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Ni C, Hong M. Oligomerization of drug transporters: Forms, functions, and mechanisms. Acta Pharm Sin B 2024; 14:1924-1938. [PMID: 38799641 PMCID: PMC11119549 DOI: 10.1016/j.apsb.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/07/2023] [Accepted: 01/05/2024] [Indexed: 05/29/2024] Open
Abstract
Drug transporters are essential players in the transmembrane transport of a wide variety of clinical drugs. The broad substrate spectra and versatile distribution pattern of these membrane proteins infer their pharmacological and clinical significance. With our accumulating knowledge on the three-dimensional structure of drug transporters, their oligomerization status has become a topic of intense study due to the possible functional roles carried out by such kind of post-translational modification (PTM). In-depth studies of oligomeric complexes formed among drug transporters as well as their interactions with other regulatory proteins can help us better understand the regulatory mechanisms of these membrane proteins, provide clues for the development of novel drugs, and improve the therapeutic efficacy. In this review, we describe different oligomerization forms as well as their structural basis of major drug transporters in the ATP-binding cassette and solute carrier superfamilies, summarize our current knowledge on the influence of oligomerization for protein expression level and transport function of these membrane proteins, and discuss the regulatory mechanisms of oligomerization. Finally, we highlight the challenges associated with the current oligomerization studies and propose some thoughts on the pharmaceutical application of this important drug transporter PTM.
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Affiliation(s)
- Chunxu Ni
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Mei Hong
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China
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2
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Fan W, Shao K, Luo M. Structural View of Cryo-Electron Microscopy-Determined ATP-Binding Cassette Transporters in Human Multidrug Resistance. Biomolecules 2024; 14:231. [PMID: 38397468 PMCID: PMC10886794 DOI: 10.3390/biom14020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
ATP-binding cassette (ABC) transporters, acting as cellular "pumps," facilitate solute translocation through membranes via ATP hydrolysis. Their overexpression is closely tied to multidrug resistance (MDR), a major obstacle in chemotherapy and neurological disorder treatment, hampering drug accumulation and delivery. Extensive research has delved into the intricate interplay between ABC transporter structure, function, and potential inhibition for MDR reversal. Cryo-electron microscopy has been instrumental in unveiling structural details of various MDR-causing ABC transporters, encompassing ABCB1, ABCC1, and ABCG2, as well as the recently revealed ABCC3 and ABCC4 structures. The newly obtained structural insight has deepened our understanding of substrate and drug binding, translocation mechanisms, and inhibitor interactions. Given the growing body of structural information available for human MDR transporters and their associated mechanisms, we believe it is timely to compile a comprehensive review of these transporters and compare their functional mechanisms in the context of multidrug resistance. Therefore, this review primarily focuses on the structural aspects of clinically significant human ABC transporters linked to MDR, with the aim of providing valuable insights to enhance the effectiveness of MDR reversal strategies in clinical therapies.
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Affiliation(s)
| | | | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore; (W.F.); (K.S.)
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3
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Baakdah F, Georges E. Epitope specific antibodies to N- and C cytoplasmic domains of the Plasmodium falciparum chloroquine resistance transporter (PfCRT) differentiate native and post-translationally modified variant. Biochem Biophys Res Commun 2023; 669:54-60. [PMID: 37267860 DOI: 10.1016/j.bbrc.2023.05.096] [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: 05/09/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Polymorphisms in Plasmodium falciparum chloroquine resistance transporter (or PfCRT) were shown to be causative of decreased sensitivity to diverse quinoline-based antimalarials. In this report we describe the identification of a post-translational variant of PfCRT using highly characterized antibodies raised against its N- and C-terminal cytoplasmic domains (e.g., 58 and 26 amino acids, respectively). Western blot analyses of P. falciparum protein extracts with anti N-PfCRT antiserum revealed two polypeptides with apparent molecular masses of 52 kDa and 42 kDa, relative to the calculated molecular mass of PfCRT of 48.7 kDa. The 52 kDa polypeptide was detectable with anti C-PfCRT antiserum, only after alkaline phosphatase treatment of P. falciparum extracts. Detailed epitope mapping of anti N- and C-PfCRT antisera revealed epitopes covering two previously identified phosphorylation sites, Ser411 and Thr416, whereby substitution of these residues with Asp amino acid, to mimic phosphorylated residues, dramatically inhibited anti C-PfCRT binding. Consistently, alkaline phosphatase treatment of P. falciparum extract unmasked the binding of anti C-PfCRT to the 52 kDa polypeptide, suggesting that the 52 kDa but not 42 kDa polypeptide is phosphorylated at its C-terminal Ser411 and Thr416. Interestingly, Pfcrt expressed in HEK-293F human kidney cells showed the same reactive polypeptides with anti N- and C-PfCRT antisera, consistent with PfCRT origin of the two polypeptides (e.g., 42 kDa and 52 kDa), but lacking PfCRT phosphorylation at its C-terminal. Immunohistochemical staining of late trophozoite-infected erythrocytes with anti N-or C-PfCRT antisera showed both polypeptides are localized to the parasite's digestive vacuole. Moreover, both polypeptides are detected in chloroquine-susceptible and -resistant strains of P. falciparum. This is the first report describing a post-translationally modified variant of PfCRT. The physiologic role of the 52 kDa phosphorylated PfCRT in P. falciparum remains to be determined.
