1
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Al Khoury C, Thoumi S, Tokajian S, Sinno A, Nemer G, El Beyrouthy M, Rahy K. ABC transporter inhibition by beauvericin partially overcomes drug resistance in Leishmania tropica. Antimicrob Agents Chemother 2024; 68:e0136823. [PMID: 38572959 PMCID: PMC11064568 DOI: 10.1128/aac.01368-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Leishmaniasis is a neglected tropical disease infecting the world's poorest populations. Miltefosine (ML) remains the primary oral drug against the cutaneous form of leishmaniasis. The ATP-binding cassette (ABC) transporters are key players in the xenobiotic efflux, and their inhibition could enhance the therapeutic index. In this study, the ability of beauvericin (BEA) to overcome ABC transporter-mediated resistance of Leishmania tropica to ML was assessed. In addition, the transcription profile of genes involved in resistance acquisition to ML was inspected. Finally, we explored the efflux mechanism of the drug and inhibitor. The efficacy of ML against all developmental stages of L. tropica in the presence or absence of BEA was evaluated using an absolute quantification assay. The expression of resistance genes was evaluated, comparing susceptible and resistant strains. Finally, the mechanisms governing the interaction between the ABC transporter and its ligands were elucidated using molecular docking and dynamic simulation. Relative quantification showed that the expression of the ABCG sub-family is mostly modulated by ML. In this study, we used BEA to impede resistance of Leishmania tropica. The IC50 values, following BEA treatment, were significantly reduced from 30.83, 48.17, and 16.83 µM using ML to 8.14, 11.1, and 7.18 µM when using a combinatorial treatment (ML + BEA) against promastigotes, axenic amastigotes, and intracellular amastigotes, respectively. We also demonstrated a favorable BEA-binding enthalpy to L. tropica ABC transporter compared to ML. Our study revealed that BEA partially reverses the resistance development of L. tropica to ML by blocking the alternate ATP hydrolysis cycle.
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Affiliation(s)
- Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Aia Sinno
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Mark El Beyrouthy
- Department of Agriculture and Food Engineering, Holy Spirit University of Kaslik, Jounieh, Lebanon
| | - Kelven Rahy
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
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2
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Di Cesare M, Kaplan E, Rendon J, Gerbaud G, Valimehr S, Gobet A, Ngo TAT, Chaptal V, Falson P, Martinho M, Dorlet P, Hanssen E, Jault JM, Orelle C. The transport activity of the multidrug ABC transporter BmrA does not require a wide separation of the nucleotide-binding domains. J Biol Chem 2024; 300:105546. [PMID: 38072053 PMCID: PMC10821409 DOI: 10.1016/j.jbc.2023.105546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
ATP-binding cassette (ABC) transporters are ubiquitous membrane proteins responsible for the translocation of a wide diversity of substrates across biological membranes. Some of them confer multidrug or antimicrobial resistance to cancer cells and pathogenic microorganisms, respectively. Despite a wealth of structural data gained in the last two decades, the molecular mechanism of these multidrug efflux pumps remains elusive, including the extent of separation between the two nucleotide-binding domains (NBDs) during the transport cycle. Based on recent outward-facing structures of BmrA, a homodimeric multidrug ABC transporter from Bacillus subtilis, we introduced a cysteine mutation near the C-terminal end of the NBDs to analyze the impact of disulfide-bond formation on BmrA function. Interestingly, the presence of the disulfide bond between the NBDs did not prevent the ATPase, nor did it affect the transport of Hoechst 33342 and doxorubicin. Yet, the 7-amino-actinomycin D was less efficiently transported, suggesting that a further opening of the transporter might improve its ability to translocate this larger compound. We solved by cryo-EM the apo structures of the cross-linked mutant and the WT protein. Both structures are highly similar, showing an intermediate opening between their NBDs while their C-terminal extremities remain in close proximity. Distance measurements obtained by electron paramagnetic resonance spectroscopy support the intermediate opening found in these 3D structures. Overall, our data suggest that the NBDs of BmrA function with a tweezers-like mechanism distinct from the related lipid A exporter MsbA.
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Affiliation(s)
- Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Elise Kaplan
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Julia Rendon
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | | | - Sepideh Valimehr
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Thu-Anh Thi Ngo
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Vincent Chaptal
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Pierre Falson
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | | | - Pierre Dorlet
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | - Eric Hanssen
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
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3
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Lacabanne D, Wiegand T, Di Cesare M, Orelle C, Ernst M, Jault JM, Meier BH, Böckmann A. Solid-State NMR Reveals Asymmetric ATP Hydrolysis in the Multidrug ABC Transporter BmrA. J Am Chem Soc 2022; 144:12431-12442. [PMID: 35776907 PMCID: PMC9284561 DOI: 10.1021/jacs.2c04287] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
The detailed mechanism
of ATP hydrolysis in ATP-binding cassette
(ABC) transporters is still not fully understood. Here, we employed 31P solid-state NMR to probe the conformational changes and
dynamics during the catalytic cycle by locking the multidrug ABC transporter
BmrA in prehydrolytic, transition, and posthydrolytic states, using
a combination of mutants and ATP analogues. The 31P spectra
reveal that ATP binds strongly in the prehydrolytic state to both
ATP-binding sites as inferred from the analysis of the nonhydrolytic
E504A mutant. In the transition state of wild-type BmrA, the symmetry
of the dimer is broken and only a single site is tightly bound to
ADP:Mg2+:vanadate, while the second site is more ‘open’
allowing exchange with the nucleotides in the solvent. In the posthydrolytic
state, weak binding, as characterized by chemical exchange with free
ADP and by asymmetric 31P–31P two-dimensional
(2D) correlation spectra, is observed for both sites. Revisiting the 13C spectra in light of these findings confirms the conformational
nonequivalence of the two nucleotide-binding sites in the transition
state. Our results show that following ATP binding, the symmetry of
the ATP-binding sites of BmrA is lost in the ATP-hydrolysis step,
but is then recovered in the posthydrolytic ADP-bound state.
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Affiliation(s)
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Margot Di Cesare
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
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4
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Structural insights into the catalytic cycle of a bacterial multidrug ABC efflux pump. J Mol Biol 2022; 434:167541. [DOI: 10.1016/j.jmb.2022.167541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/19/2022]
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Khunweeraphong N, Kuchler K. Multidrug Resistance in Mammals and Fungi-From MDR to PDR: A Rocky Road from Atomic Structures to Transport Mechanisms. Int J Mol Sci 2021; 22:4806. [PMID: 33946618 PMCID: PMC8124828 DOI: 10.3390/ijms22094806] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Multidrug resistance (MDR) can be a serious complication for the treatment of cancer as well as for microbial and parasitic infections. Dysregulated overexpression of several members of the ATP-binding cassette transporter families have been intimately linked to MDR phenomena. Three paradigm ABC transporter members, ABCB1 (P-gp), ABCC1 (MRP1) and ABCG2 (BCRP) appear to act as brothers in arms in promoting or causing MDR in a variety of therapeutic cancer settings. However, their molecular mechanisms of action, the basis for their broad and overlapping substrate selectivity, remains ill-posed. The rapidly increasing numbers of high-resolution atomic structures from X-ray crystallography or cryo-EM of mammalian ABC multidrug transporters initiated a new era towards a better understanding of structure-function relationships, and for the dynamics and mechanisms driving their transport cycles. In addition, the atomic structures offered new evolutionary perspectives in cases where transport systems have been structurally conserved from bacteria to humans, including the pleiotropic drug resistance (PDR) family in fungal pathogens for which high resolution structures are as yet unavailable. In this review, we will focus the discussion on comparative mechanisms of mammalian ABCG and fungal PDR transporters, owing to their close evolutionary relationships. In fact, the atomic structures of ABCG2 offer excellent models for a better understanding of fungal PDR transporters. Based on comparative structural models of ABCG transporters and fungal PDRs, we propose closely related or even conserved catalytic cycles, thus offering new therapeutic perspectives for preventing MDR in infectious disease settings.
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Affiliation(s)
| | - Karl Kuchler
- Center for Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter, Medical University of Vienna, Dr. Bohr-Gasse 9/2, A-1030 Vienna, Austria;
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Comparative Proteomics of Marinobacter sp. TT1 Reveals Corexit Impacts on Hydrocarbon Metabolism, Chemotactic Motility, and Biofilm Formation. Microorganisms 2020; 9:microorganisms9010003. [PMID: 33374976 PMCID: PMC7822026 DOI: 10.3390/microorganisms9010003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/19/2020] [Accepted: 12/19/2020] [Indexed: 12/12/2022] Open
Abstract
The application of chemical dispersants during marine oil spills can affect the community composition and activity of marine microorganisms. Several studies have indicated that certain marine hydrocarbon-degrading bacteria, such as Marinobacter spp., can be inhibited by chemical dispersants, resulting in lower abundances and/or reduced biodegradation rates. However, a major knowledge gap exists regarding the mechanisms underlying these physiological effects. Here, we performed comparative proteomics of the Deepwater Horizon isolate Marinobacter sp. TT1 grown under different conditions. Strain TT1 received different carbon sources (pyruvate vs. n-hexadecane) with and without added dispersant (Corexit EC9500A). Additional treatments contained crude oil in the form of a water-accommodated fraction (WAF) or chemically-enhanced WAF (CEWAF; with Corexit). For the first time, we identified the proteins associated with alkane metabolism and alginate biosynthesis in strain TT1, report on its potential for aromatic hydrocarbon biodegradation and present a protein-based proposed metabolism of Corexit components as carbon substrates. Our findings revealed that Corexit exposure affects hydrocarbon metabolism, chemotactic motility, biofilm formation, and induces solvent tolerance mechanisms, like efflux pumps, in strain TT1. This study provides novel insights into dispersant impacts on microbial hydrocarbon degraders that should be taken into consideration for future oil spill response actions.
