1
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Watterson JG. The cluster model of energy transduction in biological systems. Biosystems 2024; 240:105213. [PMID: 38616011 DOI: 10.1016/j.biosystems.2024.105213] [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: 12/19/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
The central problem in transduction is to explain how the energy caught from sunlight by chloroplasts becomes biological work. Or to express it in different terms: how does the energy remain trapped in the biological network and not get lost through thermalization into the environment? The pathway consists of an immensely large number of steps crossing hierarchical levels - some upwards, to larger assemblies, others downwards into energy rich molecules - before fuelling an action potential or a contracting cell. Accepting the assumption that steps are executed by protein domains, we expect that transduction mechanisms are the result of conformational changes, which in turn involve rearrangements of the bonds responsible for the protein fold. But why are these essential changes so difficult to detect? In this presentation, the metabolic pathway is viewed as equivalent to an energy conduit composed of equally sized units - the protein domains - rather than a row of catalysts. The flow of energy through them occurs by the same mechanism as through the cytoplasmic medium (water). This mechanism is based on the cluster-wave model of water structure, which successfully explains the transfer of energy through the liquid medium responsible for the build up of osmotic pressure. The analogy to the line of balls called "Newton's cradle" provides a useful comparison, since there the transfer is also invisible to us because the intermediate balls are motionless. It is further proposed that the spatial arrangements of the H-bonds of the α and β secondary structures support wave motion, with the linear and lateral forms of the groups of bonds belonging to the helices and sheets executing the longitudinal and transverse modes, respectively.
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2
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George AM. ABC Transporters 45 Years On. Int J Mol Sci 2023; 24:16789. [PMID: 38069112 PMCID: PMC10706759 DOI: 10.3390/ijms242316789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
ABC transporters constitute one of the largest gene families among all species [...].
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Affiliation(s)
- Anthony M George
- School of Life Sciences, University of Technology, Sydney, NSW 2007, Australia
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3
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Hu P, Liu Y, Zhu X, Kang H. ABCC Transporter Gene MoABC-R1 Is Associated with Pyraclostrobin Tolerance in Magnaporthe oryzae. J Fungi (Basel) 2023; 9:917. [PMID: 37755025 PMCID: PMC10532721 DOI: 10.3390/jof9090917] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023] Open
Abstract
Rice blast is a worldwide fungal disease that poses a threat to food security. Fungicide treatment is one of the most effective methods to control rice blast disease. However, the emergence of fungicide tolerance hampers the control efforts against rice blast. ATP-binding cassette (ABC) transporters have been found to be crucial in multidrug tolerance in various phytopathogenic fungi. This study investigated the association between polymorphisms in 50 ABC transporters and pyraclostrobin sensitivity in 90 strains of rice blast fungus. As a result, we identified MoABC-R1, a gene associated with fungicide tolerance. MoABC-R1 belongs to the ABCC-type transporter families. Deletion mutants of MoABC-R1, abc-r1, exhibited high sensitivity to pyraclostrobin at the concentration of 0.01 μg/mL. Furthermore, the pathogenicity of abc-r1 was significantly diminished. These findings indicate that MoABC-R1 not only plays a pivotal role in fungicide tolerance but also regulates the pathogenicity of rice blast. Interestingly, the combination of MoABC-R1 deletion with fungicide treatment resulted in a three-fold increase in control efficiency against rice blast. This discovery highlights MoABC-R1 as a potential target gene for the management of rice blast.
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Affiliation(s)
| | | | | | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (P.H.); (Y.L.); (X.Z.)
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4
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Mann D, Labudda K, Zimmermann S, Vocke KU, Gasper R, Kötting C, Hofmann E. ATP binding and ATP hydrolysis in full-length MsbA monitored via time-resolved Fourier transform infrared spectroscopy. Biol Chem 2023:hsz-2023-0122. [PMID: 37185095 DOI: 10.1515/hsz-2023-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
The essential Escherichia coli ATPase MsbA is a lipid flippase that serves as a prototype for multi drug resistant ABC transporters. Its physiological function is the transport of lipopolisaccharides to build up the outer membranes of gram negative bacteria. Although several structural and biochemical studies of MsbA have been conducted previously, a detailed picture of the dynamic processes that link ATP hydrolysis to allocrit transport remains elusive. We report here for the first time time-resolved Fourier transform infrared (FTIR) spectroscopic measurements of the ATP binding and ATP hydrolysis reaction of full-length MsbA and determined reaction rates at 288 K of k 1 = 0.49 ± 0.28 s-1 and k 2 = 0.014 ± 0.003 s-1, respectively. We further verified these rates with photocaged NPEcgAppNHp where only nucleotide binding was observable and the negative mutant MsbA-H537A that showed slow hydrolysis (k 2 < 2 × 10-4 s-1). Besides single turnover kinetics, FTIR measurements also deliver IR signatures of all educts, products and the protein. ADP remains protein-bound after ATP hydrolysis. In addition, the spectral changes observed for the two variants MsbA-S378A and MsbA-S482A correlated with the loss of hydrogen bonding to the γ-phosphate of ATP. This study paves the way for FTIR-spectroscopic investigations of allocrite transport in full-length MsbA.
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Affiliation(s)
- Daniel Mann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Forschungszentrum Jülich GmbH, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons / ER-C-3: Structural Biology, D-52425 Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute for Biological Information Processing / IBI-6 Cellular Structural Biology, D-52425 Jülich, Germany
| | - Kristin Labudda
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Sophie Zimmermann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Kai Ulrich Vocke
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Raphael Gasper
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Max Planck Institute of Molecular Physiology, Crystallography and Biophysics Facility, D-44227 Dortmund, Germany
| | - Carsten Kötting
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Eckhard Hofmann
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
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5
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Martins I, Mateus C, Domingues F, Oleastro M, Ferreira S. Putative Role of an ABC Efflux System in Aliarcobacter butzleri Resistance and Virulence. Antibiotics (Basel) 2023; 12:antibiotics12020339. [PMID: 36830250 PMCID: PMC9951867 DOI: 10.3390/antibiotics12020339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/22/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Aliarcobacter butzleri is considered a ubiquitous microorganism and emergent pathogen, for which increasing rates of multidrug resistance have been described. In line with this, the present work aimed to evaluate for the first time the contribution of an ABC efflux system, the YbhFSR, in the resistance and virulence of this bacterium. Following the in silico characterization of the YbhFSR transporter, a mutant strain was constructed by inactivating the gene responsible for ATP-binding. After ensuring that the mutation did not have an impact on bacterial growth, the resistance profile of parental and mutant strains to different antimicrobial agents was evaluated. The results suggest that the efflux pump may influence the resistance to benzalkonium chloride, ethidium bromide, and cadmium, and several other compounds were identified as potential substrates. Regarding the evaluation of the accumulation of ethidium bromide, a slight increase was observed for the mutant strain, demonstrating a potential role of the YbhFSR efflux pump in the extrusion of toxic compounds from A. butzleri. Subsequently, the role of this efflux pump on the A. butzleri known virulence properties was evaluated, but no difference was seen among mutant and parental strains for the motility, biofilm formation ability, susceptibility to oxidative stress, or the ability to adhere and invade Caco-2 cells. However, in contrast to the parental strain, the mutant strain showed a resistance to human serum. Overall, the results support the role of efflux pumps in A. butzleri resistance to antimicrobials, highlighting the particular role of the YbhFSR system.
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Affiliation(s)
- Inês Martins
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
| | - Cristiana Mateus
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
| | - Fernanda Domingues
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - Susana Ferreira
- CICS-UBI—Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
- Correspondence:
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6
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Alves E, Nakaya H, Guimarães E, Garcia CR. Combining IP 3 affinity chromatography and bioinformatics reveals a novel protein-IP 3 binding site on Plasmodium falciparum MDR1 transporter. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 4:100179. [PMID: 36582189 PMCID: PMC9792294 DOI: 10.1016/j.crmicr.2022.100179] [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] [Indexed: 12/23/2022] Open
Abstract
Intracellular Ca2+ mobilization induced by second messenger IP3 controls many cellular events in most of the eukaryotic groups. Despite the increasing evidence of IP3-induced Ca2+ in apicomplexan parasites like Plasmodium, responsible for malaria infection, no protein with potential function as an IP3-receptor has been identified. The use of bioinformatic analyses based on previously known sequences of IP3-receptor failed to identify potential IP3-receptor candidates in any Apicomplexa. In this work, we combine the biochemical approach of an IP3 affinity chromatography column with bioinformatic meta-analyses to identify potential vital membrane proteins that present binding with IP3 in Plasmodium falciparum. Our analyses reveal that PF3D7_0523000, a gene that codes a transport protein associated with multidrug resistance as a potential target for IP3. This work provides a new insight for probing potential candidates for IP3-receptor in Apicomplexa.
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Affiliation(s)
- Eduardo Alves
- Life Science Department, Imperial College London, London, United Kingdom
| | - Helder Nakaya
- Department of Clinical and Toxicological Analyses of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil,Computational Systems Biology Laboratory, INOVA, University of Sao Paulo, Sao Paulo, Brazil
| | - Euzébio Guimarães
- Federal University of Rio Grande do Norte, Pharmacy Department, Health Science Center, Natal, Brazil
| | - Célia R.S. Garcia
- Department of Clinical and Toxicological Analyses of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil,Corresponding author.