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Affiliation(s)
- Fadi Baakdah
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue (Montreal), Quebec, Canada
| | - Elias Georges
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue (Montreal), Quebec, Canada.
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4
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Gellen G, Klement E, Biwott K, Schlosser G, Kalló G, Csősz É, Medzihradszky KF, Bacso Z. Cross-Linking Mass Spectrometry on P-Glycoprotein. Int J Mol Sci 2023; 24:10627. [PMID: 37445813 DOI: 10.3390/ijms241310627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The ABC transporter P-glycoprotein (Pgp) has been found to be involved in multidrug resistance in tumor cells. Lipids and cholesterol have a pivotal role in Pgp's conformations; however, it is often difficult to investigate it with conventional structural biology techniques. Here, we applied robust approaches coupled with cross-linking mass spectrometry (XL-MS), where the natural lipid environment remains quasi-intact. Two experimental approaches were carried out using different cross-linkers (i) on living cells, followed by membrane preparation and immunoprecipitation enrichment of Pgp, and (ii) on-bead, subsequent to membrane preparation and immunoprecipitation. Pgp-containing complexes were enriched employing extracellular monoclonal anti-Pgp antibodies on magnetic beads, followed by on-bead enzymatic digestion. The LC-MS/MS results revealed mono-links on Pgp's solvent-accessible residues, while intraprotein cross-links confirmed a complex interplay between extracellular, transmembrane, and intracellular segments of the protein, of which several have been reported to be connected to cholesterol. Harnessing the MS results and those of molecular docking, we suggest an epitope for the 15D3 cholesterol-dependent mouse monoclonal antibody. Additionally, enriched neighbors of Pgp prove the strong connection of Pgp to the cytoskeleton and other cholesterol-regulated proteins. These findings suggest that XL-MS may be utilized for protein structure and network analyses in such convoluted systems as membrane proteins.
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Affiliation(s)
- Gabriella Gellen
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
| | - Eva Klement
- Single Cell Omics Advanced Core Facility, HCEMM, H-6728 Szeged, Hungary
- Laboratory of Proteomics Research, BRC, H-6726 Szeged, Hungary
| | - Kipchumba Biwott
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Gergő Kalló
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
| | - Éva Csősz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
| | | | - Zsolt Bacso
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Faculty of Pharmacology, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
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5
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Saib S, Hodin S, Mercier C, Paul M, Bin V, Ollier E, Delavenne X. TNF-α and IL-1β Exposure Modulates the Expression and Functionality of P-Glycoprotein in Intestinal and Renal Barriers. Mol Pharm 2022; 19:2327-2334. [PMID: 35674492 DOI: 10.1021/acs.molpharmaceut.2c00140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inflammation is characterized by an increased secretion of proinflammatory cytokines known to alter the expression and functionality of drug transporters. Since P-glycoprotein (P-gp) plays a key role in the pharmacokinetics of several drugs, these modulations could further affect drug exposure. In this context, this study aims to investigate the impact of in vitro cytokine exposure on the expression and activity of P-gp using the intestinal model Caco-2 and the human renal cells RPTEC/TERT1. Cells were exposed to various concentrations of tumor necrosis factor (TNF)-α and interleukin (IL)-1β for 24 or 72 h. Gene expression was then assessed by RT-qPCR followed by absolute quantification of P-gp using liquid chromatography coupled with mass spectrometry. Then, the activity of P-gp was assessed by the intracellular accumulation of rhodamine 123. TNF-α increased both the gene expression and P-gp activity by 15-40% in each model. Minor modulations were observed at the protein level with increases of up to 8% for RPTEC/TERT1 cells and 24% for Caco-2 cells. Conversely, IL-1β led to a downregulation of gene, protein, and functionality by 48 and 25% in intestinal and renal cells, respectively. Taken together, these data highlighted that gene expression levels and functional activity of P-gp are altered by the pro-inflammatory cytokines in intestinal and renal cells. Such pronounced changes in human P-gp could result in altered exposure to drug substrates. Further in vivo studies are needed to confirm the impact of inflammation on drug pharmacokinetics.