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7
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Dehghani-Ghahnaviyeh S, Kapoor K, Tajkhorshid E. Conformational changes in the nucleotide-binding domains of P-glycoprotein induced by ATP hydrolysis. FEBS Lett 2020; 595:735-749. [PMID: 33159693 DOI: 10.1002/1873-3468.13992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/19/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022]
Abstract
P-glycoprotein (Pgp) is a member of the ABC transporter superfamily with high physiological importance. Pgp nucleotide-binding domains (NBDs) drive the transport cycle through ATP binding and hydrolysis. We use molecular dynamics simulations to investigate the ATP hydrolysis-induced conformational changes in NBDs. Five systems, including all possible ATP/ADP combinations in the NBDs and the APO system, are simulated. ATP/ADP exchange induces conformational changes mostly within the conserved signature motif of the NBDs, resulting in relative orientational changes in the NBDs. Nucleotide removal leads to additional orientational changes in the NBDs, allowing their dissociation. Furthermore, we capture putative hydrolysis-competent configurations in which the conserved glutamate in the Walker-B motif acts as a catalytic base capturing a water molecule likely initiating ATP hydrolysis.
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Affiliation(s)
- Sepehr Dehghani-Ghahnaviyeh
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
| | - Karan Kapoor
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
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8
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Jones PM, George AM. Is the emperor wearing shorts? The published structures of ABC transporters. FEBS Lett 2020; 594:3790-3798. [PMID: 32981041 DOI: 10.1002/1873-3468.13941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/24/2020] [Accepted: 09/13/2020] [Indexed: 12/20/2022]
Abstract
ABC transporters use the energy of ATP binding and hydrolysis to transport substrates across cellular membranes. They comprise two highly conserved nucleotide binding domains and two transmembrane domains that form the transmembrane channel and contain the substrate binding sites. Structural analyses have found a variety of seemingly unrelated folds for the ABC transporter transmembrane domains, and from these, a set of diverse mechanistic models has been inferred. Nevertheless, in spite of the explosion in structure determination of ABC transporters in the last decade, advancement in certainty and clarity as to fundamental aspects of their molecular mechanisms remains elusive. With this in mind, here we put and examine the question: Could current ABC structures differ from the physiologic membrane-embedded forms?
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Affiliation(s)
- Peter M Jones
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
| | - Anthony M George
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
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9
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Goda K, Dönmez-Cakil Y, Tarapcsák S, Szalóki G, Szöllősi D, Parveen Z, Türk D, Szakács G, Chiba P, Stockner T. Human ABCB1 with an ABCB11-like degenerate nucleotide binding site maintains transport activity by avoiding nucleotide occlusion. PLoS Genet 2020; 16:e1009016. [PMID: 33031417 PMCID: PMC7544095 DOI: 10.1371/journal.pgen.1009016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 07/29/2020] [Indexed: 11/28/2022] Open
Abstract
Several ABC exporters carry a degenerate nucleotide binding site (NBS) that is unable to hydrolyze ATP at a rate sufficient for sustaining transport activity. A hallmark of a degenerate NBS is the lack of the catalytic glutamate in the Walker B motif in the nucleotide binding domain (NBD). The multidrug resistance transporter ABCB1 (P-glycoprotein) has two canonical NBSs, and mutation of the catalytic glutamate E556 in NBS1 renders ABCB1 transport-incompetent. In contrast, the closely related bile salt export pump ABCB11 (BSEP), which shares 49% sequence identity with ABCB1, naturally contains a methionine in place of the catalytic glutamate. The NBD-NBD interfaces of ABCB1 and ABCB11 differ only in four residues, all within NBS1. Mutation of the catalytic glutamate in ABCB1 results in the occlusion of ATP in NBS1, leading to the arrest of the transport cycle. Here we show that despite the catalytic glutamate mutation (E556M), ABCB1 regains its ATP-dependent transport activity, when three additional diverging residues are also replaced. Molecular dynamics simulations revealed that the rescue of ATPase activity is due to the modified geometry of NBS1, resulting in a weaker interaction with ATP, which allows the quadruple mutant to evade the conformationally locked pre-hydrolytic state to proceed to ATP-driven transport. In summary, we show that ABCB1 can be transformed into an active transporter with only one functional catalytic site by preventing the formation of the ATP-locked pre-hydrolytic state in the non-canonical site. ABC transporters are one of the largest membrane protein superfamilies, present in all organisms from archaea to humans. They transport a wide range of molecules including amino acids, sugars, vitamins, nucleotides, peptides, lipids, metabolites, antibiotics, and xenobiotics. ABC transporters energize substrate transport by hydrolyzing ATP in two symmetrically arranged nucleotide binding sites (NBSs). The human multidrug resistance transporter ABCB1 has two active NBSs, and it is generally believed that integrity and cooperation of both sites are needed for transport. Several human ABC transporters, such as the bile salt transporter ABCB11, have one degenerate NBS, which has significantly reduced ATPase activity. Interestingly, unilateral mutations affecting one of the two NBSs completely abolish the function of symmetrical ABC transporters. Here we engineered an ABCB1 variant with a degenerate, ABCB11-like NBS1, which can nevertheless transport substrates. Our results indicate that ABCB1 can mediate active transport with a single active site, questioning the validity of models assuming strictly alternating catalysis.
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Affiliation(s)
- Katalin Goda
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Yaprak Dönmez-Cakil
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- Department of Histology and Embryology, Faculty of Medicine, Maltepe University, Maltepe, Istanbul, Turkey
| | - Szabolcs Tarapcsák
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Gábor Szalóki
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
| | - Zahida Parveen
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Dóra Türk
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja, Budapest, Hungary
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja, Budapest, Hungary
- Institute of Cancer Research, Medical University of Vienna, Borschkegasse, Vienna, Austria
| | - Peter Chiba
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- * E-mail: (PC); (TS)
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- * E-mail: (PC); (TS)
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Zhang B, Zhang J, Kang Z, Liang L, Liu Y, Wang Q. On interactions of P-glycoprotein with various anti-tumor drugs by binding free energy calculations. J Biomol Struct Dyn 2020; 39:5335-5347. [PMID: 32608321 DOI: 10.1080/07391102.2020.1786456] [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] [Indexed: 10/24/2022]
Abstract
P-glycoprotein (P-gp, MDR1), one of ATP-binding cassette transporters, may confer tumor cells cross-resistance to chemotherapeutics. A large amount of P-gp inhibitors were designed to inhibit the multidrug resistance (MDR) feature of P-gp. However, no sufficient researches were reported to explore the correlation between binding capacity and drug property by experiment. Without particular drug property found to inhibit the MDR feature of P-gp, the orientation of drug design is indefinite. In this work, 10 representative cancer drugs with various properties are used to bind with P-gp by molecular dynamics simulation. Binding free energy between P-gp and 10 drugs ranges -139 to -253 kJ/mol. It reveals that the promiscuity nature of P-gp is in light of the similar binding free energy in separate P-gp-ligand binding systems. The binding effect of P-gp and drugs correlates well with the size of drugs and has no apparent correlation with the polarity of each drug. The key reason is that van der Waal's interaction occupies most of the total binding free energy, and it is led by the number of atoms in the drugs. Two transmembrane segments (TM6 and TM12) and three types of amino acids (PHE, MET, and GLN) are vital in binding drugs with van der Waal's energy, which evident the influence between binding stability and size of drugs. This work provides the cause and theoretical basis for the promiscuity nature of P-gp.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bo Zhang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Junqiao Zhang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhengzhong Kang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Lijun Liang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China.,College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Yingchun Liu
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Qi Wang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
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11
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Songkiatisak P, Ding F, Cherukuri PK, Xu XHN. Size-Dependent Inhibitory Effects of Antibiotic Nanocarriers on Filamentation of E. coli. NANOSCALE ADVANCES 2020; 2:2135-2145. [PMID: 33791510 PMCID: PMC8009294 DOI: 10.1039/c9na00697d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/30/2020] [Indexed: 06/12/2023]
Abstract
Multidrug membrane transporters exist in both prokaryotic and eukaryotic cells, which causes multidrug resistance (MDR) and urgent need of new and more effective therapeutic agencies. In this study, we used three different sized antibiotic nanocarriers to study their mode of actions and their size-dependent inhibitory effects against Escherichia coli (E. coli). The antibiotic nanocarriers (AgMUNH-Oflx NPs) with 8.6×102, 9.4×103 and 6.5×105 Oflx molecules per nanoparticle (NP) were prepared by functionalizing the Ag NPs (2.4 ± 0.7, 13.0 ± 3.1 and 92.6 ± 4.4 nm) with a monolayer of 11-amino-1-undecanethiol (MUNH2) and covalently linking ofloxacin (Oflx) with the amine group of AgMUNH2 NPs, respectively. We designed a modified cell culture medium for nanocarriers to be stable (non-aggregated) over 18 h of cell culture, which enables us to quantitatively study their size and dose dependent inhibitory effects against E. coli. We found that inhibitory effects of Oflx against E. coli highly depend upon dose of Oflx and size of nanocarriers, showing that the equal amount of Oflx delivered by the largest nanocarriers (92.6 ± 4.4 nm) were the most potent with the lowest minimum inhibitory concentration (MIC50) and created the longest and highest percentage of filamentous cells, while the smallest nanocarriers (2.4 ± 0.7) were the least potent with the highest MIC50 and produced the shortest and lowest percentage of filamentous cells. Interestingly, the same amount of Oflx on 2.4 ± 0.7 nm nanocarriers showed the 2x higher MIC and created the 2x shorter filamentous cells than free Oflx, while the Oflx on 13.0 ± 3.1 and 92.6 ± 4.4 nm nanocarriers exhibited 2x and 6x lower MICs, and produced 2x and 3x longer filamentous cell than free Oflx, respectively. Notably, three sized AgMUNH2 NPs (absence of Oflx) showed negligible inhibitory effects and did not create filamentous cells. The results show that the filamentation of E. coli highly depends upon the sizes of nanocarriers, which leads to the size-dependent inhibitory effects of nanocarriers against E. coli.