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7
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Frozen motion: how cryo-EM changes the way we look at ABC transporters. Trends Biochem Sci 2021; 47:136-148. [PMID: 34930672 DOI: 10.1016/j.tibs.2021.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022]
Abstract
ATP-binding cassette (ABC) transporters are widely present molecular machines that transfer substrates across the cell membrane. ABC transporters are involved in numerous physiological processes and are often clinical targets. Structural biology is fundamental to obtain the molecular details underlying ABC transporter function and suggest approaches to modulate it. Until recently, X-ray crystallography has been the only method capable of providing high-resolution structures of ABC transporters. However, modern cryo-electron microscopy (cryo-EM) opens entirely new ways of studying these dynamic membrane proteins. Cryo-EM enables analyses of targets that resist X-ray crystallography, challenging multicomponent complexes, and the exploration of conformational dynamics. These unique capacities have turned cryo-EM into the dominant technique for structural studies of membrane proteins, including ABC transporters.
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8
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Yeh HI, Yu YC, Kuo PL, Tsai CK, Huang HT, Hwang TC. Functional stability of CFTR depends on tight binding of ATP at its degenerate ATP-binding site. J Physiol 2021; 599:4625-4642. [PMID: 34411298 DOI: 10.1113/jp281933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/13/2021] [Indexed: 01/28/2023] Open
Abstract
Opening of the cystic fibrosis transmembrane conductance regulator (CFTR) channel is coupled to the motion of its two nucleotide-binding domains: they form a heterodimer sandwiching two functionally distinct ATP-binding sites (sites 1 and 2). While active ATP hydrolysis in site 2 triggers rapid channel closure, the functional role of stable ATP binding in the catalysis-incompetent (or degenerate) site 1, a feature conserved in many other ATP-binding cassette (ABC) transporter proteins, remains elusive. Here, we found that CFTR loses its prompt responsiveness to ATP after the channel is devoid of ATP for tens to hundreds of seconds. Mutants with weakened ATP binding in site 1 and the most prevalent disease-causing mutation, F508del, are more vulnerable to ATP depletion. In contrast, strengthening ligand binding in site 1 with N6 -(2-phenylethyl)-ATP, a high-affinity ATP analogue, or abolishing ATP hydrolysis in site 2 by the mutation D1370N, helps sustain a durable function of the otherwise unstable mutant channels. Thus, tight binding of ATP in the degenerate ATP-binding site is crucial to the functional stability of CFTR. Small molecules targeting site 1 may bear therapeutic potential to overcome the membrane instability of F508del-CFTR. KEY POINTS: During evolution, many ATP-binding cassette transporters - including the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel, whose dysfunction causes cystic fibrosis (CF) - lose the ability to hydrolyse ATP in one of the two ATP-binding sites. Here we show that tight ATP binding at this degenerate site in CFTR is central for maintaining the stable, robust function of normal CFTR. We also demonstrate that membrane instability of the most common CF-causing mutant, F508del-CFTR, can be rescued by strengthening ATP binding at CFTR's degenerate site. Our data thus explain an evolutionary puzzle and offer a potential therapeutic strategy for CF.
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Affiliation(s)
- Han-I Yeh
- Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO, 65211, USA.,Department of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ying-Chun Yu
- Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Pei-Lun Kuo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Kuang Tsai
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsin-Tuan Huang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tzyh-Chang Hwang
- Dalton Cardiovascular Research Center and Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO, 65211, USA.,Department of Pharmacology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
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9
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Bacterial Resistance to Antimicrobial Agents. Antibiotics (Basel) 2021; 10:antibiotics10050593. [PMID: 34067579 PMCID: PMC8157006 DOI: 10.3390/antibiotics10050593] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial pathogens as causative agents of infection constitute an alarming concern in the public health sector. In particular, bacteria with resistance to multiple antimicrobial agents can confound chemotherapeutic efficacy towards infectious diseases. Multidrug-resistant bacteria harbor various molecular and cellular mechanisms for antimicrobial resistance. These antimicrobial resistance mechanisms include active antimicrobial efflux, reduced drug entry into cells of pathogens, enzymatic metabolism of antimicrobial agents to inactive products, biofilm formation, altered drug targets, and protection of antimicrobial targets. These microbial systems represent suitable focuses for investigation to establish the means for their circumvention and to reestablish therapeutic effectiveness. This review briefly summarizes the various antimicrobial resistance mechanisms that are harbored within infectious bacteria.
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10
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Turner AM, Lee JYH, Gorrie CL, Howden BP, Carter GP. Genomic Insights Into Last-Line Antimicrobial Resistance in Multidrug-Resistant Staphylococcus and Vancomycin-Resistant Enterococcus. Front Microbiol 2021; 12:637656. [PMID: 33796088 PMCID: PMC8007764 DOI: 10.3389/fmicb.2021.637656] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/25/2021] [Indexed: 12/17/2022] Open
Abstract
Multidrug-resistant Staphylococcus and vancomycin-resistant Enterococcus (VRE) are important human pathogens that are resistant to most clinical antibiotics. Treatment options are limited and often require the use of 'last-line' antimicrobials such as linezolid, daptomycin, and in the case of Staphylococcus, also vancomycin. The emergence of resistance to these last-line antimicrobial agents is therefore of considerable clinical concern. This mini-review provides an overview of resistance to last-line antimicrobial agents in Staphylococcus and VRE, with a particular focus on how genomics has provided critical insights into the emergence of resistant clones, the molecular mechanisms of resistance, and the importance of mobile genetic elements in the global spread of resistance to linezolid.
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Affiliation(s)
- Adrianna M Turner
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash Health, Melbourne, VIC, Australia
| | - Claire L Gorrie
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Austin Health, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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11
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Khunweeraphong N, Kuchler K. The first intracellular loop is essential for the catalytic cycle of the human ABCG2 multidrug resistance transporter. FEBS Lett 2020; 594:4059-4075. [PMID: 33169382 PMCID: PMC7756363 DOI: 10.1002/1873-3468.13994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/03/2020] [Indexed: 12/16/2022]
Abstract
The human multidrug transporter ABCG2 is required for physiological detoxification and mediates anticancer drug resistance. Here, we identify pivotal residues in the first intracellular loop (ICL1), constituting an intrinsic part of the transmission interface. The architecture includes a triple helical bundle formed by the hot spot helix of the nucleotide‐binding domain, the elbow helix, and ICL1. We show here that the highly conserved ICL1 residues G462, Y463, and Y464 are essential for the proper cross talk of the closed nucleotide‐binding domain dimer with the transmembrane domains. Hence, ICL1 acts as a molecular spring, triggering the conformational switch of ABCG2 before substrate extrusion. These data suggest that the ABCG2 transmission interface may offer therapeutic options for the treatment of drug‐resistant malignancies.
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Affiliation(s)
- Narakorn Khunweeraphong
- Max Perutz Labs Vienna, Center for Medical Biochemistry, Campus Vienna Biocenter, Medical University of Vienna, Austria.,St. Anna Children's Cancer Research Institute-CCRI, Vienna, Austria
| | - Karl Kuchler
- Max Perutz Labs Vienna, Center for Medical Biochemistry, Campus Vienna Biocenter, Medical University of Vienna, Austria
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12
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Kohno M, Arakawa T, Sunagawa N, Mori T, Igarashi K, Nishimoto T, Fushinobu S. Molecular analysis of cyclic α-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway. PLoS One 2020; 15:e0241912. [PMID: 33211750 PMCID: PMC7676653 DOI: 10.1371/journal.pone.0241912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022] Open
Abstract
Cyclic α-maltosyl-(1→6)-maltose (CMM) is a cyclic glucotetrasaccharide with alternating α-1,4 and α-1,6 linkages. Here, we report functional and structural analyses on CMM-binding protein (CMMBP), which is a substrate-binding protein (SBP) of an ABC importer system of the bacteria Arthrobacter globiformis. Isothermal titration calorimetry analysis revealed that CMMBP specifically bound to CMM with a Kd value of 9.6 nM. The crystal structure of CMMBP was determined at a resolution of 1.47 Å, and a panose molecule was bound in a cleft between two domains. To delineate its structural features, the crystal structure of CMMBP was compared with other SBPs specific for carbohydrates, such as cyclic α-nigerosyl-(1→6)-nigerose and cyclodextrins. These results indicate that A. globiformis has a unique metabolic pathway specialized for CMM.
