salt bridge formation. This study explains how the alternating access mechanism and the flippase activity in ABC exporters could be lipid-dependent.
Collapse
|
14
|
Göddeke H, Timachi MH, Hutter CAJ, Galazzo L, Seeger MA, Karttunen M, Bordignon E, Schäfer LV. Atomistic Mechanism of Large-Scale Conformational Transition in a Heterodimeric ABC Exporter. J Am Chem Soc 2018; 140:4543-4551. [DOI: 10.1021/jacs.7b12944] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hendrik Göddeke
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - M. Hadi Timachi
- EPR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Cedric A. J. Hutter
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland
| | - Laura Galazzo
- EPR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Markus A. Seeger
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland
| | - Mikko Karttunen
- Department of Chemistry and Department of Applied Mathematics, Western University, London, Ontario N6A 3K7, Canada
| | - Enrica Bordignon
- EPR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Lars V. Schäfer
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| |
Collapse
|
15
|
Szöllősi D, Szakács G, Chiba P, Stockner T. Dissecting the Forces that Dominate Dimerization of the Nucleotide Binding Domains of ABCB1. Biophys J 2018; 114:331-342. [PMID: 29401431 PMCID: PMC5984967 DOI: 10.1016/j.bpj.2017.11.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/11/2017] [Accepted: 11/14/2017] [Indexed: 01/10/2023] Open
Abstract
P-glycoprotein, also known as multidrug resistance protein 1 or ABCB1, can export a wide range of chemically unrelated compounds, including chemotherapeutic drugs. ABCB1 consists of two transmembrane domains that form the substrate binding and translocation domain, and of two cytoplasmic nucleotide binding domains (NBDs) that energize substrate transport by ATP binding and hydrolysis. ATP binding triggers dimerization of the NBDs, which switches the transporter from an inward facing to an outward facing transmembrane domain conformation. We performed MD simulations to study the dynamic behavior of the NBD dimer in the presence or absence of nucleotides. In the apo configuration, the NBDs were overall attractive to each other as shown in the potential of mean force profile, but the energy well was shallow and broad. In contrast, a sharp and deep energy minimum (∼-42 kJ/mol) was found in the presence of ATP, leading to a well-defined conformation. Motif interaction network analyses revealed that ATP stabilizes the NBD dimer by serving as the central hub for interdomain connections. Simulations showed that forces promoting dimerization are multilayered, dominated by electrostatic interactions between the nucleotide and conserved amino acids of the signature sequence and the Walker A motif. In addition, direct and water-bridged hydrogen bonds between NBDs provided conformation-defining interactions. Importantly, we characterized a largely unrecognized but essential contribution from hydrophobic interactions between the adenine moiety of the nucleotides and a hydrophobic surface of the X-loop to the stabilization of the nucleotide-bound NBD dimer. These hydrophobic interactions lead to a sharp energy minimum, thereby conformationally restricting the nucleotide-bound state.
Collapse
Affiliation(s)
- Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Gergely Szakács
- Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Peter Chiba
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
16
|
Szöllősi D, Rose-Sperling D, Hellmich UA, Stockner T. Comparison of mechanistic transport cycle models of ABC exporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:818-832. [PMID: 29097275 PMCID: PMC7610611 DOI: 10.1016/j.bbamem.2017.10.028] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 12/25/2022]
Abstract
ABC (ATP binding cassette) transporters, ubiquitous in all kingdoms of life, carry out essential substrate transport reactions across cell membranes. Their transmembrane domains bind and translocate substrates and are connected to a pair of nucleotide binding domains, which bind and hydrolyze ATP to energize import or export of substrates. Over four decades of investigations into ABC transporters have revealed numerous details from atomic-level structural insights to their functional and physiological roles. Despite all these advances, a comprehensive understanding of the mechanistic principles of ABC transporter function remains elusive. The human multidrug resistance transporter ABCB1, also referred to as P-glycoprotein (P-gp), is one of the most intensively studied ABC exporters. Using ABCB1 as the reference point, we aim to compare the dominating mechanistic models of substrate transport and ATP hydrolysis for ABC exporters and to highlight the experimental and computational evidence in their support. In particular, we point out in silico studies that enhance and complement available biochemical data. “This article is part of a Special Issue entitled: Beyond the Structure Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.”
Collapse
Affiliation(s)
- Dániel Szöllősi
- Medical University of Vienna, Institute of Pharmacology, Waehringerstr. 13A, Vienna 1090, Austria
| | - Dania Rose-Sperling
- Johannes Gutenberg-University, Department of Pharmacy and Biochemistry, Johann-Joachim-Becher-Weg 30, Mainz 55128, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Ute A Hellmich
- Johannes Gutenberg-University, Department of Pharmacy and Biochemistry, Johann-Joachim-Becher-Weg 30, Mainz 55128, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Thomas Stockner
- Medical University of Vienna, Institute of Pharmacology, Waehringerstr. 13A, Vienna 1090, Austria.
| |
Collapse
|