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Affiliation(s)
- Preeyaporn Songkiatisak
- Department of Chemistry and Biochemistry, Old Dominion UniversityNorfolkVirginia 23529USAhttp://www.odu.edu/∼xhxu+1 (757) 683 5698+1 (757) 683 5698
| | - Feng Ding
- Department of Chemistry and Biochemistry, Old Dominion UniversityNorfolkVirginia 23529USAhttp://www.odu.edu/∼xhxu+1 (757) 683 5698+1 (757) 683 5698
| | - Pavan Kumar Cherukuri
- Department of Chemistry and Biochemistry, Old Dominion UniversityNorfolkVirginia 23529USAhttp://www.odu.edu/∼xhxu+1 (757) 683 5698+1 (757) 683 5698
| | - Xiao-Hong Nancy Xu
- Department of Chemistry and Biochemistry, Old Dominion UniversityNorfolkVirginia 23529USAhttp://www.odu.edu/∼xhxu+1 (757) 683 5698+1 (757) 683 5698
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12
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Cherukuri P, Songkiatisak P, Ding F, Jault JM, Xu XHN. Antibiotic Drug Nanocarriers for Probing of Multidrug ABC Membrane Transporter of Bacillus subtilis. ACS OMEGA 2020; 5:1625-1633. [PMID: 32010837 PMCID: PMC6990642 DOI: 10.1021/acsomega.9b03698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Multidrug membrane transporters can extrude a wide range of substrates, which cause multidrug resistance and ineffective treatment of diseases. In this study, we used three different sized antibiotic drug nanocarriers to study their size-dependent inhibitory effects against Bacillus subtilis. We functionalized 2.4 ± 0.7, 13.0 ± 3.1, and 92.6 ± 4.4 nm silver nanoparticles (Ag NPs) with a monolayer of 11-amino-1-undecanethiol and covalently linked them with antibiotics (ofloxacin, Oflx). The labeling ratios of antibiotics with NPs are 8.6 × 102, 9.4 × 103, and 6.5 × 105 Oflx molecules per NP, respectively. We designed cell culture medium in which both BmrA and ΔBmrA cells grew and functioned normally while ensuring the stabilities of nanocarriers (nonaggregation). These approaches allow us to quantitatively study the dependence of their inhibitory effect against two isogenic strains of B. subtilis, WT (normal expression of BmrA) and ΔBmrA (deletion of bmrA), upon the NP size, antibiotic dose, and BmrA expression. Our results show that the inhibitory effects of nanocarriers highly depend on NP size and antibiotic dose. The same amount of Oflx on 2.4 ± 0.7, 13.0 ± 3.1, and 92.6 ± 4.4 nm nanocarriers shows the 3× lower, nearly the same, and 10× higher inhibitory effects than that of free Oflx, against both WT and ΔBmrA, respectively. Control experiments of the respective sized AgMUNH2 NPs (absence of Oflx) show insignificant inhibitory effects toward both strains. Taken together, the results show multiple factors, such as labeling ratios, multivalent effects, and pharmacodynamics (Oflx localization and distribution), which might play the roles in the size-dependent inhibitory effects on the growth of both WT and ΔBmrA strains. Interestingly, the inhibitory effects of nanocarriers are independent of the expression of BmrA, which could be attributed to the higher efflux of nanocarriers by other membrane transporters in both strains.
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Affiliation(s)
- Pavan
Kumar Cherukuri
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529, United States
| | - Preeyaporn Songkiatisak
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529, United States
| | - Feng Ding
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529, United States
| | - Jean-Michel Jault
- UMR5086
CNRS/UCBLyon I, MMSB-IBCP, 7 Passage du Vercors, 69367 Lyon cedex 07, France
| | - Xiao-Hong Nancy Xu
- Department
of Chemistry and Biochemistry, Old Dominion
University, Norfolk, Virginia 23529, United States
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13
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Hassler M, Shaltiel IA, Kschonsak M, Simon B, Merkel F, Thärichen L, Bailey HJ, Macošek J, Bravo S, Metz J, Hennig J, Haering CH. Structural Basis of an Asymmetric Condensin ATPase Cycle. Mol Cell 2020; 74:1175-1188.e9. [PMID: 31226277 PMCID: PMC6591010 DOI: 10.1016/j.molcel.2019.03.037] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/16/2019] [Accepted: 03/27/2019] [Indexed: 01/20/2023]
Abstract
The condensin protein complex plays a key role in the structural organization of genomes. How the ATPase activity of its SMC subunits drives large-scale changes in chromosome topology has remained unknown. Here we reconstruct, at near-atomic resolution, the sequence of events that take place during the condensin ATPase cycle. We show that ATP binding induces a conformational switch in the Smc4 head domain that releases its hitherto undescribed interaction with the Ycs4 HEAT-repeat subunit and promotes its engagement with the Smc2 head into an asymmetric heterodimer. SMC head dimerization subsequently enables nucleotide binding at the second active site and disengages the Brn1 kleisin subunit from the Smc2 coiled coil to open the condensin ring. These large-scale transitions in the condensin architecture lay out a mechanistic path for its ability to extrude DNA helices into large loop structures.
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Affiliation(s)
- Markus Hassler
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Indra A Shaltiel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Marc Kschonsak
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Fabian Merkel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Collaboration for Joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Lena Thärichen
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Henry J Bailey
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sol Bravo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jutta Metz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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14
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van Veen HW, Singh H, Agboh K, Fagg LA, Guo D, Swain B, de Kruijf RF, Guffick C. Energy coupling in ABC exporters. Res Microbiol 2019; 170:392-398. [PMID: 31442612 DOI: 10.1016/j.resmic.2019.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/27/2019] [Accepted: 08/12/2019] [Indexed: 11/19/2022]
Abstract
Multidrug transporters are important and interesting molecular machines that extrude a wide variety of cytotoxic drugs from target cells. This review summarizes novel insights in the energetics and mechanisms of bacterial ATP-binding cassette multidrug transporters as well as recent advances connecting multidrug transport to ion and lipid translocation processes in other membrane proteins.
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Affiliation(s)
- Hendrik W van Veen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
| | - Himansha Singh
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Kelvin Agboh
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Lisa A Fagg
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Dawei Guo
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Brendan Swain
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Robbin F de Kruijf
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Charlotte Guffick
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
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15
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Duan W, Li X, Ge Y, Yu Z, Li P, Li J, Qin L, Xie J. Mycobacterium tuberculosis Rv1473 is a novel macrolides ABC Efflux Pump regulated by WhiB7. Future Microbiol 2018; 14:47-59. [PMID: 30539658 DOI: 10.2217/fmb-2018-0207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
AIM To characterize a novel macrolide ATP binding cassette efflux pump encoding gene Rv1473 which might be involved in antibiotic resistance. METHODS Mycobacterium smegmatis was used as a surrogate model for pathogenic mycobacteria, drug susceptibility assays and ethidium bromide accumulation assay were harnessed to verify drug resistance. The real-time quantitative PCR was used to evaluate the transcription levels of WhiB7 and Ms3140 upon exposure to macrolides. RESULTS Rv1473 contributes to macrolides resistance via efflux mechanisms, and was positively regulated by the transcription factor WhiB7 upon macrolides exposure. CONCLUSION Rv1473 is a novel ATP binding cassette efflux pump involved in mycobacterium intrinsic antibiotics resistance via efflux mechanism. This finding will facilitate novel antibiotic discovery and the treatment of pathogen, especially for nontuberculous mycobacteria.
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Affiliation(s)
- Wei Duan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Xue Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Yan Ge
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Zhaoxiao Yu
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Ping Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Jiang Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
| | - Lianhua Qin
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Shanghai 200433, PR China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment & Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, PR China
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16
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Graham WJ, Putnam CD, Kolodner RD. The properties of Msh2-Msh6 ATP binding mutants suggest a signal amplification mechanism in DNA mismatch repair. J Biol Chem 2018; 293:18055-18070. [PMID: 30237169 PMCID: PMC6254361 DOI: 10.1074/jbc.ra118.005439] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 09/17/2018] [Indexed: 11/30/2022] Open
Abstract
DNA mismatch repair (MMR) corrects mispaired DNA bases and small insertion/deletion loops generated by DNA replication errors. After binding a mispair, the eukaryotic mispair recognition complex Msh2–Msh6 binds ATP in both of its nucleotide-binding sites, which induces a conformational change resulting in the formation of an Msh2–Msh6 sliding clamp that releases from the mispair and slides freely along the DNA. However, the roles that Msh2–Msh6 sliding clamps play in MMR remain poorly understood. Here, using Saccharomyces cerevisiae, we created Msh2 and Msh6 Walker A nucleotide–binding site mutants that have defects in ATP binding in one or both nucleotide-binding sites of the Msh2–Msh6 heterodimer. We found that these mutations cause a complete MMR defect in vivo. The mutant Msh2–Msh6 complexes exhibited normal mispair recognition and were proficient at recruiting the MMR endonuclease Mlh1–Pms1 to mispaired DNA. At physiological (2.5 mm) ATP concentration, the mutant complexes displayed modest partial defects in supporting MMR in reconstituted Mlh1–Pms1-independent and Mlh1–Pms1-dependent MMR reactions in vitro and in activation of the Mlh1–Pms1 endonuclease and showed a more severe defect at low (0.1 mm) ATP concentration. In contrast, five of the mutants were completely defective and one was mostly defective for sliding clamp formation at high and low ATP concentrations. These findings suggest that mispair-dependent sliding clamp formation triggers binding of additional Msh2–Msh6 complexes and that further recruitment of additional downstream MMR proteins is required for signal amplification of mispair binding during MMR.
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Affiliation(s)
| | - Christopher D Putnam
- From the Ludwig Institute for Cancer Research San Diego,; Departments of Medicine and
| | - Richard D Kolodner
- From the Ludwig Institute for Cancer Research San Diego,; Cellular and Molecular Medicine,; Moores-UCSD Cancer Center, and; Institute of Genomic Medicine, University of California School of Medicine, San Diego, La Jolla, California 92093-0669.