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Affiliation(s)
- Masaki Kohno
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- R&D Division, HAYASHIBARA CO., LTD., Okayama, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
| | - Tetsuya Mori
- R&D Division, HAYASHIBARA CO., LTD., Okayama, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
- * E-mail:
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13
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Mishra A, Dhiman S, George SJ. ATP‐Driven Synthetic Supramolecular Assemblies: From ATP as a Template to Fuel. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006614] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ananya Mishra
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
| | - Shikha Dhiman
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
| | - Subi J. George
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
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14
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Mishra A, Dhiman S, George SJ. ATP‐Driven Synthetic Supramolecular Assemblies: From ATP as a Template to Fuel. Angew Chem Int Ed Engl 2020; 60:2740-2756. [DOI: 10.1002/anie.202006614] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/09/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Ananya Mishra
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
| | - Shikha Dhiman
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
| | - Subi J. George
- Supramolecular Chemistry Laboratory New Chemistry Unit School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Bangalore 560064 India
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15
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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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16
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Remali J, Aizat WM, Ng CL, Lim YC, Mohamed-Hussein ZA, Fazry S. In silico analysis on the functional and structural impact of Rad50 mutations involved in DNA strand break repair. PeerJ 2020; 8:e9197. [PMID: 32509463 PMCID: PMC7247530 DOI: 10.7717/peerj.9197] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 04/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND DNA double strand break repair is important to preserve the fidelity of our genetic makeup after DNA damage. Rad50 is one of the components in MRN complex important for DNA repair mechanism. Rad50 mutations can lead to microcephaly, mental retardation and growth retardation in human. However, Rad50 mutations in human and other organisms have never been gathered and heuristically compared for their deleterious effects. It is important to assess the conserved region in Rad50 and its homolog to identify vital mutations that can affect functions of the protein. METHOD In this study, Rad50 mutations were retrieved from SNPeffect 4.0 database and literature. Each of the mutations was analyzed using various bioinformatic analyses such as PredictSNP, MutPred, SNPeffect 4.0, I-Mutant and MuPro to identify its impact on molecular mechanism, biological function and protein stability, respectively. RESULTS We identified 103 mostly occurred mutations in the Rad50 protein domains and motifs, which only 42 mutations were classified as most deleterious. These mutations are mainly situated at the specific motifs such as Walker A, Q-loop, Walker B, D-loop and signature motif of the Rad50 protein. Some of these mutations were predicted to negatively affect several important functional sites that play important roles in DNA repair mechanism and cell cycle signaling pathway, highlighting Rad50 crucial role in this process. Interestingly, mutations located at non-conserved regions were predicted to have neutral/non-damaging effects, in contrast with previous experimental studies that showed deleterious effects. This suggests that software used in this study may have limitations in predicting mutations in non-conserved regions, implying further improvement in their algorithm is needed. In conclusion, this study reveals the priority of acid substitution associated with the genetic disorders. This finding highlights the vital roles of certain residues such as K42E, C681A/S, CC684R/S, S1202R, E1232Q and D1238N/A located in Rad50 conserved regions, which can be considered for a more targeted future studies.
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Affiliation(s)
- Juwairiah Remali
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Yi Chieh Lim
- Danish Cancer Society, Research Centre Strand Boulevard, Copenhagen, Denmark
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Shazrul Fazry
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Pusat Penyelidikan Tasik Chini, Fakulti Sains dan Teknologi, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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17
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Feng Z, Liu D, Wang L, Wang Y, Zang Z, Liu Z, Song B, Gu L, Fan Z, Yang S, Chen J, Cui Y. A Putative Efflux Transporter of the ABC Family, YbhFSR, in Escherichia coli Functions in Tetracycline Efflux and Na +(Li +)/H + Transport. Front Microbiol 2020; 11:556. [PMID: 32390957 PMCID: PMC7190983 DOI: 10.3389/fmicb.2020.00556] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/16/2020] [Indexed: 12/20/2022] Open
Abstract
ATP-binding cassette transporters are ubiquitous in almost all organisms. The Escherichia coli genome is predicted to encode 69 ABC transporters. Eleven of the ABC transporters are presumed to be exporters, of which seven are possible drug export transporters. There has been minimal research on the function of YbhFSR, which is one of the putative drug resistance exporters. In this study, the ybhF gene of this transporter was characterized. Overexpression and knockout strains of ybhF were constructed. The ATPase activity of YbhF was studied using the malachite green assay, and the efflux abilities of knockout strains were demonstrated by using ethidium bromide (EB) as a substrate. The substrates of YbhFSR efflux, examined with the minimum inhibitory concentration (MIC), were determined to be tetracycline, oxytetracycline, chlortetracycline, doxycycline, EB, and Hoechst33342. Furthermore, tetracycline and EB efflux and accumulation experiments confirmed that the substrates of YbhFSR were tetracyclines and EB. The MIC assay and the fluorescence test results showed that tetracyclines are likely to be the major antibiotic substrate of YbhFSR. The existence of the signature NatA motif suggested that YbhFSR may also function as a Na+/H+ transporter. Overexpression of YbhF in E. coli KNabc lacking crucial Na+/H+ transporters conferred tolerance to NaCl, LiCl, and an alkaline pH. Together, the results showed that YbhFSR exhibited dual functions as a drug efflux pump and a Na+ (Li+)/H+ antiporter.
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Affiliation(s)
- Zhenyue Feng
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Defu Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Lizi Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yanhong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhongjing Zang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhenhua Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Baifen Song
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Liwei Gu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhaowei Fan
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Siyu Yang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jing Chen
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yudong Cui
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
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18
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Miyake M, Terada T, Shimokawa M, Sugimoto N, Arakawa T, Shimizu K, Igarashi K, Fujita K, Fushinobu S. Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum. FEBS J 2020; 287:5114-5129. [PMID: 32246585 DOI: 10.1111/febs.15315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/09/2020] [Accepted: 03/26/2020] [Indexed: 12/29/2022]
Abstract
Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for β-arabinooligosaccharides, which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for α-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting β-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the β-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-β1,2-Araf (β-Ara2 ) with a Kd of 0.150 μm, but did not bind L-arabinose or methyl-β-Ara2 . Therefore, the SBP was termed β-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with β-Ara2 were determined at resolutions of up to 1.78 Å. The findings showed that β-Ara2 was bound to BABP within a short tunnel between two lobes as an α-anomeric form at its reducing end. BABP forms extensive interactions with β-Ara2 , and its binding mode was unique among SBPs. A molecular dynamics simulation revealed that the closed conformation of substrate-bound BABP is stable, whereas substrate-free form can adopt a fully open and two distinct semi-open states. The importer system specific for β-Ara2 may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates. DATABASE: Atomic coordinates and structure factors (codes 6LCE and 6LCF) have been deposited in the Protein Data Bank (http://wwpdb.org/).
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Affiliation(s)
| | - Tohru Terada
- The Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | | | - Naohisa Sugimoto
- Department of Biomaterial Sciences, The University of Tokyo, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | | | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, The University of Tokyo, Japan.,VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
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19
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Mächtel R, Narducci A, Griffith DA, Cordes T, Orelle C. An integrated transport mechanism of the maltose ABC importer. Res Microbiol 2019; 170:321-337. [PMID: 31560984 PMCID: PMC6906923 DOI: 10.1016/j.resmic.2019.09.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/27/2022]
Abstract
ATP-binding cassette (ABC) transporters use the energy of ATP hydrolysis to transport a large diversity of molecules actively across biological membranes. A combination of biochemical, biophysical, and structural studies has established the maltose transporter MalFGK2 as one of the best characterized proteins of the ABC family. MalF and MalG are the transmembrane domains, and two MalKs form a homodimer of nucleotide-binding domains. A periplasmic maltose-binding protein (MalE) delivers maltose and other maltodextrins to the transporter, and triggers its ATPase activity. Substrate import occurs in a unidirectional manner by ATP-driven conformational changes in MalK2 that allow alternating access of the substrate-binding site in MalF to each side of the membrane. In this review, we present an integrated molecular mechanism of the transport process considering all currently available information. Furthermore, we summarize remaining inconsistencies and outline possible future routes to decipher the full mechanistic details of transport by MalEFGK2 complex and that of related importer systems.
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Affiliation(s)
- Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Douglas A Griffith
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany.
| | - Cédric Orelle
- Université de Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 passage du Vercors, 69367 Lyon, France.
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20
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Beis K, Rebuffat S. Multifaceted ABC transporters associated to microcin and bacteriocin export. Res Microbiol 2019; 170:399-406. [DOI: 10.1016/j.resmic.2019.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/12/2019] [Accepted: 07/17/2019] [Indexed: 12/30/2022]
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21
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Shvarev D, Maldener I. ATP-binding cassette transporters of the multicellular cyanobacterium Anabaena sp. PCC 7120: a wide variety for a complex lifestyle. FEMS Microbiol Lett 2019; 365:4817535. [PMID: 29360977 DOI: 10.1093/femsle/fny012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/18/2018] [Indexed: 01/29/2023] Open
Abstract
Two hundred genes or 3% of the known or putative protein-coding genes of the filamentous freshwater cyanobacterium Anabaena sp. PCC 7120 encode domains of ATP-binding cassette (ABC) transporters. Detailed characterization of some of these transporters (14-15 importers and 5 exporters) has revealed their crucial roles in the complex lifestyle of this multicellular photoautotroph, which is able to differentiate specialized cells for nitrogen fixation. This review summarizes the characteristics of the ABC transporters of Anabaena sp. PCC 7120 known to date.
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Affiliation(s)
- Dmitry Shvarev
- Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Iris Maldener
- Organismic Interactions, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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22
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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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23
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Arana MR, Altenberg GA. ATP-binding Cassette Exporters: Structure and Mechanism with a Focus on P-glycoprotein and MRP1. Curr Med Chem 2019; 26:1062-1078. [PMID: 29022498 DOI: 10.2174/0929867324666171012105143] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 08/03/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Proteins that belong to the ATP-binding cassette superfamily include transporters that mediate the efflux of substrates from cells. Among these exporters, P-glycoprotein and MRP1 are involved in cancer multidrug resistance, protection from endo and xenobiotics, determination of drug pharmacokinetics, and the pathophysiology of a variety of disorders. OBJECTIVE To review the information available on ATP-binding cassette exporters, with a focus on Pglycoprotein, MRP1 and related proteins. We describe tissue localization and function of these transporters in health and disease, and discuss the mechanisms of substrate transport. We also correlate recent structural information with the function of the exporters, and discuss details of their molecular mechanism with a focus on the nucleotide-binding domains. METHODS Evaluation of selected publications on the structure and function of ATP-binding cassette proteins. CONCLUSIONS Conformational changes on the nucleotide-binding domains side of the exporters switch the accessibility of the substrate-binding pocket between the inside and outside, which is coupled to substrate efflux. However, there is no agreement on the magnitude and nature of the changes at the nucleotide- binding domains side that drive the alternate-accessibility. Comparison of the structures of Pglycoprotein and MRP1 helps explain differences in substrate selectivity and the bases for polyspecificity. P-glycoprotein substrates are hydrophobic and/or weak bases, and polyspecificity is explained by a flexible hydrophobic multi-binding site that has a few acidic patches. MRP1 substrates are mostly organic acids, and its polyspecificity is due to a single bipartite binding site that is flexible and displays positive charge.