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Affiliation(s)
- Sonia Saib
- INSERM U1059, Dysfonction Vasculaire et Hémostase (DVH), Université Jean Monnet, Saint-Etienne F-42023, France
| | - Sophie Hodin
- INSERM U1059, Dysfonction Vasculaire et Hémostase (DVH), Université Jean Monnet, Saint-Etienne F-42023, France
| | - Clément Mercier
- INSERM U1059, Dysfonction Vasculaire et Hémostase (DVH), Université Jean Monnet, Saint-Etienne F-42023, France
| | - Mireille Paul
- INSERM U1059, Laboratoire de Biologie Intégrative du Tissu Osseux (LBTO), Université Jean Monnet, Saint-Etienne F-42023, France
| | - Valérie Bin
- INSERM U1059, Dysfonction Vasculaire et Hémostase (DVH), Université Jean Monnet, Saint-Etienne F-42023, France
| | - Edouard Ollier
- INSERM U1059, Dysfonction Vasculaire et Hémostase (DVH), Université Jean Monnet, Saint-Etienne F-42023, France
| | - Xavier Delavenne
- INSERM U1059, Dysfonction Vasculaire et Hémostase (DVH), Université Jean Monnet, Saint-Etienne F-42023, France.,Laboratoire de Pharmacologie Toxicologie Gaz du sang, CHU de Saint-Etienne, Saint-Etienne CS 82301, France
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6
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Baakdah F, Georges E. Epitope-specific IgG pools identify PfCRT monomer and homodimer polypeptides that are differentially phosphorylated at Ser 411 in Plasmodium falciparum. Biochem Biophys Res Commun 2021; 557:261-266. [PMID: 33894412 DOI: 10.1016/j.bbrc.2021.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/17/2022]
Abstract
The Plasmodium falciparum chloroquine resistance transporter (PfCRT) is a phospho-protein with three identified phosphorylation sites (Ser33, Ser411 and Thr416) at its cytosolic N- and C-termini. In this study, we report on the characterization of PfCRT anti-serum and show the presence of three epitope-specific immunoglobulin (IgG) pools (i.e., IgG-P1, P2, and P3), each recognizing a different epitope in PfCRT cytoplasmic C-terminal. IgG-P2 bound the heptapeptide sequence (408NEDSEGE414), including Ser411. The effect of Ser411 phosphorylation on the binding specificity of IgG-P2 was confirmed using heptapeptides and full-length PfCRT with substitutions of Ser411 with aspartic acid (phospho-serine mimic) and alanine residues. Moreover, using purified IgG-P2, we show the presence of PfCRT homodimer that has un-phosphorylated Ser411 and migrates with an apparent molecular mass of 90 kDa on SDS-PAGE. In addition, parasite lysates showed PfCRT to be more phosphorylated at Ser411 in CQ-sensitive (3D7) than CQ-resistant (Dd2-H) strains of P. falciparum. Taken together, the findings of this study suggest a role for Ser411 phosphorylation in PfCRT structure-function.
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Affiliation(s)
- Fadi Baakdah
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Québec, Canada
| | - Elias Georges
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Québec, Canada.
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7
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Linker Domains: Why ABC Transporters 'Live in Fragments no Longer'. Trends Biochem Sci 2019; 45:137-148. [PMID: 31839525 DOI: 10.1016/j.tibs.2019.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/30/2019] [Accepted: 11/13/2019] [Indexed: 11/20/2022]
Abstract
ATP-binding cassette (ABC) transporters are membrane proteins present in all kingdoms of life. We have considered the disordered region that connects the N- and C-terminal halves in many eukaryotic ABC transporters, allowing all four consensus functional domains to be linked. The recent availability of structures of ABC transporters containing linker regions has allowed us to identify the start and end points of the connectors as well as hinting at their localisation. We address questions such as: Where did the linker regions come from? Why do some ABC transporters have connectors and others not? What are the rules and roles of the linker regions? What are the consequences of mutations in these connector regions for disease in humans?
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8
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Abstract
Drug transporter proteins are critical to the distribution of a wide range of endogenous compounds and xenobiotics such as hormones, bile acids, peptides, lipids, sugars, and drugs. There are two classes of drug transporters- the solute carrier (SLC) transporters and ATP-binding cassette (ABC) transporters -which predominantly differ in the energy source utilized to transport substrates across a membrane barrier. Despite their hydrophobic nature and residence in the membrane bilayer, drug transporters have dynamic structures and adopt many conformations during the translocation process. Whereas there is significant literature evidence for the substrate specificity and structure-function relationship for clinically relevant drug transporters proteins, there is less of an understanding in the regulatory mechanisms that contribute to the functional expression of these proteins. Post-translational modifications have been shown to modulate drug transporter functional expression via a wide range of molecular mechanisms. These modifications commonly occur through the addition of a functional group (e.g. phosphorylation), a small protein (e.g. ubiquitination), sugar chains (e.g. glycosylation), or lipids (e.g. palmitoylation) on solvent accessible amino acid residues. These covalent additions often occur as a result of a signaling cascade and may be reversible depending on the type of modification and the intended fate of the signaling event. Here, we review the significant role in which post-translational modifications contribute to the dynamic regulation and functional consequences of SLC and ABC drug transporters and highlight recent progress in understanding their roles in transporter structure, function, and regulation.