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17
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Condensin ATPase motifs contribute differentially to the maintenance of chromosome morphology and genome stability. PLoS Biol 2018; 16:e2003980. [PMID: 29949571 PMCID: PMC6039025 DOI: 10.1371/journal.pbio.2003980] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 07/10/2018] [Accepted: 06/12/2018] [Indexed: 02/06/2023] Open
Abstract
Effective transfer of genetic information during cell division requires a major reorganization of chromosome structure. This process is triggered by condensin, a conserved pentameric ATPase essential for chromosome condensation. How condensin harnesses the energy of ATP hydrolysis to promote chromatin reorganization is unknown. To address this issue, we performed a genetic screen specifically focused on the ATPase domain of Smc4, a core subunit of condensin. Our screen identified mutational hotspots that impair condensin’s ability to condense chromosomes to various degrees. These mutations have distinct effects on viability, genome stability, and chromosome morphology, revealing unique thresholds for condensin enzymatic activity in the execution of its cellular functions. Biochemical analyses indicate that inactivation of Smc4 ATPase activity can result in cell lethality because it favors a specific configuration of condensin that locks ATP in the enzyme. Together, our results provide critical insights into the mechanism used by condensin to harness the energy of ATP hydrolysis for the compaction of chromatin. In eukaryotes, the deletion of a single copy of most genes shows little or no detectable phenotype under standard proliferative conditions. This implies that a large reduction in the level of a gene product can be tolerated by eukaryotic organisms and that a “reserve capacity” is built in the protein machinery that drives most cellular processes. Here, we test if the main effector of chromosome condensation—the condensin complex—operates with a reserve enzymatic capacity in the execution of its multiple functions in vivo. To achieve this, we created an allelic series of mutations that selectively inactivate condensin ATPase activity in a graded manner. We show that many core functions of condensin can be maintained even at low levels of ATPase activity. Our data also reveal the existence of various thresholds of ATPase activity that are necessary and sufficient for the execution of different cellular functions by condensin. Notably, loss of genome stability at repetitive DNA is only observed when condensin ATPase activity is severely impaired. Taken together, our results reveal key insights into the process of ATP hydrolysis by condensin and how the energy it releases promotes genome remodeling and stability during cell division.
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18
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Dibutyl phthalate alters the metabolic pathways of microbes in black soils. Sci Rep 2018; 8:2605. [PMID: 29422490 PMCID: PMC5805725 DOI: 10.1038/s41598-018-21030-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 01/29/2018] [Indexed: 01/08/2023] Open
Abstract
Dibutyl phthalate (DBP) is well known as a high-priority pollutant. This study explored the impacts of DBP on the metabolic pathways of microbes in black soils in the short term (20 days). The results showed that the microbial communities were changed in black soils with DBP. In nitrogen cycling, the abundances of the genes were elevated by DBP. DBP contamination facilitated 3'-phosphoadenosine-5'-phosphosulfate (PAPS) formation, and the gene flux of sulfate metabolism was increased. The total abundances of ABC transporters and the gene abundances of the monosaccharide-transporting ATPases MalK and MsmK were increased by DBP. The total abundance of two-component system (TCS) genes and the gene abundances of malate dehydrogenase, histidine kinase and citryl-CoA lyase were increased after DBP contamination. The total abundance of phosphotransferase system (PTS) genes and the gene abundances of phosphotransferase, Crr and BglF were raised by DBP. The increased gene abundances of ABC transporters, TCS and PTS could be the reasons for the acceleration of nitrogen, carbon and sulfate metabolism. The degrading-genes of DBP were increased markedly in soil exposed to DBP. In summary, DBP contamination altered the microbial community and enhanced the gene abundances of the carbon, nitrogen and sulfur metabolism in black soils in the short term.
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19
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Pan X, Zhang Q, Qu S, Huang S, Wang H, Mei H. Allosteric effects of ATP binding on the nucleotide-binding domain of a heterodimeric ATP-binding cassette transporter. Integr Biol (Camb) 2017; 8:1158-1169. [PMID: 27731447 DOI: 10.1039/c6ib00136j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ATP-binding cassette (ABC) exporters mediate vital transport of a variety of molecules across the lipid bilayer in all organisms. To explore the allosteric effect of ATP binding at the asymmetric ATPase sites, molecular dynamics simulations were performed on the nucleotide-binding domains (NBDs) of a heterodimeric exporter TM287/288 in 4 different ATP-bound states. The results showed that ATP bound at the degenerate site can maintain a semi-open conformation of NBD1-NBD2, which may be defective in ATP hydrolysis. By contrast, when bound at the consensus site, ATP can induce an intra-domain rotation of the α-helical subdomain towards the RecA-like subdomain of NBD2 at the degenerate site. The rotation of the α-helical subdomain rearranged the hydrogen bond networks at the NBD1-NBD2 interface, induced a significant conformational change in the D-loop at the degenerate site and inter- and intra-domain communications at both sites, and eventually elicited dimerization of NBD1-NBD2. These findings indicate that the asymmetric ATPase sites of the heterodimeric exporter are structurally and functionally distinct.
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Affiliation(s)
- Xianchao Pan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400044, China. and College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Qiaoxia Zhang
- Chongqing Research Institute of Chemical Industry, Chongqing 400021, China
| | - Sujun Qu
- College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Shuheng Huang
- College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Huicong Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400044, China. and College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400044, China. and College of Bioengineering, Chongqing University, Chongqing 400044, China
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20
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Zoghbi ME, Mok L, Swartz DJ, Singh A, Fendley GA, Urbatsch IL, Altenberg GA. Substrate-induced conformational changes in the nucleotide-binding domains of lipid bilayer-associated P-glycoprotein during ATP hydrolysis. J Biol Chem 2017; 292:20412-20424. [PMID: 29018094 DOI: 10.1074/jbc.m117.814186] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/25/2017] [Indexed: 11/06/2022] Open
Abstract
P-glycoprotein (Pgp) is an efflux pump important in multidrug resistance of cancer cells and in determining drug pharmacokinetics. Pgp is a prototype ATP-binding cassette transporter with two nucleotide-binding domains (NBDs) that bind and hydrolyze ATP. Conformational changes at the NBDs (the Pgp engines) lead to changes across Pgp transmembrane domains that result in substrate translocation. According to current alternating access models (substrate-binding pocket accessible only to one side of the membrane at a time), binding of ATP promotes NBD dimerization, resulting in external accessibility of the drug-binding site (outward-facing, closed NBD conformation), and ATP hydrolysis leads to dissociation of the NBDs with the subsequent return of the accessibility of the binding site to the cytoplasmic side (inward-facing, open NBD conformation). However, previous work has not investigated these events under near-physiological conditions in a lipid bilayer and in the presence of transport substrate. Here, we used luminescence resonance energy transfer (LRET) to measure the distances between the two Pgp NBDs. Pgp was labeled with LRET probes, reconstituted in lipid nanodiscs, and the distance between the NBDs was measured at 37 °C. In the presence of verapamil, a substrate that activates ATP hydrolysis, the NBDs of Pgp reconstituted in nanodiscs were never far apart during the hydrolysis cycle, and we never observed the NBD-NBD distances of tens of Å that have previously been reported. However, we found two main conformations that coexist in a dynamic equilibrium under all conditions studied. Our observations highlight the importance of performing studies of efflux pumps under near-physiological conditions, in a lipid bilayer, at 37 °C, and during substrate-stimulated hydrolysis.
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Affiliation(s)
- Maria E Zoghbi
- From the Department of Cell Physiology and Molecular Biophysics
| | - Leo Mok
- Department of Cell Biology and Biochemistry, and
| | | | | | | | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, and .,Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
| | - Guillermo A Altenberg
- From the Department of Cell Physiology and Molecular Biophysics, .,Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430
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21
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Genovese I, Ilari A, Assaraf YG, Fazi F, Colotti G. Not only P-glycoprotein: Amplification of the ABCB1- containing chromosome region 7q21 confers multidrug resistance upon cancer cells by coordinated overexpression of an assortment of resistance-related proteins. Drug Resist Updat 2017; 32:23-46. [DOI: 10.1016/j.drup.2017.10.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/01/2017] [Accepted: 10/11/2017] [Indexed: 02/07/2023]
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22
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Xia X, Cole SPC, Cai T, Cai Y. Effect of traditional Chinese medicine components on multidrug resistance in tumors mediated by P-glycoprotein. Oncol Lett 2017; 13:3989-3996. [PMID: 28588693 PMCID: PMC5452909 DOI: 10.3892/ol.2017.5976] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 02/07/2017] [Indexed: 12/03/2022] Open
Abstract
Multidrug resistance (MDR) is a major cause of chemotherapy failure. It occurs when an organism is resistant to one type of drug, but also develops resistance to other drugs with different structures and targets. There is a high incidence of MDR in cancer chemotherapy, therefore, finding an effective and non-toxic MDR reversal agent is an important goal, particularly for P-glycoprotein-mediated MDR in cancer. Improvements continue to be made to the status and understanding of traditional Chinese medicine (TCM), due to the advantages of low toxicity and relatively minor side effects. Therefore TCM is currently being used in the treatment of various types of diseases. In recent years, numerous components of TCM have been identified to be effective in reversing MDR by downregulating expression of the drug transporter membrane protein, recovering changes in enzymes involved in detoxification and metabolism and repairing the cell apoptosis pathway. The present study summarizes the anticancerous properties and MDR reversing components of traditional medicinal plants commonly used in the treatment of cancer.