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Affiliation(s)
- Maite Rocío Arana
- Instituto de Fisiología Experimental, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 570, 2000 Rosario, Argentina
| | - Guillermo Alejandro Altenberg
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430-6551, United States
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24
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Jorda A, Cauli O, Santonja JM, Aldasoro M, Aldasoro C, Obrador E, Vila JM, Mauricio MD, Iradi A, Guerra-Ojeda S, Marchio P, Valles SL. Changes in Chemokines and Chemokine Receptors Expression in a Mouse Model of Alzheimer's Disease. Int J Biol Sci 2019; 15:453-463. [PMID: 30745834 PMCID: PMC6367555 DOI: 10.7150/ijbs.26703] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/21/2018] [Indexed: 11/18/2022] Open
Abstract
The amyloid precursor protein plus presenilin-1 (APP/PS1) mice are a frequently-used model for Alzheimer's disease studies (AD). However, the data relevant to which proteins are involved in inflammatory mechanism are not sufficiently well-studied using the AD mouse model. Using behavioral studies, quantitative RT-PCR and Western-blot techniques, significant findings were determined by the expression of proteins involved in inflammation comparing APP/PS1 and Wild type mice. Increased GFAP expression could be associated with the elevation in number of reactive astrocytes. IL-3 is involved in inflammation and ABDF1 intervenes normally in the transport across cell membranes and both were found up-regulated in APP/PS1 mice compared to Wild type mice. Furthermore, CCR5 expression was decreased and both CCL3 and CCL4 chemokines were highly expressed indicating a possible gliosis and probably an increase in chemotaxis from lymphocytes and T cell generation. We also noted for the first time, a CCR8 increase expression with diminution of its CCL1 chemokine, both normally involved in protection from bacterial infection and demyelination. Control of inflammatory proteins will be the next step in understanding the progression of AD and also in determining the mechanisms that can develop in this disease.
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Affiliation(s)
- Adrián Jorda
- Department of Physiology, School of Medicine, University of Valencia. Spain
| | - Omar Cauli
- Faculty of Surgery and Chiropody, University of Valencia. Spain
| | | | - Martin Aldasoro
- Department of Physiology, School of Medicine, University of Valencia. Spain
| | - Constanza Aldasoro
- Department of Physiology, School of Medicine, University of Valencia. Spain
| | - Elena Obrador
- Department of Physiology, School of Medicine, University of Valencia. Spain
| | - Jose Ma Vila
- Department of Physiology, School of Medicine, University of Valencia. Spain
| | | | - Antonio Iradi
- Department of Physiology, School of Medicine, University of Valencia. Spain
| | - Sol Guerra-Ojeda
- Department of Physiology, School of Medicine, University of Valencia. Spain
| | - Patricia Marchio
- Department of Physiology, School of Medicine, University of Valencia. Spain
| | - Soraya L Valles
- Department of Physiology, School of Medicine, University of Valencia. Spain
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25
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FK506 Resistance of Saccharomyces cerevisiae Pdr5 and Candida albicans Cdr1 Involves Mutations in the Transmembrane Domains and Extracellular Loops. Antimicrob Agents Chemother 2018; 63:AAC.01146-18. [PMID: 30348662 DOI: 10.1128/aac.01146-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
The 23-membered-ring macrolide tacrolimus, a commonly used immunosuppressant, also known as FK506, is a broad-spectrum inhibitor and an efflux pump substrate of pleiotropic drug resistance (PDR) ATP-binding cassette (ABC) transporters. Little, however, is known about the molecular mechanism by which FK506 inhibits PDR transporter drug efflux. Thus, to obtain further insights we searched for FK506-resistant mutants of Saccharomyces cerevisiae cells overexpressing either the endogenous multidrug efflux pump Pdr5 or its Candida albicans orthologue, Cdr1. A simple but powerful screen gave 69 FK506-resistant mutants with, between them, 72 mutations in either Pdr5 or Cdr1. Twenty mutations were in just three Pdr5/Cdr1 equivalent amino acid positions, T550/T540 and T552/S542 of extracellular loop 1 (EL1) and A723/A713 of EL3. Sixty of the 72 mutations were either in the ELs or the extracellular halves of individual transmembrane spans (TMSs), while 11 mutations were found near the center of individual TMSs, mostly in predicted TMS-TMS contact points, and only two mutations were in the cytosolic nucleotide-binding domains of Pdr5. We propose that FK506 inhibits Pdr5 and Cdr1 drug efflux by slowing transporter opening and/or substrate release, and that FK506 resistance of Pdr5/Cdr1 drug efflux is achieved by modifying critical intramolecular contact points that, when mutated, enable the cotransport of FK506 with other pump substrates. This may also explain why the 35 Cdr1 mutations that caused FK506 insensitivity of fluconazole efflux differed from the 13 Cdr1 mutations that caused FK506 insensitivity of cycloheximide efflux.
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26
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Prieß M, Göddeke H, Groenhof G, Schäfer LV. Molecular Mechanism of ATP Hydrolysis in an ABC Transporter. ACS CENTRAL SCIENCE 2018; 4:1334-1343. [PMID: 30410971 PMCID: PMC6202651 DOI: 10.1021/acscentsci.8b00369] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Indexed: 05/28/2023]
Abstract
Hydrolysis of nucleoside triphosphate (NTP) plays a key role for the function of many biomolecular systems. However, the chemistry of the catalytic reaction in terms of an atomic-level understanding of the structural, dynamic, and free energy changes associated with it often remains unknown. Here, we report the molecular mechanism of adenosine triphosphate (ATP) hydrolysis in the ATP-binding cassette (ABC) transporter BtuCD-F. Free energy profiles obtained from hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations show that the hydrolysis reaction proceeds in a stepwise manner. First, nucleophilic attack of an activated lytic water molecule at the ATP γ-phosphate yields ADP + HPO4 2- as intermediate product. A conserved glutamate that is located very close to the γ-phosphate transiently accepts a proton and thus acts as catalytic base. In the second step, the proton is transferred back from the catalytic base to the γ-phosphate, yielding ADP + H2PO4 -. These two chemical reaction steps are followed by rearrangements of the hydrogen bond network and the coordination of the Mg2+ ion. The rate constant estimated from the computed free energy barriers is in very good agreement with experiments. The overall free energy change of the reaction is close to zero, suggesting that phosphate bond cleavage itself does not provide a power stroke for conformational changes. Instead, ATP binding is essential for tight dimerization of the nucleotide-binding domains and the transition of the transmembrane domains from inward- to outward-facing, whereas ATP hydrolysis resets the conformational cycle. The mechanism is likely relevant for all ABC transporters and might have implications also for other NTPases, as many residues involved in nucleotide binding and hydrolysis are strictly conserved.
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Affiliation(s)
- Marten Prieß
- Theoretical
Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Hendrik Göddeke
- Theoretical
Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Gerrit Groenhof
- Department
of Chemistry and Nanoscience Center, University
of Jyväskylä, P.O. Box
35, FI-40014 Jyväskylä, Finland
| | - Lars V. Schäfer
- Theoretical
Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
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27
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The ABC Transporter Components HgdB and HgdC are Important for Glycolipid Layer Composition and Function of Heterocysts in Anabaena sp. PCC 7120. Life (Basel) 2018; 8:life8030026. [PMID: 30004454 PMCID: PMC6161253 DOI: 10.3390/life8030026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 06/21/2018] [Accepted: 06/28/2018] [Indexed: 12/13/2022] Open
Abstract
Anabaena sp. PCC 7120 is a filamentous cyanobacterium able to fix atmospheric nitrogen in semi-regularly spaced heterocysts. For correct heterocyst function, a special cell envelope consisting of a glycolipid layer and a polysaccharide layer is essential. We investigated the role of the genes hgdB and hgdC, encoding domains of a putative ABC transporter, in heterocyst maturation. We investigated the subcellular localization of the fusion protein HgdC-GFP and followed the differential expression of the hgdB and hgdC genes during heterocyst maturation. Using a single recombination approach, we created a mutant in hgdB gene and studied its phenotype by microscopy and analytical chromatography. Although heterocysts are formed in the mutant, the structure of the glycolipid layer is aberrant and also contains an atypical ratio of the two major glycolipids. As shown by a pull-down assay, HgdB interacts with the outer membrane protein TolC, which indicates a function as a type 1 secretion system. We show that the hgdB-hgdC genes are essential for the creation of micro-oxic conditions by influencing the correct composition of the glycolipid layer for heterocyst function. Our observations confirm the significance of the hgdB-hgdC gene cluster and shed light on a novel mode of regulation of heterocyst envelope formation.