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Affiliation(s)
- Lindsay C Czuba
- Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA
| | | | - Peter W Swaan
- Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
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9
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Santos JMLD, Vasconcelos JF, Frota GA, Ribeiro WLC, André WPP, Vieira LDS, Teixeira M, Bevilaqua CML, Monteiro JP. Haemonchus contortus β-tubulin isotype 1 gene F200Y and F167Y SNPs are both selected by ivermectin and oxfendazole treatments with differing impacts on anthelmintic resistance. Vet Parasitol 2017; 248:90-95. [DOI: 10.1016/j.vetpar.2017.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/13/2017] [Accepted: 11/06/2017] [Indexed: 11/15/2022]
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10
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Pokharel D, Roseblade A, Oenarto V, Lu JF, Bebawy M. Proteins regulating the intercellular transfer and function of P-glycoprotein in multidrug-resistant cancer. Ecancermedicalscience 2017; 11:768. [PMID: 29062386 PMCID: PMC5636210 DOI: 10.3332/ecancer.2017.768] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Indexed: 12/15/2022] Open
Abstract
Chemotherapy is an essential part of anticancer treatment. However, the overexpression of P-glycoprotein (P-gp) and the subsequent emergence of multidrug resistance (MDR) hampers successful treatment clinically. P-gp is a multidrug efflux transporter that functions to protect cells from xenobiotics by exporting them out from the plasma membrane to the extracellular space. P-gp inhibitors have been developed in an attempt to overcome P-gp-mediated MDR; however, lack of specificity and dose limiting toxicity have limited their effectiveness clinically. Recent studies report on accessory proteins that either directly or indirectly regulate P-gp expression and function and which are necessary for the establishment of the functional phenotype in cancer cells. This review discusses the role of these proteins, some of which have been recently proposed to comprise an interactive complex, and discusses their contribution towards MDR. We also discuss the role of other pathways and proteins in regulating P-gp expression in cells. The potential for these proteins as novel therapeutic targets provides new opportunities to circumvent MDR clinically.
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Affiliation(s)
- Deep Pokharel
- Discipline of Pharmacy, The Graduate School of Health, The University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Ariane Roseblade
- Discipline of Pharmacy, The Graduate School of Health, The University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Vici Oenarto
- Discipline of Pharmacy, The Graduate School of Health, The University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Jamie F Lu
- Discipline of Pharmacy, The Graduate School of Health, The University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Mary Bebawy
- Discipline of Pharmacy, The Graduate School of Health, The University of Technology Sydney, Sydney, NSW 2007, Australia.,Laboratory of Cancer Cell Biology and Therapeutics, The University of Technology Sydney, Sydney, NSW 2007, Australia
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11
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Sequences in Linker-1 domain of the multidrug resistance associated protein (MRP1 or ABCC1) bind to tubulin and their binding is modulated by phosphorylation. Biochem Biophys Res Commun 2016; 482:1001-1006. [PMID: 27908733 DOI: 10.1016/j.bbrc.2016.11.147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 11/27/2016] [Indexed: 11/22/2022]
Abstract
The multidrug resistant associated protein 1 (or MRP1, ABCC1) encodes two cytoplasmic linker domains (L0 and L1) composed of highly charged sequences with multiple protein kinase A/C phosphorylation sites. In this report we made use of the scanning peptide approach to identify MRP1 linker L1 (L1MRP1) interacting proteins. Scanning heptapeptides covering L1MRP1 126 amino acids (Ile846- Leu972) were synthesized and used in pull-down assays to isolate proteins from cell extracts (human multidrug resistant SCLC cell line; H69/AR). The results show four high affinity binding sequences in L1MRP1 domain [866FLRTYAST867; 906SAGKQLQRQLSSS912; 925ISRHHNSTA927 and 954AQTGQVKLSVYW959] that bound ∼55 kDa and 110 kDa polypeptides. The latter polypeptides were identified by mass spectrometry as α- and β-tubulin monomers and dimers. Western blotting with monoclonal antibodies to α- and β-tubulin proteins confirmed the mass-spectrometry results. Moreover, using recombinant full-length GST-Linker 1 fusion polypeptide (GST-L1MRP1), we confirmed the peptide scanning approach demonstrating specific binding of tubulin to GST-L1MRP1. Intriguingly, substitutions of serine residues in L1MRP1 by aspartic acid, but not alanine, abolished its binding to tubulin, suggesting that phosphorylation of Ser871, 915, 930, and 961 within L1MRP1 may modulate its binding to tubulin. Taken together, the results of this study suggest possible interaction between MRP1 and tubulin that is modulated by phosphorylation of specific sequences in the L1MRP1 domain.