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Affiliation(s)
- Xi Xia
- School of Pharmacy, Institute of Oncology, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Susan P C Cole
- Department of Pathology and Molecular Medicine, Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Kingston, ON K7L 3N6, Canada
| | - Tiange Cai
- School of Life Science, Liaoning University, Shenyang, Liaoning 110036, P.R. China
| | - Yu Cai
- School of Pharmacy, Institute of Oncology, Jinan University, Guangzhou, Guangdong 510632, P.R. China
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23
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Bugde P, Biswas R, Merien F, Lu J, Liu DX, Chen M, Zhou S, Li Y. The therapeutic potential of targeting ABC transporters to combat multi-drug resistance. Expert Opin Ther Targets 2017; 21:511-530. [DOI: 10.1080/14728222.2017.1310841] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Piyush Bugde
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Riya Biswas
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Fabrice Merien
- School of Science, Auckland University of Technology, Auckland, New Zealand
- School of Science, AUT Roche Diagnostic Laboratory, Auckland University of Technology, Auckland, New Zealand
| | - Jun Lu
- School of Science, Auckland University of Technology, Auckland, New Zealand
- School of Interprofessional Health Studies, Auckland University of Technology, Auckland, New Zealand
| | - Dong-Xu Liu
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Mingwei Chen
- Department of Respiratory Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shufeng Zhou
- Department of Biotechnology and Bioengineering, College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Yan Li
- School of Science, Auckland University of Technology, Auckland, New Zealand
- School of Interprofessional Health Studies, Auckland University of Technology, Auckland, New Zealand
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24
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Jones PM, George AM. How Intrinsic Dynamics Mediates the Allosteric Mechanism in the ABC Transporter Nucleotide Binding Domain Dimer. J Chem Theory Comput 2017; 13:1712-1722. [PMID: 28240893 DOI: 10.1021/acs.jctc.6b00839] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A protein's architecture facilitates specific motions-intrinsic dynamic modes-that are employed to effect function. Here we used molecular dynamics (MD) simulations to investigate the dynamics of the MJ0796 ABC transporter nucleotide-binding domain (NBD). ABC transporter NBDs form a rotationally symmetric dimer whereby two equivalent active sites are formed at their interface; in complex with a dimer of transmembrane domains they hydrolyze ATP to energize translocation of substrates across cellular membranes. Our data suggest the ABC NBD's ensemble of functional states can be understood predominately in terms of conformational changes between its major subdomains, occurring along two orthogonal dynamic modes. The data show that ligands and oligomeric interactions modulate the equilibrium conformation of the NBD with respect to these motions, suggesting that allostery is achieved by affecting the energetic profile along these two modes. The observed dynamics and allostery integrate consonantly and logically within a mechanistic framework for the ABC NBD dimer, which is supported by a large body of experimental and theoretical data, providing a higher resolution view of the enzyme's dynamic cycle. Our study shows how valuable mechanistic inferences can be derived from accessible short-time scale MD simulations of an enzyme's substructures.
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Affiliation(s)
- Peter M Jones
- School of Life Sciences, University of Technology Sydney , P.O. Box 123, Broadway, New South Wales 2007, Australia
| | - Anthony M George
- School of Life Sciences, University of Technology Sydney , P.O. Box 123, Broadway, New South Wales 2007, Australia
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25
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Verhalen B, Dastvan R, Thangapandian S, Peskova Y, Koteiche HA, Nakamoto RK, Tajkhorshid E, Mchaourab HS. Energy transduction and alternating access of the mammalian ABC transporter P-glycoprotein. Nature 2017; 543:738-741. [PMID: 28289287 PMCID: PMC5558441 DOI: 10.1038/nature21414] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 01/23/2017] [Indexed: 12/15/2022]
Abstract
ATP binding cassette (ABC) transporters of the exporter class harness the energy of ATP hydrolysis in the nucleotide-binding domains (NBDs) to power the energetically uphill efflux of substrates by a dedicated transmembrane domain (TMD). Although numerous investigations have described the mechanism of ATP hydrolysis and defined the architecture of ABC exporters, a detailed structural dynamic understanding of the transduction of ATP energy to the work of substrate translocation remains elusive. Here we used double electron-electron resonance and molecular dynamics simulations to describe the ATP- and substrate-coupled conformational cycle of the mouse ABC efflux transporter P-glycoprotein (Pgp; also known as ABCB1), which has a central role in the clearance of xenobiotics and in cancer resistance to chemotherapy. Pairs of spin labels were introduced at residues selected to track the putative inward-facing to outward-facing transition. Our findings illuminate how ATP energy is harnessed in the NBDs in a two-stroke cycle and elucidate the consequent conformational motion that reconfigures the TMD, two critical aspects of Pgp transport mechanism. Along with a fully atomistic model of the outward-facing conformation in membranes, the insight into Pgp conformational dynamics harmonizes mechanistic and structural data into a novel perspective on ATP-coupled transport and reveals mechanistic divergence within the efflux class of ABC transporters.
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Affiliation(s)
- Brandy Verhalen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Reza Dastvan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Sundarapandian Thangapandian
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yelena Peskova
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Hanane A Koteiche
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Robert K Nakamoto
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, USA
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Kaur H, Lakatos-Karoly A, Vogel R, Nöll A, Tampé R, Glaubitz C. Coupled ATPase-adenylate kinase activity in ABC transporters. Nat Commun 2016; 7:13864. [PMID: 28004795 PMCID: PMC5192220 DOI: 10.1038/ncomms13864] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/04/2016] [Indexed: 12/24/2022] Open
Abstract
ATP-binding cassette (ABC) transporters, a superfamily of integral membrane proteins, catalyse the translocation of substrates across the cellular membrane by ATP hydrolysis. Here we demonstrate by nucleotide turnover and binding studies based on 31P solid-state NMR spectroscopy that the ABC exporter and lipid A flippase MsbA can couple ATP hydrolysis to an adenylate kinase activity, where ADP is converted into AMP and ATP. Single-point mutations reveal that both ATPase and adenylate kinase mechanisms are associated with the same conserved motifs of the nucleotide-binding domain. Based on these results, we propose a model for the coupled ATPase-adenylate kinase mechanism, involving the canonical and an additional nucleotide-binding site. We extend these findings to other prokaryotic ABC exporters, namely LmrA and TmrAB, suggesting that the coupled activities are a general feature of ABC exporters.
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Affiliation(s)
- Hundeep Kaur
- Institute for Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Andrea Lakatos-Karoly
- Institute for Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Ramona Vogel
- Institute for Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Anne Nöll
- Institute for Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Robert Tampé
- Institute for Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
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27
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Glycolipid substrates for ABC transporters required for the assembly of bacterial cell-envelope and cell-surface glycoconjugates. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1394-1403. [PMID: 27793707 DOI: 10.1016/j.bbalip.2016.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 01/07/2023]
Abstract
Glycoconjugates, molecules that contain sugar components, are major components of the cell envelopes of bacteria and cover much of their exposed surfaces. These molecules are involved in interactions with the surrounding environment and, in pathogens, play critical roles in the interplay with the host immune system. Despite the remarkable diversity in glycoconjugate structures, most are assembled by glycosyltransferases that act on lipid acceptors at the cytosolic membrane. The resulting glycolipids are then transported to the cell surface in processes that frequently begin with ATP-binding cassette transporters. This review summarizes current understanding of the structure and biosynthesis of glycolipid substrates and the structure and functions of their transporters. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Yang Z, Zhou Q, Mok L, Singh A, Swartz DJ, Urbatsch IL, Brouillette CG. Interactions and cooperativity between P-glycoprotein structural domains determined by thermal unfolding provides insights into its solution structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:48-60. [PMID: 27783926 DOI: 10.1016/j.bbamem.2016.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/19/2016] [Accepted: 10/21/2016] [Indexed: 12/16/2022]
Abstract
Structural changes in mouse P-glycoprotein (Pgp) induced by thermal unfolding were studied by differential scanning calorimetry (DSC), circular dichroism and fluorescence spectroscopy to gain insight into the solution conformation(s) of this ABC transporter that may not be apparent from current crystal structures. DSC of reconstituted Pgp showed two thermal unfolding transitions in the absence of MgATP, suggesting that each transition involved the cooperative unfolding of two or more interacting structural domains. A low calorimetric unfolding enthalpy and minimal structural changes were observed, which are hallmarks of the thermal unfolding of α-helical membrane proteins, because generally only the extramembranous regions undergo significant unfolding. Nucleotide binding increased the unfolding temperature of both transitions to the same extent, suggesting that one nucleotide binding domain (NBD) unfolds with each transition. Combined with the results from the two isolated NBDs, we propose that each DSC transition represents the cooperative unfolding of one NBD and the two contacting intracellular loops. Further, the presence of two transitions in both apo and MgATP bound wild-type Pgp suggests the NBD-dimeric conformation is transient, and that Pgp resides predominantly in the crystallographically observed inward-facing conformation with NBDs separated, even under conditions supporting continuous MgATP hydrolysis. In contrast, DSC of the vanadate-trapped MgADP·Pgp complex and the MgATP-bound catalytically inactive mutant, E552A/E1197A, show an additional transition at much higher temperature, corresponding to the unfolding of the nucleotide-trapped NBD-dimeric outward-facing conformation. The collective results indicate a strong preference for an NBD dissociated, inward-facing conformation of Pgp.
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Affiliation(s)
- Zhengrong Yang
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Qingxian Zhou
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leo Mok
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Anukriti Singh
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Douglas J Swartz
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Christie G Brouillette
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, USA.
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Kaur H, Lakatos A, Spadaccini R, Vogel R, Hoffmann C, Becker-Baldus J, Ouari O, Tordo P, Mchaourab H, Glaubitz C. The ABC exporter MsbA probed by solid state NMR – challenges and opportunities. Biol Chem 2016; 396:1135-49. [PMID: 25849794 DOI: 10.1515/hsz-2015-0119] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/26/2015] [Indexed: 01/20/2023]
Abstract
ATP binding cassette (ABC) transporters form a superfamily of integral membrane proteins involved in translocation of substrates across the membrane driven by ATP hydrolysis. Despite available crystal structures and extensive biochemical data, many open questions regarding their transport mechanisms remain. Therefore, there is a need to explore spectroscopic techniques such as solid state NMR in order to bridge the gap between structural and mechanistic data. In this study, we investigate the feasibility of using Escherichia coli MsbA as a model ABC transporter for solid state NMR studies. We show that optimised solubilisation and reconstitution procedures enable preparing stable and homogenous protein samples. Depending on the duration of solubilisation, MsbA can be obtained in either an apo- or in a native lipid A bound form. Building onto these optimisations, the first promising MAS-NMR spectra with narrow lines have been recorded. However, further sensitivity improvements are required so that complex NMR experiments can be recorded within a reasonable amount of time. We therefore demonstrate the usability of paramagnetic doping for rapid data acquisition and explore dynamic nuclear polarisation as a method for general signal enhancement. Our results demonstrate that solid state NMR provides an opportunity to address important biological questions related to complex mechanisms of ABC transporters.