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28
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Göddeke H, Timachi MH, Hutter CAJ, Galazzo L, Seeger MA, Karttunen M, Bordignon E, Schäfer LV. Atomistic Mechanism of Large-Scale Conformational Transition in a Heterodimeric ABC Exporter. J Am Chem Soc 2018; 140:4543-4551. [DOI: 10.1021/jacs.7b12944] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hendrik Göddeke
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - M. Hadi Timachi
- EPR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Cedric A. J. Hutter
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland
| | - Laura Galazzo
- EPR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Markus A. Seeger
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland
| | - Mikko Karttunen
- Department of Chemistry and Department of Applied Mathematics, Western University, London, Ontario N6A 3K7, Canada
| | - Enrica Bordignon
- EPR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Lars V. Schäfer
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
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29
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Karasik A, Ledwitch KV, Arányi T, Váradi A, Roberts A, Szeri F. Boosted coupling of ATP hydrolysis to substrate transport upon cooperative estradiol-17-β-D-glucuronide binding in a Drosophila ATP binding cassette type-C transporter. FASEB J 2018; 32:669-680. [PMID: 28939593 DOI: 10.1096/fj.201700606r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ATP binding cassette type-C (ABCC) transporters move molecules across cell membranes upon hydrolysis of ATP; however, their coupling of ATP hydrolysis to substrate transport remains elusive. Drosophila multidrug resistance-associated protein (DMRP) is the functional ortholog of human long ABCC transporters, with similar substrate and inhibitor specificity, but higher activity. Exploiting its high activity, we kinetically dissected the catalytic mechanism of DMRP by using E2-d-glucuronide (E2G), the physiologic substrate of human ABCC. We examined the DMRP-mediated interdependence of ATP and E2G in biochemical assays. We observed E2G-dependent ATPase activity to be biphasic at subsaturating ATP concentrations, which implies at least 2 E2G binding sites on DMRP. Furthermore, transport measurements indicated strong nonreciprocal cooperativity between ATP and E2G. In addition to confirming these findings, our kinetic modeling with the Complex Pathway Simulator indicated a 10-fold decrease in the E2G-mediated activation of ATP hydrolysis upon saturation of the second E2G binding site. Surprisingly, the binding of the second E2G allowed for substrate transport with a constant rate, which tightly coupled ATP hydrolysis to transport. In summary, we show that the second E2G binding-similar to human ABCC2-allosterically stimulates transport activity of DMRP. Our data suggest that this is achieved by a significant increase in the coupling of ATP hydrolysis to transport.-Karasik, A., Ledwitch, K. V., Arányi, T., Váradi, A., Roberts, A., Szeri, F. Boosted coupling of ATP hydrolysis to substrate transport upon cooperative estradiol-17-β-D-glucuronide binding in a Drosophila ATP binding cassette type-C transporter.
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Affiliation(s)
- Agnes Karasik
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | | | - Tamás Arányi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - András Váradi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Arthur Roberts
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, USA
| | - Flóra Szeri
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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30
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Szöllősi D, Rose-Sperling D, Hellmich UA, Stockner T. Comparison of mechanistic transport cycle models of ABC exporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:818-832. [PMID: 29097275 PMCID: PMC7610611 DOI: 10.1016/j.bbamem.2017.10.028] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 12/25/2022]
Abstract
ABC (ATP binding cassette) transporters, ubiquitous in all kingdoms of life, carry out essential substrate transport reactions across cell membranes. Their transmembrane domains bind and translocate substrates and are connected to a pair of nucleotide binding domains, which bind and hydrolyze ATP to energize import or export of substrates. Over four decades of investigations into ABC transporters have revealed numerous details from atomic-level structural insights to their functional and physiological roles. Despite all these advances, a comprehensive understanding of the mechanistic principles of ABC transporter function remains elusive. The human multidrug resistance transporter ABCB1, also referred to as P-glycoprotein (P-gp), is one of the most intensively studied ABC exporters. Using ABCB1 as the reference point, we aim to compare the dominating mechanistic models of substrate transport and ATP hydrolysis for ABC exporters and to highlight the experimental and computational evidence in their support. In particular, we point out in silico studies that enhance and complement available biochemical data. “This article is part of a Special Issue entitled: Beyond the Structure Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.”
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Affiliation(s)
- Dániel Szöllősi
- Medical University of Vienna, Institute of Pharmacology, Waehringerstr. 13A, Vienna 1090, Austria
| | - Dania Rose-Sperling
- Johannes Gutenberg-University, Department of Pharmacy and Biochemistry, Johann-Joachim-Becher-Weg 30, Mainz 55128, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Ute A Hellmich
- Johannes Gutenberg-University, Department of Pharmacy and Biochemistry, Johann-Joachim-Becher-Weg 30, Mainz 55128, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Thomas Stockner
- Medical University of Vienna, Institute of Pharmacology, Waehringerstr. 13A, Vienna 1090, Austria.
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31
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Khunweeraphong N, Stockner T, Kuchler K. The structure of the human ABC transporter ABCG2 reveals a novel mechanism for drug extrusion. Sci Rep 2017; 7:13767. [PMID: 29061978 PMCID: PMC5653816 DOI: 10.1038/s41598-017-11794-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/31/2017] [Indexed: 12/13/2022] Open
Abstract
The human ABC transporter ABCG2 (Breast Cancer Resistance Protein, BCRP) is implicated in anticancer resistance, in detoxification across barriers and linked to gout. Here, we generate a novel atomic model of ABCG2 using the crystal structure of ABCG5/G8. Extensive mutagenesis verifies the structure, disclosing hitherto unrecognized essential residues and domains in the homodimeric ABCG2 transporter. The elbow helix, the first intracellular loop (ICL1) and the nucleotide-binding domain (NBD) constitute pivotal elements of the architecture building the transmission interface that borders a central cavity which acts as a drug trap. The transmission interface is stabilized by salt-bridge interactions between the elbow helix and ICL1, as well as within ICL1, which is essential to control the conformational switch of ABCG2 to the outward-open drug-releasing conformation. Importantly, we propose that ICL1 operates like a molecular spring that holds the NBD dimer close to the membrane, thereby enabling efficient coupling of ATP hydrolysis during the catalytic cycle. These novel mechanistic data open new opportunities to therapeutically target ABCG2 in the context of related diseases.
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Affiliation(s)
- Narakorn Khunweeraphong
- Center for Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/2, A-1030, Vienna, Austria
| | - Thomas Stockner
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University Vienna, Währingerstrasse 13A, A-1090, Vienna, Austria
| | - Karl Kuchler
- Center for Medical Biochemistry, Max F. Perutz Laboratories, Medical University of Vienna, Campus Vienna Biocenter, Dr. Bohr-Gasse 9/2, A-1030, Vienna, Austria.
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32
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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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33
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Seguin A, Takahashi-Makise N, Yien YY, Huston NC, Whitman JC, Musso G, Wallace JA, Bradley T, Bergonia HA, Kafina MD, Matsumoto M, Igarashi K, Phillips JD, Paw BH, Kaplan J, Ward DM. Reductions in the mitochondrial ABC transporter Abcb10 affect the transcriptional profile of heme biosynthesis genes. J Biol Chem 2017; 292:16284-16299. [PMID: 28808058 DOI: 10.1074/jbc.m117.797415] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/09/2017] [Indexed: 11/06/2022] Open
Abstract
ATP-binding cassette subfamily B member 10 (Abcb10) is a mitochondrial ATP-binding cassette (ABC) transporter that complexes with mitoferrin1 and ferrochelatase to enhance heme biosynthesis in developing red blood cells. Reductions in Abcb10 levels have been shown to reduce mitoferrin1 protein levels and iron import into mitochondria, resulting in reduced heme biosynthesis. As an ABC transporter, Abcb10 binds and hydrolyzes ATP, but its transported substrate is unknown. Here, we determined that decreases in Abcb10 did not result in protoporphyrin IX accumulation in morphant-treated zebrafish embryos or in differentiated Abcb10-specific shRNA murine Friend erythroleukemia (MEL) cells in which Abcb10 was specifically silenced with shRNA. We also found that the ATPase activity of Abcb10 is necessary for hemoglobinization in MEL cells, suggesting that the substrate transported by Abcb10 is important in mediating increased heme biosynthesis during erythroid development. Inhibition of 5-aminolevulinic acid dehydratase (EC 4.2.1.24) with succinylacetone resulted in both 5-aminolevulinic acid (ALA) accumulation in control and Abcb10-specific shRNA MEL cells, demonstrating that reductions in Abcb10 do not affect ALA export from mitochondria and indicating that Abcb10 does not transport ALA. Abcb10 silencing resulted in an alteration in the heme biosynthesis transcriptional profile due to repression by the transcriptional regulator Bach1, which could be partially rescued by overexpression of Alas2 or Gata1, providing a mechanistic explanation for why Abcb10 shRNA MEL cells exhibit reduced hemoglobinization. In conclusion, our findings rule out that Abcb10 transports ALA and indicate that Abcb10's ATP-hydrolysis activity is critical for hemoglobinization and that the substrate transported by Abcb10 provides a signal that optimizes hemoglobinization.