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12
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Macrocyclic lactones and their relationship to the SNPs related to benzimidazole resistance. Mol Biochem Parasitol 2015; 201:128-34. [PMID: 26253426 DOI: 10.1016/j.molbiopara.2015.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/08/2015] [Accepted: 07/31/2015] [Indexed: 11/22/2022]
Abstract
Haemonchus contortus is an abomasal nematode of ruminants that is widely present across the world. Its ability to cause death of infected animals and rapidly develop anthelmintic resistance makes it a dangerous pathogen. Ivermectin (IVM) and moxidectin (MOX) are macrocyclic lactones (MLs). They have been successfully used to treat parasitic nematodes over the last three decades. A genetic association between IVM selection and single nucleotide polymorphisms (SNPs) on the β-tubulin isotype 1 gene was reported in H. contortus. These SNPs result in replacing phenylalanine (F, TTC) with tyrosine (Y, TAC) at position 167 or 200 on the β-tubulin protein. Recently we reported a direct interaction of IVM with α- and β-tubulin. It had been hypothesized that the SNPs (F167Y and F200Y) may change tubulin dynamics and directly affect IVM binding. The goal of the current study was to observe the effects of SNPs (F167Y and F200Y) on tubulin polymerization and IVM binding. It was also of interest to evaluate the differences between IVM and MOX on tubulin polymerization. We conclude that the SNPs cause no difference in the polymerization of wild and mutant tubulins. Furthermore, neither of the SNPs reduced IVM binding. Varying results were obtained in the degree of polymerization of parasitic and mammalian tubulin for IVM and MOX, i.e., the extent of polymerization was greater for IVM compared with MOX, for H. contortus tubulin, and vice versa for mammalian tubulin. Molecular modeling showed that IVM and MOX docked into the taxane binding pocket of both mammalian and parasitic wild type and mutant tubulins. However the binding was stronger for mammalian tubulin as compared to parasitic tubulin.
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13
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Ashraf S, Beech RN, Hancock MA, Prichard RK. Ivermectin binds to Haemonchus contortus tubulins and promotes stability of microtubules. Int J Parasitol 2015; 45:647-54. [DOI: 10.1016/j.ijpara.2015.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/27/2015] [Accepted: 03/30/2015] [Indexed: 11/16/2022]
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14
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Ma J, Biggin PC. Substrate versus inhibitor dynamics of P-glycoprotein. Proteins 2013; 81:1653-68. [PMID: 23670856 DOI: 10.1002/prot.24324] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/24/2013] [Accepted: 04/19/2013] [Indexed: 12/20/2022]
Abstract
By far the most studied multidrug resistance protein is P-glycoprotein. Despite recent structural data, key questions about its function remain. P-glycoprotein (P-gp) is flexible and undergoes large conformational changes as part of its function and in this respect, details not only of the export cycle, but also the recognition stage are currently lacking. Given the flexibility, molecular dynamics (MD) simulations provide an ideal tool to examine this aspect in detail. We have performed MD simulations to examine the behaviour of P-gp. In agreement with previous reports, we found that P-gp undergoes large conformational changes which tended to result in the nucleotide-binding domains coming closer together. In all simulations, the approach of the NBDs was asymmetrical in agreement with previous observations for other ABC transporter proteins. To validate the simulations, we make extensive comparison to previous cross-linking data. Our results show very good agreement with the available data. We then went on to compare the influence of inhibitor compounds bound with simulations of a substrate (daunorubicin) bound. Our results suggest that inhibitors may work by keeping the NBDs apart, thus preventing ATP-hydrolysis. On the other hand, repeat simulations of daunorubicin (substrate) in one particular binding pose suggest that the approach of the NBDs is not impaired and that the structure would be still be competent to perform ATP hydrolysis, thus providing a model for inhibition or substrate transport. Finally we compare the latter to earlier QSAR data to provide a model for the first part of substrate transport within P-gp.
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Affiliation(s)
- Jerome Ma
- Department of Biochemistry, Structural Bioinformatics and Computational Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
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15
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Ferreira RJ, Ferreira MJU, Dos Santos DJVA. Assessing the Stabilization of P-Glycoprotein's Nucleotide-Binding Domains by the Linker, Using Molecular Dynamics. Mol Inform 2013; 32:529-40. [PMID: 27481670 DOI: 10.1002/minf.201200175] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 04/17/2012] [Indexed: 01/25/2023]
Abstract
This paper focuses on the importance of the intermediate linker sequence for the stabilization of the cytoplasmic portion of murine P-glycoprotein, an ABC transporter involved in Multidrug Resistance (MDR) in cancer. Three putative protein-protein interaction areas were predicted to exist, two of them next to the C-terminal nucleotide-binding domain (NBD2) and the third one next to the inner leaflet interface of the lipid bilayer. These contact spots were confirmed by detailed contact maps from structures obtained before and after a 100 ns molecular dynamics production run, allowing a more thorough characterization of the type and number of residues involved in protein-protein contacts. It was found that these contact surfaces are located next to several highly conserved motifs of ABC transporters, serving as anchor points and assisting the linker's 'damper' function.