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Szöllősi D, Erdei Á, Gyimesi G, Magyar C, Hegedűs T. Access Path to the Ligand Binding Pocket May Play a Role in Xenobiotics Selection by AhR. PLoS One 2016; 11:e0146066. [PMID: 26727491 PMCID: PMC4699818 DOI: 10.1371/journal.pone.0146066] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/11/2015] [Indexed: 11/23/2022] Open
Abstract
Understanding of multidrug binding at the atomic level would facilitate drug design and strategies to modulate drug metabolism, including drug transport, oxidation, and conjugation. Therefore we explored the mechanism of promiscuous binding of small molecules by studying the ligand binding domain, the PAS-B domain of the aryl hydrocarbon receptor (AhR). Because of the low sequence identities of PAS domains to be used for homology modeling, structural features of the widely employed HIF-2α and a more recent suitable template, CLOCK were compared. These structures were used to build AhR PAS-B homology models. We performed molecular dynamics simulations to characterize dynamic properties of the PAS-B domain and the generated conformational ensembles were employed in in silico docking. In order to understand structural and ligand binding features we compared the stability and dynamics of the promiscuous AhR PAS-B to other PAS domains exhibiting specific interactions or no ligand binding function. Our exhaustive in silico binding studies, in which we dock a wide spectrum of ligand molecules to the conformational ensembles, suggest that ligand specificity and selection may be determined not only by the PAS-B domain itself, but also by other parts of AhR and its protein interacting partners. We propose that ligand binding pocket and access channels leading to the pocket play equally important roles in discrimination of endogenous molecules and xenobiotics.
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Affiliation(s)
- Dániel Szöllősi
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, 1094, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary
| | - Áron Erdei
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, 1094, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, 1083, Hungary
| | - Gergely Gyimesi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, 3012, Switzerland
| | - Csaba Magyar
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - Tamás Hegedűs
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences, Budapest, 1094, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary
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31
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Jones PM, George AM. The Nucleotide-Free State of the Multidrug Resistance ABC Transporter LmrA: Sulfhydryl Cross-Linking Supports a Constant Contact, Head-to-Tail Configuration of the Nucleotide-Binding Domains. PLoS One 2015; 10:e0131505. [PMID: 26120849 PMCID: PMC4485892 DOI: 10.1371/journal.pone.0131505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/03/2015] [Indexed: 12/12/2022] Open
Abstract
ABC transporters are integral membrane pumps that are responsible for the import or export of a diverse range of molecules across cell membranes. ABC transporters have been implicated in many phenomena of medical importance, including cystic fibrosis and multidrug resistance in humans. The molecular architecture of ABC transporters comprises two transmembrane domains and two ATP-binding cassettes, or nucleotide-binding domains (NBDs), which are highly conserved and contain motifs that are crucial to ATP binding and hydrolysis. Despite the improved clarity of recent structural, biophysical, and biochemical data, the seemingly simple process of ATP binding and hydrolysis remains controversial, with a major unresolved issue being whether the NBD protomers separate during the catalytic cycle. Here chemical cross-linking data is presented for the bacterial ABC multidrug resistance (MDR) transporter LmrA. These indicate that in the absence of nucleotide or substrate, the NBDs come into contact to a significant extent, even at 4°C, where ATPase activity is abrogated. The data are clearly not in accord with an inward-closed conformation akin to that observed in a crystal structure of V. cholerae MsbA. Rather, they suggest a head-to-tail configuration ‘sandwich’ dimer similar to that observed in crystal structures of nucleotide-bound ABC NBDs. We argue the data are more readily reconciled with the notion that the NBDs are in proximity while undergoing intra-domain motions, than with an NBD ‘Switch’ mechanism in which the NBD monomers separate in between ATP hydrolysis cycles.
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Affiliation(s)
- Peter M Jones
- School of Life Sciences, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia
| | - Anthony M George
- School of Life Sciences, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia
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32
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Shah AH, Banerjee A, Rawal MK, Saxena AK, Mondal AK, Prasad R. ABC transporter Cdr1p harbors charged residues in the intracellular loop and nucleotide-binding domain critical for protein trafficking and drug resistance. FEMS Yeast Res 2015; 15:fov036. [DOI: 10.1093/femsyr/fov036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2015] [Indexed: 12/26/2022] Open
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33
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Antigen Translocation Machineries in Adaptive Immunity and Viral Immune Evasion. J Mol Biol 2015; 427:1102-18. [DOI: 10.1016/j.jmb.2014.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/04/2014] [Accepted: 09/05/2014] [Indexed: 11/23/2022]
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Uchea C, Owen SF, Chipman JK. Functional xenobiotic metabolism and efflux transporters in trout hepatocyte spheroid cultures. Toxicol Res (Camb) 2015; 4:494-507. [PMID: 25893091 PMCID: PMC4384106 DOI: 10.1039/c4tx00160e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/28/2015] [Indexed: 12/12/2022] Open
Abstract
Prediction of xenobiotic fate in fish is important for the regulatory assessment of chemicals under current legislation.
Prediction of xenobiotic fate in fish is important for the regulatory assessment of chemicals under current legislation. Trout hepatocyte spheroids are a promising in vitro model for this assessment. In this investigation, the gene expression and function for xenobiotic metabolism and cellular efflux were characterised. Using fluorescence, transport and real time PCR analysis, the expression and functionality of a variety of genes related to xenobiotic metabolism and drug efflux were assessed in a range of trout hepatocyte culture preparations. Significantly greater levels of expression of genes involved in xenobiotic metabolism and efflux were measured in spheroids (which have been shown to remain viable in excess of 30 days), compared to hepatocytes cultured using conventional suspension and monolayer culture techniques. A transient decline in the expression of genes related to both xenobiotic metabolism and transport was determined during spheroid development, with a subsequent recovery in older spheroids. The most mature spheroids also exhibited an expression profile most comparable to that reported in vivo. Functionality of efflux transporters in spheroids was also demonstrated using fluorescent markers and specific inhibitors. In conclusion, the more physiologically relevant architecture in spheroid cultures provides a high functional integrity in relation to xenobiotic metabolism and efflux. Together with the enhanced gene expression and longevity of the model, hepatocytes in spheroid culture may prove to be an accurate alternative model to study the mechanisms of these processes in fish liver and provide an assay to determine the bioaccumulation potential of environmental contaminants.
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Affiliation(s)
- Chibuzor Uchea
- University of Birmingham , School of Biosciences , Birmingham , B15 2TT , UK ; AstraZeneca , Alderley Park , Macclesfield , Cheshire , SK10 4TF , UK .
| | - Stewart F Owen
- AstraZeneca , Alderley Park , Macclesfield , Cheshire , SK10 4TF , UK .
| | - J Kevin Chipman
- University of Birmingham , School of Biosciences , Birmingham , B15 2TT , UK
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Albareda M, Rodrigue A, Brito B, Ruiz-Argüeso T, Imperial J, Mandrand-Berthelot MA, Palacios J. Rhizobium leguminosarum HupE is a highly-specific diffusion facilitator for nickel uptake. Metallomics 2015; 7:691-701. [DOI: 10.1039/c4mt00298a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Functional and topological analysis ofRhizobium leguminosarumHupE, the founding member of the HupE/UreJ family of nickel permeases, provides new hints on how bacteria manage nickel provision for metalloenzyme synthesis.
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Affiliation(s)
- Marta Albareda
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
| | - Agnès Rodrigue
- Microbiologie
- Adaptation et Pathogénie
- F-69622 Villeurbanne Cedex, France
| | - Belén Brito
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
| | - Tomás Ruiz-Argüeso
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
| | - Juan Imperial
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
| | | | - Jose Palacios
- Departamento de Biotecnología
- Escuela Técnica Superior de Ingenieros Agrónomos and Centro de Biotecnología y Genómica de Plantas (C.B.G.P.)
- Universidad Politécnica de Madrid
- Campus de Montegancedo
- 28223 Pozuelo de Alarcón, Spain
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36
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Zhao R, Liu L, Wang Y, Xiao Z. Vinegar-baked Radix Bupleuri modulates the cell membrane constituents and inhibits the P-gp activity in rat hepatocytes. Altern Ther Health Med 2014; 14:357. [PMID: 25256115 PMCID: PMC4192444 DOI: 10.1186/1472-6882-14-357] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 09/22/2014] [Indexed: 12/12/2022]
Abstract
Background Vinegar-baked Radix Bupleuri (VBRB) enhances the effects of other drugs on the liver by increasing drug distribution to the liver, but the mechanism of action remains unclear. The present study was designed to determine the effects of VBRB on the membrane permeability, constituents, and P-glycoprotein (P-gp) activity of hepatocyte BRL cells, in order to interpret the liver targeting enhancing effects of VBRB. Methods The membrane permeability and P-gp expression were analyzed by flow cytometry. The membrane constituents were determined by an automatic biochemistry analyzer and thin-layer chromatography. Results The results showed that, compared with the control, VBRB enhanced the membrane permeability by 41-67% (P < 0.05), which occurred in the absence of any cytotoxicity. VBRB had marginal effects on the cholesterol content, but significantly affected the total protein contents and the lipid constituents of the cell membrane in a dose- and time-dependent manner. VBRB inhibited P-gp expression in the cell membrane by 59-86% (P < 0.01). Conclusion VBRB affects the constituents of BRL cells and increases its permeability, which may help explain its liver-targeting effects.