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Affiliation(s)
- Alexandra Seguin
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | | | | | | | | | - Gabriel Musso
- the Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Jared A Wallace
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Thomas Bradley
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Hector A Bergonia
- the Division of Hematology-Oncology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | | | - Mitsuyo Matsumoto
- the Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - Kazuhiko Igarashi
- the Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - John D Phillips
- the Division of Hematology-Oncology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | - Barry H Paw
- the Division of Hematology and.,the Division of Hematology-Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, and.,the Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Jerry Kaplan
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Diane M Ward
- From the Division of Microbiology and Immunology, Department of Pathology, and
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34
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Zoghbi ME, Altenberg GA. Luminescence resonance energy transfer spectroscopy of ATP-binding cassette proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:854-867. [PMID: 28801111 DOI: 10.1016/j.bbamem.2017.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022]
Abstract
The ATP-binding cassette (ABC) superfamily includes regulatory and transport proteins. Most human ABC exporters pump substrates out of cells using energy from ATP hydrolysis. Although major advances have been made toward understanding the molecular mechanism of ABC exporters, there are still many issues unresolved. During the last few years, luminescence resonance energy transfer has been used to detect conformational changes in real time, with atomic resolution, in isolated ABC nucleotide binding domains (NBDs) and full-length ABC exporters. NBDs are particularly interesting because they provide the power stroke for substrate transport. Luminescence resonance energy transfer (LRET) is a spectroscopic technique that can provide dynamic information with atomic-resolution of protein conformational changes under physiological conditions. Using LRET, it has been shown that NBD dimerization, a critical step in ABC proteins catalytic cycle, requires binding of ATP to two nucleotide binding sites. However, hydrolysis at just one of the sites can drive dissociation of the NBD dimer. It was also found that the NBDs of the bacterial ABC exporter MsbA reconstituted in a lipid bilayer membrane and studied at 37°C never separate as much as suggested by crystal structures. This observation stresses the importance of performing structural/functional studies of ABC exporters under physiologic conditions. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Maria E Zoghbi
- School of Natural Sciences, University of California, Merced, 4225 N. Hospital Road, Atwater, CA, USA
| | - Guillermo A Altenberg
- Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79423-6551, USA.
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35
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D-helix influences dimerization of the ATP-binding cassette (ABC) transporter associated with antigen processing 1 (TAP1) nucleotide-binding domain. PLoS One 2017; 12:e0178238. [PMID: 28542489 PMCID: PMC5441636 DOI: 10.1371/journal.pone.0178238] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/10/2017] [Indexed: 12/13/2022] Open
Abstract
ATP-binding cassette (ABC) transporters form a large family of transmembrane importers and exporters. Using two nucleotide-binding domains (NBDs), which form a canonical ATP-sandwich dimer at some point within the transport cycle, the transporters harness the energy from ATP binding and hydrolysis to drive substrate transport. However the structural elements that enable and tune the dimerization propensity of the NBDs have not been fully elucidated. Here we compared the biochemical properties of the NBDs of human and rat TAP1, a subunit of the heterodimeric transporter associated with antigen processing (TAP). The isolated human TAP1 NBD was monomeric in solution, in contrast to the previously observed ATP-mediated homodimerization of the isolated rat TAP1 NBD. Using a series of human-rat chimeric constructs, we identified the D-helix, an α-helix N-terminal to the conserved D-loop motif, as an important determinant of NBD dimerization. The ATPase activity of our panel of TAP1 NBD constructs largely correlated with dimerization ability, indicating that the observed dimerization uses the canonical ATP-sandwich interface. The N-terminus of the D-helix from one protomer interacts with the ATP-binding Walker A motif of the second protomer at the ATP-sandwich interface. However, our mutational analysis indicated that residues farther from the interface, within the second and third turn of the D-helix, also influence dimerization. Overall, our data suggest that although the D-helix sequence is not conserved in ABC transporters, its precise positioning within the NBD structure has a critical role in NBD dimerization.
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36
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Wilcox SM, Arora H, Munro L, Xin J, Fenninger F, Johnson LA, Pfeifer CG, Choi KB, Hou J, Hoodless PA, Jefferies WA. The role of the innate immune response regulatory gene ABCF1 in mammalian embryogenesis and development. PLoS One 2017; 12:e0175918. [PMID: 28542262 PMCID: PMC5438103 DOI: 10.1371/journal.pone.0175918] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/03/2017] [Indexed: 12/15/2022] Open
Abstract
ABCF1 is an ABC transporter family protein that has been shown to regulate innate immune response and is a risk gene for autoimmune pancreatitis and arthritis. Unlike other members of ABC transporter family, ABCF1 lacks trans-membrane domains and is thought to function in translation initiation through an interaction with eukaryotic translation initiation factor 2 (eIF2). To study ABCF1 expression and function in development and disease, we used a single gene trap insertion in the Abcf1 gene in murine embryonic stem cells (ES cells) that allowed lineage tracing of the endogenous Abcf1 promoter by following the expression of a β-galactosidase reporter gene. From the ES cells, heterozygous mice (Abcf1+/-) were produced. No live born Abcf1-/- progeny were ever generated, and the lethality was not mouse strain-specific. Thus, we have determined that Abcf1 is an essential gene in development. Abcf1-/- mice were found to be embryonic lethal at 3.5 days post coitum (dpc), while Abcf1+/- mice appeared developmentally normal. Abcf1+/- mice were fertile and showed no significant differences in their anatomy when compared with their wild type littermates. The Abcf1 promoter was found to be active in all organs in adult mice, but varies in levels of expression in specific cell types within tissues. Furthermore, we observed high promoter activity in the blastocysts and embryos. Overall, Abcf1 expression in embryos is required for development and its expression in adults was highly correlated with actively proliferating and differentiating cell types.
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Affiliation(s)
- Sara M. Wilcox
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Hitesh Arora
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lonna Munro
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jian Xin
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Franz Fenninger
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura A. Johnson
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Cheryl G. Pfeifer
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyung Bok Choi
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Juan Hou
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Pamela A. Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Developmental and Cell Biology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Wilfred A. Jefferies
- The Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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37
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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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38
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Esser L, Zhou F, Pluchino KM, Shiloach J, Ma J, Tang WK, Gutierrez C, Zhang A, Shukla S, Madigan JP, Zhou T, Kwong PD, Ambudkar SV, Gottesman MM, Xia D. Structures of the Multidrug Transporter P-glycoprotein Reveal Asymmetric ATP Binding and the Mechanism of Polyspecificity. J Biol Chem 2016; 292:446-461. [PMID: 27864369 DOI: 10.1074/jbc.m116.755884] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/15/2016] [Indexed: 12/25/2022] Open
Abstract
P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancer; it plays important roles in determining the pharmacokinetics of many drugs. Understanding the structural basis of P-gp, substrate polyspecificity has been hampered by its intrinsic flexibility, which is facilitated by a 75-residue linker that connects the two halves of P-gp. Here we constructed a mutant murine P-gp with a shortened linker to facilitate structural determination. Despite dramatic reduction in rhodamine 123 and calcein-AM transport, the linker-shortened mutant P-gp possesses basal ATPase activity and binds ATP only in its N-terminal nucleotide-binding domain. Nine independently determined structures of wild type, the linker mutant, and a methylated P-gp at up to 3.3 Å resolution display significant movements of individual transmembrane domain helices, which correlated with the opening and closing motion of the two halves of P-gp. The open-and-close motion alters the surface topology of P-gp within the drug-binding pocket, providing a mechanistic explanation for the polyspecificity of P-gp in substrate interactions.
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Affiliation(s)
- Lothar Esser
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI
| | - Fei Zhou
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI
| | | | | | - Jichun Ma
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI
| | - Wai-Kwan Tang
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI
| | - Camilo Gutierrez
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI
| | - Alex Zhang
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI
| | - Suneet Shukla
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI
| | - James P Madigan
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI
| | - Tongqing Zhou
- the Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Peter D Kwong
- the Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Suresh V Ambudkar
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI
| | | | - Di Xia
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI,
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39
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Hsu WL, Furuta T, Sakurai M. ATP Hydrolysis Mechanism in a Maltose Transporter Explored by QM/MM Metadynamics Simulation. J Phys Chem B 2016; 120:11102-11112. [PMID: 27712074 DOI: 10.1021/acs.jpcb.6b07332] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Translocation of substrates across the cell membrane by adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporters depends on the energy provided by ATP hydrolysis within the nucleotide-binding domains (NBDs). However, the detailed mechanism remains unclear. In this study, we focused on maltose transporter NBDs (MalK2) and performed a quantum mechanical/molecular mechanical (QM/MM) well-tempered metadynamics simulation to address this issue. We explored the free-energy profile along an assigned collective variable. As a result, it was determined that the activation free energy is approximately 10.5 kcal/mol, and the reaction released approximately 3.8 kcal/mol of free energy, indicating that the reaction of interest is a one-step exothermic reaction. The dissociation of the ATP γ-phosphate seems to be the rate-limiting step, which supports the so-called dissociative model. Moreover, Glu159, located in the Walker B motif, acts as a base to abstract the proton from the lytic water, but is not the catalytic base, which corresponds to an atypical general base catalysis model. We also observed two interesting proton transfers: transfer from the His192 ε-position nitrogen to the dissociated inorganic phosphate, Pi, and transfer from the Lys42 side chain to adenosine 5'-diphosphate β-phosphate. These proton transfers would stabilize the posthydrolysis state. Our study provides significant insight into the ATP hydrolysis mechanism in MalK2 from a dynamical viewpoint, and this insight would be applicable to other ABC transporters.