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Affiliation(s)
- Ricardo J Ferreira
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Medicinal Chemistry, Av. Prof. Gama Pinto, Lisbon, Portugal phone: 217946400; fax: 217946470
| | - Maria-José U Ferreira
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Medicinal Chemistry, Av. Prof. Gama Pinto, Lisbon, Portugal phone: 217946400; fax: 217946470
| | - Daniel J V A Dos Santos
- Research Institute for Medicines and Pharmaceutical Sciences (iMed.UL), Medicinal Chemistry, Av. Prof. Gama Pinto, Lisbon, Portugal phone: 217946400; fax: 217946470. .,Faculty of Sciences, University of Porto, REQUIMTE, Department of Chemistry and Biochemistry, Porto, Portugal.
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16
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Suo SB, Qiu JD, Shi SP, Sun XY, Huang SY, Chen X, Liang RP. Position-specific analysis and prediction for protein lysine acetylation based on multiple features. PLoS One 2012; 7:e49108. [PMID: 23173045 PMCID: PMC3500252 DOI: 10.1371/journal.pone.0049108] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 10/04/2012] [Indexed: 11/17/2022] Open
Abstract
Protein lysine acetylation is a type of reversible post-translational modification that plays a vital role in many cellular processes, such as transcriptional regulation, apoptosis and cytokine signaling. To fully decipher the molecular mechanisms of acetylation-related biological processes, an initial but crucial step is the recognition of acetylated substrates and the corresponding acetylation sites. In this study, we developed a position-specific method named PSKAcePred for lysine acetylation prediction based on support vector machines. The residues around the acetylation sites were selected or excluded based on their entropy values. We incorporated features of amino acid composition information, evolutionary similarity and physicochemical properties to predict lysine acetylation sites. The prediction model achieved an accuracy of 79.84% and a Matthews correlation coefficient of 59.72% using the 10-fold cross-validation on balanced positive and negative samples. A feature analysis showed that all features applied in this method contributed to the acetylation process. A position-specific analysis showed that the features derived from the critical neighboring residues contributed profoundly to the acetylation site determination. The detailed analysis in this paper can help us to understand more of the acetylation mechanism and can provide guidance for the related experimental validation.
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Affiliation(s)
- Sheng-Bao Suo
- Department of Chemistry, Nanchang University, Nanchang, China
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17
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Yang Y, Li Z, Mo W, Ambadipudi R, Arnold RJ, Hrncirova P, Novotny MV, Georges E, Zhang JT. Human ABCC1 interacts and colocalizes with ATP synthase α, revealed by interactive proteomics analysis. J Proteome Res 2012; 11:1364-72. [PMID: 22188235 DOI: 10.1021/pr201003g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Human ABCC1 is a member of the ATP-binding cassette (ABC) transporter superfamily, and its overexpression has been shown to cause multidrug resistance by active efflux of a wide variety of anticancer drugs. ABCC1 has been shown to exist and possibly function as a homodimer. However, a possible heterocomplex involving ABCC1 has been indicated. In this study, we performed an interactive proteomics study to examine proteins that bind to and form heterocomplexes with ABCC1 using coimmunoprecipitation and tandem mass spectrometry (MS/MS) analyses. We found that ATP synthase α binds to ABCC1 in plasma membranes with a ratio of 2:1. The ATP synthase α binding site in ABCC1 is located in the linker domain at the carboxyl core of ABCC1, and phosphorylation of the linker domain at the protein kinase A site enhances ATP synthase α binding. The interaction between ABCC1 and ATP synthase α in a heterocomplex may indicate a novel function of ABCC1 in regulating extracellular ATP level and purinergic signaling cascade.