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37
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He L, Aleksandrov AA, An J, Cui L, Yang Z, Brouillette CG, Riordan JR. Restoration of NBD1 thermal stability is necessary and sufficient to correct ∆F508 CFTR folding and assembly. J Mol Biol 2014; 427:106-20. [PMID: 25083918 DOI: 10.1016/j.jmb.2014.07.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 07/09/2014] [Accepted: 07/11/2014] [Indexed: 11/29/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) (ABCC7), unique among ABC exporters as an ion channel, regulates ion and fluid transport in epithelial tissues. Loss of function due to mutations in the cftr gene causes cystic fibrosis. The most common cystic-fibrosis-causing mutation, the deletion of F508 (ΔF508) from the first nucleotide binding domain (NBD1) of CFTR, results in misfolding of the protein and clearance by cellular quality control systems. The ΔF508 mutation has two major impacts on CFTR: reduced thermal stability of NBD1 and disruption of its interface with membrane-spanning domains (MSDs). It is unknown if these two defects are independent and need to be targeted separately. To address this question, we varied the extent of stabilization of NBD1 using different second-site mutations and NBD1 binding small molecules with or without NBD1/MSD interface mutation. Combinations of different NBD1 changes had additive corrective effects on ∆F508 maturation that correlated with their ability to increase NBD1 thermostability. These effects were much larger than those caused by interface modification alone and accounted for most of the correction achieved by modifying both the domain and the interface. Thus, NBD1 stabilization plays a dominant role in overcoming the ΔF508 defect. Furthermore, the dual target approach resulted in a locked-open ion channel that was constitutively active in the absence of the normally obligatory dependence on phosphorylation by protein kinase A. Thus, simultaneous targeting of both the domain and the interface, as well as being non-essential for correction of biogenesis, may disrupt normal regulation of channel function.
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Affiliation(s)
- Lihua He
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Andrei A Aleksandrov
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jianli An
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Liying Cui
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Zhengrong Yang
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Christie G Brouillette
- Center for Structural Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - John R Riordan
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
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38
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Loo TW, Clarke DM. Cysteines introduced into extracellular loops 1 and 4 of human P-glycoprotein that are close only in the open conformation spontaneously form a disulfide bond that inhibits drug efflux and ATPase activity. J Biol Chem 2014; 289:24749-58. [PMID: 25053414 DOI: 10.1074/jbc.m114.583021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
P-glycoprotein (P-gp) is an ATP-binding cassette drug pump that protects us from toxic compounds and confers multidrug resistance. The protein is organized into two halves. The halves contain a transmembrane domain (TMD) with six transmembrane segments and a nucleotide-binding domain (NBD). The drug- and ATP-binding sites reside at the TMD1/TMD2 and NBD1/NBD2 interfaces, respectively. ATP-dependent drug efflux involves changes between the open inward-facing (NBDs apart, extracellular loops (ECLs) close together) and the closed outward-facing (NBDs close together, ECLs apart) conformations. It is controversial, however, whether the open conformation only exists transiently in intact cells because of the presence of high levels of ATP. To test for the presence of an open conformation in intact cells, reporter cysteines were placed in extracellular loops 1 (A80C, N half) and 4 (R741C, C half). The rationale was that cysteines A80C/R741C would only come close enough to form a disulfide bond in an open conformation (6.9 Å apart) because they are separated widely (30.4 Å apart) in the closed conformation. It was observed that the mutant A80C/R741C cross-linked spontaneously (>90%) when expressed in cells. In contrast to previous reports showing that trapping P-gp in a closed conformation highly activated ATPase activity, here we show that A80C/R741C cross-linking inhibited ATPase activity and drug efflux. Both activities were restored when the cross-linked mutant was treated with a thiol-reducing agent. The results show that an open conformation can be readily detected in cells and that cross-linking of cysteines placed in ECLs 1 and 4 inhibits activity.
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Affiliation(s)
- Tip W Loo
- From the Departments of Medicine and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David M Clarke
- From the Departments of Medicine and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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ABC transporters in adaptive immunity. Biochim Biophys Acta Gen Subj 2014; 1850:449-60. [PMID: 24923865 DOI: 10.1016/j.bbagen.2014.05.022] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 05/24/2014] [Accepted: 05/29/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND ABC transporters ubiquitously found in all kingdoms of life move a broad range of solutes across membranes. Crystal structures of four distinct types of ABC transport systems have been solved, shedding light on different conformational states within the transport process. Briefly, ATP-dependent flipping between inward- and outward-facing conformations allows directional transport of various solutes. SCOPE OF REVIEW The heterodimeric transporter associated with antigen processing TAP1/2 (ABCB2/3) is a crucial element of the adaptive immune system. The ABC transport complex shuttles proteasomal degradation products into the endoplasmic reticulum. These antigenic peptides are loaded onto major histocompatibility complex class I molecules and presented on the cell surface. We detail the functional modules of TAP, its ATPase and transport cycle, and its interaction with and modulation by other cellular components. In particular, we emphasize how viral factors inhibit TAP activity and thereby prevent detection of the infected host cell by cytotoxic T-cells. MAJOR CONCLUSIONS Merging functional details on TAP with structural insights from related ABC transporters refines the understanding of solute transport. Although human ABC transporters are extremely diverse, they still may employ conceptually related transport mechanisms. Appropriately, we delineate a working model of the transport cycle and how viral factors arrest TAP in distinct conformations. GENERAL SIGNIFICANCE Deciphering the transport cycle of human ABC proteins is the major issue in the field. The defined peptidic substrate, various inhibitory viral factors, and its role in adaptive immunity provide unique tools for the investigation of TAP, making it an ideal model system for ABC transporters in general. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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40
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Kinetic validation of the models for P-glycoprotein ATP hydrolysis and vanadate-induced trapping. Proposal for additional steps. PLoS One 2014; 9:e98804. [PMID: 24897122 PMCID: PMC4045855 DOI: 10.1371/journal.pone.0098804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/07/2014] [Indexed: 11/20/2022] Open
Abstract
P-Glycoprotein, a member of the ATP-binding cassette (ABC) superfamily, is a multidrug transporter responsible for cellular efflux of hundreds of structurally unrelated compounds, including natural products, many clinically used drugs and anti-cancer agents. Expression of P-glycoprotein has been linked to multidrug resistance in human cancers. ABC transporters are driven by ATP hydrolysis at their two cytoplasmic nucleotide-binding domains, which interact to form a closed ATP-bound sandwich dimer. Intimate knowledge of the catalytic cycle of these proteins is clearly essential for understanding their mechanism of action. P-Glycoprotein has been proposed to hydrolyse ATP by an alternating mechanism, for which there is substantial experimental evidence, including inhibition of catalytic activity by trapping of ortho-vanadate at one nucleotide-binding domain, and the observation of an asymmetric occluded state. Despite many studies of P-glycoprotein ATPase activity over the past 20 years, no comprehensive kinetic analysis has yet been carried out, and some puzzling features of its behaviour remain unexplained. In this work, we have built several progressively more complex kinetic models, and then carried out simulations and detailed analysis, to test the validity of the proposed reaction pathway employed by P-glycoprotein for ATP hydrolysis. To establish kinetic parameters for the catalytic cycle, we made use of the large amount of published data on ATP hydrolysis by hamster P-glycoprotein, both purified and in membrane vesicles. The proposed kinetic scheme(s) include a high affinity priming reaction for binding of the first ATP molecule, and an independent pathway for ADP binding outside the main catalytic cycle. They can reproduce to varying degrees the observed behavior of the protein's ATPase activity and its inhibition by ortho-vanadate. The results provide new insights into the mode of action of P-glycoprotein, and some hypotheses about the nature of the occluded nucleotide-bound state.
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41
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Abstract
AbstractABC transporters comprise a large, diverse, and ubiquitous superfamily of membrane active transporters. Their core architecture is a dimer of dimers, comprising two transmembrane (TM) domains that bind substrate, and two ATP-binding cassettes, which use the cell's energy currency to couple substrate translocation to ATP hydrolysis. Despite the availability of over a dozen resolved structures and a wealth of biochemical and biophysical data, this field is bedeviled by controversy and long-standing mechanistic questions remain unresolved. The prevailing paradigm for the ABC transport mechanism is the Switch Model, in which the ATP-binding cassettes dimerize upon binding two ATP molecules, and thence dissociate upon sequential ATP hydrolysis. This cycle of nucleotide-binding domain (NBD) dimerization and dissociation is coupled to a switch between inward- or outward facing conformations of a single TM channel; this alternating access enables substrate binding on one face of the membrane and its release at the other. Notwithstanding widespread acceptance of the Switch Model, there is substantial evidence that the NBDs do not separate very much, if at all, and thus physical separation of the ATP cassettes observed in crystallographic structures may be an artefact. An alternative Constant Contact Model has been proposed, in which ATP hydrolysis occurs alternately at the two ATP-binding sites, with one of the sites remaining closed and containing occluded nucleotide at all times. In this model, the cassettes remain in contact and the active sites swing open in an alternately seesawing motion. Whilst the concept of NBD association/dissociation in the Switch Model is naturally compatible with a single alternating-access channel, the asymmetric functioning proposed by the Constant Contact model suggests an alternating or reciprocating function in the TMDs. Here, a new model for the function of ABC transporters is proposed in which the sequence of ATP binding, hydrolysis, and product release in each active site is directly coupled to the analogous sequence of substrate binding, translocation and release in one of two functionally separate substrate translocation pathways. Each translocation pathway functions 180° out of phase. A wide and diverse selection of data for both ABC importers and exporters is examined, and the ability of the Switch and Reciprocating Models to explain the data is compared and contrasted. This analysis shows that not only can the Reciprocating Model readily explain the data; it also suggests straightforward explanations for the function of a number of atypical ABC transporters. This study represents the most coherent and complete attempt at an all-encompassing scheme to explain how these important proteins work, one that is consistent with sound biochemical and biophysical evidence.