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Affiliation(s)
- Wei-Lin Hsu
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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40
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Wątły J, Potocki S, Rowińska-Żyrek M. Zinc Homeostasis at the Bacteria/Host Interface-From Coordination Chemistry to Nutritional Immunity. Chemistry 2016; 22:15992-16010. [DOI: 10.1002/chem.201602376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry; University of Wroclaw; F. Joliot-Curie 14 50-383 Wroclaw Poland
| | - Sławomir Potocki
- Faculty of Chemistry; University of Wroclaw; F. Joliot-Curie 14 50-383 Wroclaw Poland
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41
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Tsao S, Weber S, Cameron C, Nehme D, Ahmadzadeh E, Raymond M. Positive regulation of the Candida albicans multidrug efflux pump Cdr1p function by phosphorylation of its N-terminal extension. J Antimicrob Chemother 2016; 71:3125-3134. [PMID: 27402010 DOI: 10.1093/jac/dkw252] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/10/2016] [Accepted: 05/24/2016] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES Overexpression of ATP-binding cassette (ABC) transporters is a frequent cause of multidrug resistance in cancer cells and pathogenic microorganisms. One example is the Cdr1p transporter from the human fungal pathogen Candida albicans that belongs to the pleiotropic drug resistance (PDR) subfamily of ABC transporters found in fungi and plants. Cdr1p is overexpressed in several azole-resistant clinical isolates, causing azole efflux and treatment failure. Cdr1p appears as a doublet band in western blot analyses, suggesting that the protein is post-translationally modified. We investigated whether Cdr1p is phosphorylated and the function of this modification. METHODS Phosphorylated residues were identified by MS. Their function was investigated by site-directed mutagenesis and expression of the mutants in a C. albicans endogenous system that exploits a hyperactive allele of the Tac1p transcription factor to drive high levels of Cdr1p expression. Fluconazole resistance was measured by microtitre plate and spot assays and transport activity by Nile red accumulation. RESULTS We identified a cluster of seven phosphorylated amino acids in the N-terminal extension (NTE) of Cdr1p. Mutating all seven sites to alanine dramatically diminished the ability of Cdr1p to confer fluconazole resistance and transport Nile red, without affecting Cdr1p localization. Conversely, a Cdr1p mutant in which the seven amino acids were replaced by glutamate was able to confer high levels of fluconazole resistance and to export Nile red. CONCLUSIONS Our results demonstrate that the NTE of Cdr1p is phosphorylated and that NTE phosphorylation plays a major role in regulating Cdr1p and possibly other PDR transporter function.
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Affiliation(s)
- Sarah Tsao
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Sandra Weber
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Christine Cameron
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Dominic Nehme
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Elaheh Ahmadzadeh
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Martine Raymond
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC H3T 1J4, Canada .,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada
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42
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Zhou Y, Ojeda-May P, Nagaraju M, Pu J. Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method. Methods Enzymol 2016; 577:185-212. [PMID: 27498639 PMCID: PMC4985252 DOI: 10.1016/bs.mie.2016.05.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are ubiquitous ATP-dependent membrane proteins involved in translocations of a wide variety of substrates across cellular membranes. To understand the chemomechanical coupling mechanism as well as functional asymmetry in these systems, a quantitative description of how ABC transporters hydrolyze ATP is needed. Complementary to experimental approaches, computer simulations based on combined quantum mechanical and molecular mechanical (QM/MM) potentials have provided new insights into the catalytic mechanism in ABC transporters. Quantitatively reliable determination of the free energy requirement for enzymatic ATP hydrolysis, however, requires substantial statistical sampling on QM/MM potential. A case study shows that brute force sampling of ab initio QM/MM (AI/MM) potential energy surfaces is computationally impractical for enzyme simulations of ABC transporters. On the other hand, existing semiempirical QM/MM (SE/MM) methods, although affordable for free energy sampling, are unreliable for studying ATP hydrolysis. To close this gap, a multiscale QM/MM approach named reaction path-force matching (RP-FM) has been developed. In RP-FM, specific reaction parameters for a selected SE method are optimized against AI reference data along reaction paths by employing the force matching technique. The feasibility of the method is demonstrated for a proton transfer reaction in the gas phase and in solution. The RP-FM method may offer a general tool for simulating complex enzyme systems such as ABC transporters.
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Affiliation(s)
- Y Zhou
- Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - P Ojeda-May
- Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - M Nagaraju
- Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - J Pu
- Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States.
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43
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Rijpma SR, van der Velden M, Annoura T, Matz JM, Kenthirapalan S, Kooij TWA, Matuschewski K, van Gemert GJ, van de Vegte-Bolmer M, Siebelink-Stoter R, Graumans W, Ramesar J, Klop O, Russel FGM, Sauerwein RW, Janse CJ, Franke-Fayard BM, Koenderink JB. Vital and dispensable roles of Plasmodium multidrug resistance transporters during blood- and mosquito-stage development. Mol Microbiol 2016; 101:78-91. [PMID: 26991313 DOI: 10.1111/mmi.13373] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2016] [Indexed: 11/29/2022]
Abstract
Multidrug resistance (MDR) proteins belong to the B subfamily of the ATP Binding Cassette (ABC) transporters, which export a wide range of compounds including pharmaceuticals. In this study, we used reverse genetics to study the role of all seven Plasmodium MDR proteins during the life cycle of malaria parasites. Four P. berghei genes (encoding MDR1, 4, 6 and 7) were refractory to deletion, indicating a vital role during blood stage multiplication and validating them as potential targets for antimalarial drugs. Mutants lacking expression of MDR2, MDR3 and MDR5 were generated in both P. berghei and P. falciparum, indicating a dispensable role for blood stage development. Whereas P. berghei mutants lacking MDR3 and MDR5 had a reduced blood stage multiplication in vivo, blood stage growth of P. falciparum mutants in vitro was not significantly different. Oocyst maturation and sporozoite formation in Plasmodium mutants lacking MDR2 or MDR5 was reduced. Sporozoites of these P. berghei mutants were capable of infecting mice and life cycle completion, indicating the absence of vital roles during liver stage development. Our results demonstrate vital and dispensable roles of MDR proteins during blood stages and an important function in sporogony for MDR2 and MDR5 in both Plasmodium species.
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Affiliation(s)
- Sanna R Rijpma
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Maarten van der Velden
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Takeshi Annoura
- Department of Tropical Medicine, The Jikei University School of Medicine, Post code 105-8461 Nishi-shinbashi 3-25-8, Minato-ku, Tokyo, Japan
| | - Joachim M Matz
- Department of Medical Microbiology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Sanketha Kenthirapalan
- Parasitology Unit, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Taco W A Kooij
- Department of Medical Microbiology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Kai Matuschewski
- Parasitology Unit, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117, Berlin, Germany.,Institute of Biology, Humboldt University, 10117, Berlin, Germany
| | - Geert-Jan van Gemert
- Department of Medical Microbiology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Marga van de Vegte-Bolmer
- Department of Medical Microbiology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Rianne Siebelink-Stoter
- Department of Medical Microbiology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Wouter Graumans
- Department of Medical Microbiology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Jai Ramesar
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Onny Klop
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Frans G M Russel
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Robert W Sauerwein
- Department of Medical Microbiology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
| | - Chris J Janse
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Blandine M Franke-Fayard
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Jan B Koenderink
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Geert-Grooteplein 28, 6525, GA, Nijmegen, The Netherlands
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44
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Zoghbi ME, Cooper RS, Altenberg GA. The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter. J Biol Chem 2016; 291:4453-61. [PMID: 26725230 DOI: 10.1074/jbc.m115.698498] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 12/22/2022] Open
Abstract
ATP-binding cassette exporters use the energy of ATP hydrolysis to transport substrates across membranes by switching between inward- and outward-facing conformations. Essentially all structural studies of these proteins have been performed with the proteins in detergent micelles, locked in specific conformations and/or at low temperature. Here, we used luminescence resonance energy transfer spectroscopy to study the prototypical ATP-binding cassette exporter MsbA reconstituted in nanodiscs at 37 °C while it performs ATP hydrolysis. We found major differences when comparing MsbA in these native-like conditions with double electron-electron resonance data and the crystal structure of MsbA in the open inward-facing conformation. The most striking differences include a significantly smaller separation between the nucleotide-binding domains and a larger fraction of molecules with associated nucleotide-binding domains in the nucleotide-free apo state. These studies stress the importance of studying membrane proteins in an environment that approaches physiological conditions.
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Affiliation(s)
- Maria E Zoghbi
- From the Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430-6551
| | - Rebecca S Cooper
- From the Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430-6551
| | - Guillermo A Altenberg
- From the Department of Cell Physiology and Molecular Biophysics, and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, Texas 79430-6551
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45
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Groothuizen FS, Sixma TK. The conserved molecular machinery in DNA mismatch repair enzyme structures. DNA Repair (Amst) 2015; 38:14-23. [PMID: 26796427 DOI: 10.1016/j.dnarep.2015.11.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/05/2015] [Accepted: 11/30/2015] [Indexed: 12/25/2022]
Abstract
The machinery of DNA mismatch repair enzymes is highly conserved in evolution. The process is initiated by recognition of a DNA mismatch, and validated by ATP and the presence of a processivity clamp or a methylation mark. Several events in MMR promote conformational changes that lead to progression of the repair process. Here we discuss functional conformational changes in the MMR proteins and we compare the enzymes to paralogs in other systems.