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Affiliation(s)
- Youyun Yang
- Department of Pharmacology and Toxicology and IU Simon Cancer Center, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
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18
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Lespine A, Ménez C, Bourguinat C, Prichard RK. P-glycoproteins and other multidrug resistance transporters in the pharmacology of anthelmintics: Prospects for reversing transport-dependent anthelmintic resistance. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2011; 2:58-75. [PMID: 24533264 DOI: 10.1016/j.ijpddr.2011.10.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 10/11/2011] [Accepted: 10/13/2011] [Indexed: 12/24/2022]
Abstract
Parasitic helminths cause significant disease in animals and humans. In the absence of alternative treatments, anthelmintics remain the principal agents for their control. Resistance extends to the most important class of anthelmintics, the macrocyclic lactone endectocides (MLs), such as ivermectin, and presents serious problems for the livestock industries and threatens to severely limit current parasite control strategies in humans. Understanding drug resistance is important for optimizing and monitoring control, and reducing further selection for resistance. Multidrug resistance (MDR) ABC transporters have been implicated in ML resistance and contribute to resistance to a number of other anthelmintics. MDR transporters, such as P-glycoproteins, are essential for many cellular processes that require the transport of substrates across cell membranes. Being overexpressed in response to chemotherapy in tumour cells and to ML-based treatment in nematodes, they lead to therapy failure by decreasing drug concentration at the target. Several anthelmintics are inhibitors of these efflux pumps and appropriate combinations can result in higher treatment efficacy against parasites and reversal of resistance. However, this needs to be balanced against possible increased toxicity to the host, or the components of the combination selecting on the same genes involved in the resistance. Increased efficacy could result from modifying anthelmintic pharmacokinetics in the host or by blocking parasite transporters involved in resistance. Combination of anthelmintics can be beneficial for delaying selection for resistance. However, it should be based on knowledge of resistance mechanisms and not simply on mode of action classes, and is best started before resistance has been selected to any member of the combination. Increasing knowledge of the MDR transporters involved in anthelmintic resistance in helminths will play an important role in allowing for the identification of markers to monitor the spread of resistance and to evaluate new tools and management practices aimed at delaying its spread.
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Affiliation(s)
- Anne Lespine
- INRA UMR1331, Université de Toulouse, INP, TOXALIM, F-31027 Toulouse, France
| | - Cécile Ménez
- INRA UMR1331, Université de Toulouse, INP, TOXALIM, F-31027 Toulouse, France
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19
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Ferrándiz-Huertas C, Fernández-Carvajal A, Ferrer-Montiel A. Rab4 interacts with the human P-glycoprotein and modulates its surface expression in multidrug resistant K562 cells. Int J Cancer 2010; 128:192-205. [PMID: 20209493 DOI: 10.1002/ijc.25310] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
P-glycoprotein (P-gp) is a plasma membrane glycoprotein that has been signaled as a primary cause of multidrug resistance (MDR) in tumors. We performed a yeast 2-hybrid screen using the C-terminal domain of P-gp and identified 2 small GTPases involved in vesicular trafficking, Rab4 and Rab14, which complex with P-gp. The overexpression of GFP-Rab4, either transiently or stably, but not of Rab14, in K562ADR cells decreased the presence of P-gp in the cell surface. As a result, expression of this GTPase reduced the MDR phenotype of K562ADR cells, by augmenting the intracellular accumulation of daunomycin (DNM). This effect was mimicked by the constitutively active Rab4Q72L mutant, but not by the dominant negative Rab4S27N mutant. Rab4 regulated excocytotic P-gp trafficking to the plasma membrane from intracellular compartments, and this modulation required the interaction of both proteins and the GTPase activity. Noteworthy, K562ADR cells exhibited a significant reduction of Rab4 levels, but not of other Rab GTPases, as compared with the sensitive parental cell line, suggesting that the development of the MDR phenotype in these cells involves upregulation of P-gp and a concomitant downregulation of proteins that regulate its surface expression. Attenuation of endogenous Rab4 levels in K562ADR by RNA interference enhanced the expression of P-gp in the cell surface, and reduced the uptake of DNM. Accordingly, these findings substantiate the notion that modulation of the temporal and spatial distribution of P-gp in cancer cells may be a valid therapeutic strategy to alleviate the MDR phenotype, and signal to Rab4 as a potential target.
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Affiliation(s)
- Clotilde Ferrándiz-Huertas
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Av de la Universidad s/n, 03202 Elche, Alicante, Spain
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20
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MDR1 function is sensitive to the phosphorylation state of myosin regulatory light chain. Biochem Biophys Res Commun 2010; 398:7-12. [PMID: 20510202 DOI: 10.1016/j.bbrc.2010.05.084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 05/14/2010] [Indexed: 11/24/2022]
Abstract
Multiple drug resistance protein 1 (MDR1) is composed of two homologous halves separated by an intracellular linker region. The linker has been reported to bind myosin regulatory light chain (RLC), but it is not clear how this can occur in the context of a myosin II complex. We characterized MDR1-RLC interactions and determined that binding occurs via the amino terminal of the RLC, a domain that typically binds myosin heavy chain. MDR1-RLC interactions were sensitive to the phosphorylation state of the light chain in that phosphorylation by myosin light chain kinase (MLCK) resulted in a loss of binding in vitro. We used ML-7, a specific inhibitor of MLCK, to study the functional consequences of disrupting RLC phosphorylation in intact cells. Pretreatment of polarized Madin-Darby canine kidney cells stably expressing MDR1 with ML-7 produced a significant increase in apical to basal permeability and a corresponding decrease in the efflux ratio (threefold; p<0.01) of [(3)H]-digoxin, a classic MDR1 substrate. Together these data show that MDR1-mediated transport of [(3)H]-digoxin can be modulated by pharmacological manipulation of myosin RLC, but direct MDR1-RLC interactions are atypical and not explained by the structure of the myosin II holoenzyme.