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42
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Szakács G, Hall MD, Gottesman MM, Boumendjel A, Kachadourian R, Day BJ, Baubichon-Cortay H, Di Pietro A. Targeting the Achilles heel of multidrug-resistant cancer by exploiting the fitness cost of resistance. Chem Rev 2014; 114:5753-74. [PMID: 24758331 PMCID: PMC4059772 DOI: 10.1021/cr4006236] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar tudósok körútja 2, Budapest 1117, Hungary
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43
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Structure and mechanism of ATP-dependent phospholipid transporters. Biochim Biophys Acta Gen Subj 2014; 1850:461-75. [PMID: 24746984 DOI: 10.1016/j.bbagen.2014.04.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 01/09/2023]
Abstract
BACKGROUND ATP-binding cassette (ABC) transporters and P4-ATPases are two large and seemingly unrelated families of primary active pumps involved in moving phospholipids from one leaflet of a biological membrane to the other. SCOPE OF REVIEW This review aims to identify common mechanistic features in the way phospholipid flipping is carried out by two evolutionarily unrelated families of transporters. MAJOR CONCLUSIONS Both protein families hydrolyze ATP, although they employ different mechanisms to use it, and have a comparable size with twelve transmembrane segments in the functional unit. Further, despite differences in overall architecture, both appear to operate by an alternating access mechanism and during transport they might allow access of phospholipids to the internal part of the transmembrane domain. The latter feature is obvious for ABC transporters, but phospholipids and other hydrophobic molecules have also been found embedded in P-type ATPase crystal structures. Taken together, in two diverse groups of pumps, nature appears to have evolved quite similar ways of flipping phospholipids. GENERAL SIGNIFICANCE Our understanding of the structural basis for phospholipid flipping is still limited but it seems plausible that a general mechanism for phospholipid flipping exists in nature. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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44
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Abstract
ATP-binding cassette (ABC) transporters form a large superfamily of ATP-dependent protein complexes that mediate transport of a vast array of substrates across membranes. The 14 currently available structures of ABC transporters have greatly advanced insight into the transport mechanism and revealed a tremendous structural diversity. Whereas the domains that hydrolyze ATP are structurally related in all ABC transporters, the membrane-embedded domains, where the substrates are translocated, adopt four different unrelated folds. Here, we review the structural characteristics of ABC transporters and discuss the implications of this structural diversity for mechanistic diversity.
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Affiliation(s)
- Josy ter Beek
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
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45
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O’Mara ML, Mark AE. Structural characterization of two metastable ATP-bound states of P-glycoprotein. PLoS One 2014; 9:e91916. [PMID: 24632881 PMCID: PMC3954865 DOI: 10.1371/journal.pone.0091916] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/18/2014] [Indexed: 12/30/2022] Open
Abstract
ATP Binding Cassette (ABC) transporters couple the binding and hydrolysis of ATP to the transport of substrate molecules across the membrane. The mechanism by which ATP binding and/or hydrolysis drives the conformational changes associated with substrate transport has not yet been characterized fully. Here, changes in the conformation of the ABC export protein P-glycoprotein on ATP binding are examined in a series of molecular dynamics simulations. When one molecule of ATP is placed at the ATP binding site associated with each of the two nucleotide binding domains (NBDs), the membrane-embedded P-glycoprotein crystal structure adopts two distinct metastable conformations. In one, each ATP molecule interacts primarily with the Walker A motif of the corresponding NBD. In the other, the ATP molecules interacts with both Walker A motif of one NBD and the Signature motif of the opposite NBD inducing the partial dimerization of the NBDs. This interaction is more extensive in one of the two ATP binding site, leading to an asymmetric structure. The overall conformation of the transmembrane domains is not altered in either of these metastable states, indicating that the conformational changes associated with ATP binding observed in the simulations in the absence of substrate do not lead to the outward-facing conformation and thus would be insufficient in themselves to drive transport. Nevertheless, the metastable intermediate ATP-bound conformations observed are compatible with a wide range of experimental cross-linking data demonstrating the simulations do capture physiologically important conformations. Analysis of the interaction between ATP and its cofactor Mg(2+) with each NBD indicates that the coordination of ATP and Mg(2+) differs between the two NBDs. The role structural asymmetry may play in ATP binding and hydrolysis is discussed. Furthermore, we demonstrate that our results are not heavily influenced by the crystal structure chosen for initiation of the simulations.
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Affiliation(s)
- Megan L. O’Mara
- School of Chemistry and Molecular Biosciences (SCMB), The Institute for Molecular Biosciences (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Mathematics and Physics (SMP), The Institute for Molecular Biosciences (IMB), The University of Queensland, Brisbane, Queensland, Australia
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences (SCMB), The Institute for Molecular Biosciences (IMB), The University of Queensland, Brisbane, Queensland, Australia
- The Institute for Molecular Biosciences (IMB), The University of Queensland, Brisbane, Queensland, Australia
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46
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Sharom FJ. Complex Interplay between the P-Glycoprotein Multidrug Efflux Pump and the Membrane: Its Role in Modulating Protein Function. Front Oncol 2014; 4:41. [PMID: 24624364 PMCID: PMC3939933 DOI: 10.3389/fonc.2014.00041] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/17/2014] [Indexed: 11/16/2022] Open
Abstract
Multidrug resistance in cancer is linked to expression of the P-glycoprotein multidrug transporter (Pgp, ABCB1), which exports many structurally diverse compounds from cells. Substrates first partition into the bilayer and then interact with a large flexible binding pocket within the transporter's transmembrane regions. Pgp has been described as a hydrophobic vacuum cleaner or an outwardly directed drug/lipid flippase. Recent X-ray crystal structures have shed some light on the nature of the drug-binding pocket and suggested routes by which substrates can enter it from the membrane. Detergents have profound effects on Pgp function, and several appear to be substrates. Biochemical and biophysical studies in vitro, some using purified reconstituted protein, have explored the effects of the membrane environment. They have demonstrated that Pgp is involved in a complex relationship with its lipid environment, which modulates the behavior of its substrates, as well as various functions of the protein, including ATP hydrolysis, drug binding, and drug transport. Membrane lipid composition and fluidity, phospholipid headgroup and acyl chain length all influence Pgp function. Recent studies focusing on thermodynamics and kinetics have revealed some important principles governing Pgp-lipid and substrate-lipid interactions, and how these affect drug-binding and transport. In some cells, Pgp is associated with cholesterol-rich microdomains, which may modulate its functions. The relationship between Pgp and cholesterol remains an open question; however, it clearly affects several aspects of its function in addition to substrate-membrane partitioning. The action of Pgp modulators appears to depend on their membrane permeability, and membrane fluidizers and surfactants reverse drug resistance, likely via an indirect mechanism. A detailed understanding of how the membrane affects Pgp substrates and Pgp's catalytic cycle may lead to new strategies to combat clinical drug resistance.
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Affiliation(s)
- Frances Jane Sharom
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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Abstract
Lipopolysaccharide molecules represent a unique family of glycolipids based on a highly conserved lipid moiety known as lipid A. These molecules are produced by most gram-negative bacteria, in which they play important roles in the integrity of the outer-membrane permeability barrier and participate extensively in host-pathogen interplay. Few bacteria contain lipopolysaccharide molecules composed only of lipid A. In most forms, lipid A is glycosylated by addition of the core oligosaccharide that, in some bacteria, provides an attachment site for a long-chain O-antigenic polysaccharide. The complexity of lipopolysaccharide structures is reflected in the processes used for their biosynthesis and export. Rapid growth and cell division depend on the bacterial cell's capacity to synthesize and export lipopolysaccharide efficiently and in large amounts. We review recent advances in those processes, emphasizing the reactions that are essential for viability.
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Affiliation(s)
- Chris Whitfield
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada;
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Loo TW, Clarke DM. Identification of the distance between the homologous halves of P-glycoprotein that triggers the high/low ATPase activity switch. J Biol Chem 2014; 289:8484-92. [PMID: 24523403 DOI: 10.1074/jbc.m114.552075] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
P-glycoprotein (P-gp, ABCB1) is an ATP-binding cassette drug pump that protects us from toxic compounds and confers multidrug resistance. Each homologous half contains a transmembrane domain with six transmembrane segments followed by a nucleotide-binding domain (NBD). The drug- and ATP-binding sites reside at the interface between the transmembrane domain and NBDs, respectively. Drug binding activates ATPase activity by an unknown mechanism. There is no high resolution structure of human P-gp, but homology models based on the crystal structures of bacterial, mouse, and Caenorhabditis elegans ATP-binding cassette drug pumps yield both open (NBDs apart) and closed (NBDs together) conformations. Molecular dynamics simulations predict that the NBDs can be separated over a range of distances (over 20 Å). To determine the distance that show high or low ATPase activity, we cross-linked reporter cysteines L175C (N-half) and N820C (C-half) with cross-linkers of various lengths that separated the halves between 6 and 30 Å (α-carbons). We observed that ATPase activity increased over 10-fold when the cysteines were cross-linked at distances between 6 and 19 Å, although cross-linking at distances greater than 20 Å yielded basal levels of activity. The results suggest that the ATPase activation switch appears to be turned on or off when L175C/N820 are clamped at distances less than or greater than 20 Å, respectively. We predict that the high/low ATPase activity switch may occur at a distance where the NBDs are predicted in molecular dynamic simulations to undergo pronounced twisting as they approach each other (Wise, J. G. (2012) Biochemistry 51, 5125-5141).
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Affiliation(s)
- Tip W Loo
- From the Departments of Medicine and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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49
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The Maltose ABC Transporter: Where Structure Meets Function. SPRINGER SERIES IN BIOPHYSICS 2014. [DOI: 10.1007/978-3-642-53839-1_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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50
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Tarling EJ, de Aguiar Vallim TQ, Edwards PA. Role of ABC transporters in lipid transport and human disease. Trends Endocrinol Metab 2013; 24:342-50. [PMID: 23415156 PMCID: PMC3659191 DOI: 10.1016/j.tem.2013.01.006] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/16/2013] [Accepted: 01/18/2013] [Indexed: 12/28/2022]
Abstract
Almost half of the 48 human ATP-binding cassette (ABC) transporter proteins are thought to facilitate the ATP-dependent translocation of lipids or lipid-related compounds. Such substrates include cholesterol, plant sterols, bile acids, phospholipids, and sphingolipids. Mutations in a substantial number of the 48 human ABC transporters have been linked to human disease. Indeed the finding that 12 diseases have been associated with abnormal lipid transport and/or homeostasis demonstrates the importance of this family of transporters in cell physiology. This review highlights the role of ABC transporters in lipid transport and movement, in addition to discussing their roles in cellular homeostasis and inherited disorders.
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Affiliation(s)
- Elizabeth J Tarling
- Department of Biological Chemistry, David Geffen School of Medicine at the University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA.
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