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Affiliation(s)
- Flora S Groothuizen
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K Sixma
- Division of Biochemistry and CGC.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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46
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Rijpma SR, van der Velden M, González-Pons M, Annoura T, van Schaijk BCL, van Gemert GJ, van den Heuvel JJMW, Ramesar J, Chevalley-Maurel S, Ploemen IH, Khan SM, Franetich JF, Mazier D, de Wilt JHW, Serrano AE, Russel FGM, Janse CJ, Sauerwein RW, Koenderink JB, Franke-Fayard BM. Multidrug ATP-binding cassette transporters are essential for hepatic development of Plasmodium sporozoites. Cell Microbiol 2015; 18:369-83. [PMID: 26332724 DOI: 10.1111/cmi.12517] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/11/2015] [Accepted: 08/24/2015] [Indexed: 12/23/2022]
Abstract
Multidrug resistance-associated proteins (MRPs) belong to the C-family of ATP-binding cassette (ABC) transport proteins and are known to transport a variety of physiologically important compounds and to be involved in the extrusion of pharmaceuticals. Rodent malaria parasites encode a single ABC transporter subfamily C protein, whereas human parasites encode two: MRP1 and MRP2. Although associated with drug resistance, their biological function and substrates remain unknown. To elucidate the role of MRP throughout the parasite life cycle, Plasmodium berghei and Plasmodium falciparum mutants lacking MRP expression were generated. P. berghei mutants lacking expression of the single MRP as well as P. falciparum mutants lacking MRP1, MRP2 or both proteins have similar blood stage growth kinetics and drug-sensitivity profiles as wild type parasites. We show that MRP1-deficient parasites readily invade primary human hepatocytes and develop into mature liver stages. In contrast, both P. falciparum MRP2-deficient parasites and P. berghei mutants lacking MRP protein expression abort in mid to late liver stage development, failing to produce mature liver stages. The combined P. berghei and P. falciparum data are the first demonstration of a critical role of an ABC transporter during Plasmodium liver stage development.
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Affiliation(s)
- Sanna R Rijpma
- Department of Pharmacology and Toxicology, Radboud University Medical Centre, Geert-Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Maarten van der Velden
- Department of Pharmacology and Toxicology, Radboud University Medical Centre, Geert-Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Maria González-Pons
- Department of Microbiology and Medical Zoology, University of Puerto Rico, School of Medicine, PR 00936-5067, San Juan, Puerto Rico, USA
| | - Takeshi Annoura
- Department of Tropical Medicine, The Jikei University School of Medicine, Post code 105-8461, Nishi-shinbashi 3-25-8, Minato-ku, Tokyo, Japan
| | - Ben C L van Schaijk
- Department of Medical Microbiology, Radboud University Medical Centre, Geert-Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Geert-Jan van Gemert
- Department of Medical Microbiology, Radboud University Medical Centre, Geert-Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Jeroen J M W van den Heuvel
- Department of Pharmacology and Toxicology, Radboud University Medical Centre, Geert-Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Jai Ramesar
- Department of Parasitology, Center of Infectious Diseases, Leiden Malaria Research Group, Leiden, The Netherlands
| | - Severine Chevalley-Maurel
- Department of Parasitology, Center of Infectious Diseases, Leiden Malaria Research Group, Leiden, The Netherlands
| | - Ivo H Ploemen
- Department of Medical Microbiology, Radboud University Medical Centre, Geert-Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Shahid M Khan
- Department of Tropical Medicine, The Jikei University School of Medicine, Post code 105-8461, Nishi-shinbashi 3-25-8, Minato-ku, Tokyo, Japan
| | - Jean-Francois Franetich
- AP-HP, Groupe hospitalier Pitié-Salpêtrière, Service Parasitologie-Mycologie, 47-83 Boulevard de l'Hôpital, 75651, Paris, France
| | - Dominique Mazier
- AP-HP, Groupe hospitalier Pitié-Salpêtrière, Service Parasitologie-Mycologie, 47-83 Boulevard de l'Hôpital, 75651, Paris, France.,CIMI-Paris (UPMC UMRS CR7 - Inserm U1135 - CNRS ERL 8255), Paris, France
| | - Johannes H W de Wilt
- Department of Surgery, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Adelfa E Serrano
- Department of Microbiology and Medical Zoology, University of Puerto Rico, School of Medicine, PR 00936-5067, San Juan, Puerto Rico, USA
| | - Frans G M Russel
- Department of Pharmacology and Toxicology, Radboud University Medical Centre, Geert-Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Chris J Janse
- Department of Parasitology, Center of Infectious Diseases, Leiden Malaria Research Group, Leiden, The Netherlands
| | - Robert W Sauerwein
- Department of Medical Microbiology, Radboud University Medical Centre, Geert-Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Jan B Koenderink
- Department of Pharmacology and Toxicology, Radboud University Medical Centre, Geert-Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Blandine M Franke-Fayard
- Department of Parasitology, Center of Infectious Diseases, Leiden Malaria Research Group, Leiden, The Netherlands
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47
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Watching conformational dynamics of ABC transporters with single-molecule tools. Biochem Soc Trans 2015; 43:1041-7. [DOI: 10.1042/bst20150140] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
ATP-binding cassette (ABC) transporters play crucial roles in cellular processes, such as nutrient uptake, drug resistance, cell-volume regulation and others. Despite their importance, all proposed molecular models for transport are based on indirect evidence, i.e. functional interpretation of static crystal structures and ensemble measurements of function and structure. Thus, classical biophysical and biochemical techniques do not readily visualize dynamic structural changes. We recently started to use single-molecule fluorescence techniques to study conformational states and changes of ABC transporters in vitro, in order to observe directly how the different steps during transport are coordinated. This review summarizes our scientific strategy and some of the key experimental advances that allowed the substrate-binding mechanism of prokaryotic ABC importers and the transport cycle to be explored. The conformational states and transitions of ABC-associated substrate-binding domains (SBDs) were visualized with single-molecule FRET, permitting a direct correlation of structural and kinetic information of SBDs. We also delineated the different steps of the transport cycle. Since information in such assays are restricted by proper labelling of proteins with fluorescent dyes, we present a simple approach to increase the amount of protein with FRET information based on non-specific interactions between a dye and the size-exclusion chromatography (SEC) column material used for final purification.
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48
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Abstract
It is almost 40 years since the drug efflux pump P-glycoprotein (permeability glycoprotein or P-gp) was shown to confer multi-drug resistance in cancer cells. This protein has been one of the most extensively investigated transport proteins due to its intriguing mechanism and its affect in oncology. P-gp is known to interact with over 300 compounds and the ability to achieve this has not yet been revealed. Following the binding of substrate and nucleotide, a complex series of conformational changes in the membrane and cytosolic domains translocates substrate across the membrane. Despite over 30 years of biochemical investigation, the availability of structural data and a plethora of chemical tools to modulate its function, the molecular mechanism remains a mystery. In addition, overcoming its activity in resistant cancer cells has not been achieved in the clinic, thereby garnering some degree of pessimism in the field. This review highlights the progress that has been achieved in understanding this complex protein and the value of undertaking molecular studies.
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Affiliation(s)
- Richard Callaghan
- Division of Biomedical Science & Biochemistry, Research School of Biology, The Australian National University Canberra, ACT 0200, Australia
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49
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Zhang XC, Han L, Zhao Y. Thermodynamics of ABC transporters. Protein Cell 2015; 7:17-27. [PMID: 26408021 PMCID: PMC4707154 DOI: 10.1007/s13238-015-0211-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/11/2015] [Indexed: 01/09/2023] Open
Abstract
ABC transporters form the largest of all transporter families, and their structural study has made tremendous progress over recent years. However, despite such advances, the precise mechanisms that determine the energy-coupling between ATP hydrolysis and the conformational changes following substrate binding remain to be elucidated. Here, we present our thermodynamic analysis for both ABC importers and exporters, and introduce the two new concepts of differential-binding energy and elastic conformational energy into the discussion. We hope that the structural analysis of ABC transporters will henceforth take thermodynamic aspects of transport mechanisms into account as well.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lei Han
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Zhao
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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50
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Bao H, Dalal K, Cytrynbaum E, Duong F. Sequential Action of MalE and Maltose Allows Coupling ATP Hydrolysis to Translocation in the MalFGK2 Transporter. J Biol Chem 2015; 290:25452-60. [PMID: 26338707 DOI: 10.1074/jbc.m115.671826] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Indexed: 01/05/2023] Open
Abstract
ATP-binding cassette (ABC) transporters have evolved an ATP-dependent alternating-access mechanism to transport substrates across membranes. Despite important progress, especially in their structural analysis, it is still unknown how the substrate stimulates ATP hydrolysis, the hallmark of ABC transporters. In this study, we measure the ATP turnover cycle of MalFGK2 in steady and pre-steady state conditions. We show that (i) the basal ATPase activity of MalFGK2 is very low because the cleavage of ATP is rate-limiting, (ii) the binding of open-state MalE to the transporter induces ATP cleavage but leaves release of Pi limiting, and (iii) the additional presence of maltose stimulates release of Pi, and therefore increases the overall ATP turnover cycle. We conclude that open-state MalE stabilizes MalFGK2 in the outward-facing conformation until maltose triggers return to the inward-facing state for substrate and Pi release. This concerted action explains why ATPase activity of MalFGK2 depends on maltose, and why MalE is essential for transport.
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Affiliation(s)
- Huan Bao
- From the Departments of Biochemistry and Molecular Biology and
| | - Kush Dalal
- From the Departments of Biochemistry and Molecular Biology and
| | - Eric Cytrynbaum
- Mathematics, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | - Franck Duong
- From the Departments of Biochemistry and Molecular Biology and
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