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21
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Yang ZR. Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy. BMC Bioinformatics 2009; 10:361. [PMID: 19874585 PMCID: PMC2777180 DOI: 10.1186/1471-2105-10-361] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 10/29/2009] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Tyrosine sulfation is one of the most important posttranslational modifications. Due to its relevance to various disease developments, tyrosine sulfation has become the target for drug design. In order to facilitate efficient drug design, accurate prediction of sulfotyrosine sites is desirable. A predictor published seven years ago has been very successful with claimed prediction accuracy of 98%. However, it has a particularly low sensitivity when predicting sulfotyrosine sites in some newly sequenced proteins. RESULTS A new approach has been developed for predicting sulfotyrosine sites using the random forest algorithm after a careful evaluation of seven machine learning algorithms. Peptides are formed by consecutive residues symmetrically flanking tyrosine sites. They are then encoded using an amino acid hydrophobicity scale. This new approach has increased the sensitivity by 22%, the specificity by 3%, and the total prediction accuracy by 10% compared with the previous predictor using the same blind data. Meanwhile, both negative and positive predictive powers have been increased by 9%. In addition, the random forest model has an excellent feature for ranking the residues flanking tyrosine sites, hence providing more information for further investigating the tyrosine sulfation mechanism. A web tool has been implemented at http://ecsb.ex.ac.uk/sulfotyrosine for public use. CONCLUSION The random forest algorithm is able to deliver a better model compared with the Hidden Markov Model, the support vector machine, artificial neural networks, and others for predicting sulfotyrosine sites. The success shows that the random forest algorithm together with an amino acid hydrophobicity scale encoding can be a good candidate for peptide classification.
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Affiliation(s)
- Zheng Rong Yang
- School of Biosciences, University of Exeter, Exeter EX4 5DE, UK.
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22
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Sato T, Kodan A, Kimura Y, Ueda K, Nakatsu T, Kato H. Functional role of the linker region in purified human P-glycoprotein. FEBS J 2009; 276:3504-16. [PMID: 19490125 DOI: 10.1111/j.1742-4658.2009.07072.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human P-glycoprotein (P-gp), which conveys multidrug resistance, is an ATP-dependent drug efflux pump that transports a wide variety of structurally unrelated compounds out of cells. P-gp possesses a 'linker region' of approximately 75 amino acids that connects two homologous halves, each of which contain a transmembrane domain followed by a nucleotide-binding domain. To investigate the role of the linker region, purified human P-gp was cleaved by proteases at the linker region and then compared with native P-gp. Based on a verapamil-stimulated ATP hydrolase assay, size-exclusion chromatography analysis and a thermo-stability assay, cleavage of the P-gp linker did not directly affect the preservation of the overall structure or the catalytic process in ATP hydrolysis. However, linker cleavage increased the k(cat) values both with substrate (k(sub)) and without substrate (k(basal)), but decreased the k(sub)/k(basal) values of all 10 tested substrates. The former result indicates that cleaving the linker activates P-gp, while the latter result suggests that the linker region maintains the tightness of coupling between the ATP hydrolase reaction and substrate recognition. Inspection of structures of the P-gp homolog, MsbA, suggests that linker-cleaved P-gp has increased ATP hydrolase activity because the linker interferes with a conformational change that accompanies the ATP hydrolase reaction. Moreover, linker cleavage affected the specificity constants [k(sub)/K(m(D))] for some substrates (i.e. linker cleavage probably shifts the substrate specificity profile of P-gp). Thus, this result also suggests that the linker region regulates the inherent substrate specificity of P-gp.
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Affiliation(s)
- Tomomi Sato
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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23
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Wolff J. Plasma membrane tubulin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1415-33. [PMID: 19328773 DOI: 10.1016/j.bbamem.2009.03.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/13/2009] [Accepted: 03/19/2009] [Indexed: 01/17/2023]
Abstract
The association of tubulin with the plasma membrane comprises multiple levels of penetration into the bilayer: from integral membrane protein, to attachment via palmitoylation, to surface binding, and to microtubules attached by linker proteins to proteins in the membrane. Here we discuss the soundness and weaknesses of the chemical and biochemical evidence marshaled to support these associations, as well as the mechanisms by which tubulin or microtubules may regulate functions at the plasma membrane.
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Affiliation(s)
- J Wolff
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Genetic analysis of a relationship between macrocyclic lactone and benzimidazole anthelmintic selection on Haemonchus contortus. Pharmacogenet Genomics 2008; 18:129-40. [DOI: 10.1097/fpc.0b013e3282f4711d] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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