1
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Lindt KA, Frühschulz S, Tampé R, Abele R. Interdomain communication in a homodimeric ABC transporter. J Biol Chem 2024; 300:107440. [PMID: 38844133 PMCID: PMC11267003 DOI: 10.1016/j.jbc.2024.107440] [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: 08/26/2023] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 07/02/2024] Open
Abstract
ABC transporters are found in all organisms and almost every cellular compartment. They mediate the transport of various solutes across membranes, energized by ATP binding and hydrolysis. Dysfunctions can result in severe diseases, such as cystic fibrosis or antibiotic resistance. In type IV ABC transporters, each of the two nucleotide-binding domains is connected to a transmembrane domain by two coupling helices, which are part of cytosolic loops. Although there are many structural snapshots of different conformations, the interdomain communication is still enigmatic. Therefore, we analyzed the function of three conserved charged residues in the intracytosolic loop 1 of the human homodimeric, lysosomal peptide transporter TAPL (transporter associated with antigen processing-like). Substitution of D278 in coupling helix 1 by alanine interrupted peptide transport by impeding ATP hydrolysis. Alanine substitution of R288 and D292, both localized next to the coupling helix 1 extending to transmembrane helix 3, reduced peptide transport but increased basal ATPase activity. Surprisingly, the ATPase activity of the R288A variant dropped in a peptide-dependent manner, whereas ATPase activity of wildtype and D292A was unaffected. Interestingly, R288A and D292A mutants did not differentiate between ATP and GTP in respect of hydrolysis. However, in contrast to wildtye TAPL, only ATP energized peptide transport. In sum, D278 seems to be involved in bidirectional interdomain communication mediated by network of polar interactions, whereas the two residues in the cytosolic extension of transmembrane helix 3 are involved in regulation of ATP hydrolysis, most likely by stabilization of the outward-facing conformation.
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Affiliation(s)
| | - Stefan Frühschulz
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Rupert Abele
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany.
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2
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Yao L, Liu Q, Lei Z, Sun T. Development and challenges of antimicrobial peptide delivery strategies in bacterial therapy: A review. Int J Biol Macromol 2023; 253:126819. [PMID: 37709236 DOI: 10.1016/j.ijbiomac.2023.126819] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023]
Abstract
The escalating global prevalence of antimicrobial resistance poses a critical threat, prompting concerns about its impact on public health. This predicament is exacerbated by the acute shortage of novel antimicrobial agents, a scarcity attributed to the rapid surge in bacterial resistance. This review delves into the realm of antimicrobial peptides, a diverse class of compounds ubiquitously present in plants and animals across various natural organisms. Renowned for their intrinsic antibacterial activity, these peptides provide a promising avenue to tackle the intricate challenge of bacterial resistance. However, the clinical utility of peptide-based drugs is hindered by limited bioavailability and susceptibility to rapid degradation, constraining efforts to enhance the efficacy of bacterial infection treatments. The emergence of nanocarriers marks a transformative approach poised to revolutionize peptide delivery strategies. This review elucidates a promising framework involving nanocarriers within the realm of antimicrobial peptides. This paradigm enables meticulous and controlled peptide release at infection sites by detecting dynamic shifts in microenvironmental factors, including pH, ROS, GSH, and reactive enzymes. Furthermore, a glimpse into the future reveals the potential of targeted delivery mechanisms, harnessing inflammatory responses and intricate signaling pathways, including adenosine triphosphate, macrophage receptors, and pathogenic nucleic acid entities. This approach holds promise in fortifying immunity, thereby amplifying the potency of peptide-based treatments. In summary, this review spotlights peptide nanosystems as prospective solutions for combating bacterial infections. By bridging antimicrobial peptides with advanced nanomedicine, a new therapeutic era emerges, poised to confront the formidable challenge of antimicrobial resistance head-on.
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Affiliation(s)
- Longfukang Yao
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China; Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Qianying Liu
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhixin Lei
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China; Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
| | - Taolei Sun
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China; Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
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3
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Rudolph M, Tampé R, Joseph B. Time-Resolved Mn 2+ -NO and NO-NO Distance Measurements Reveal That Catalytic Asymmetry Regulates Alternating Access in an ABC Transporter. Angew Chem Int Ed Engl 2023; 62:e202307091. [PMID: 37459565 DOI: 10.1002/anie.202307091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
ATP-binding cassette (ABC) transporters shuttle diverse substrates across biological membranes. Transport is often achieved through a transition between an inward-facing (IF) and an outward-facing (OF) conformation of the transmembrane domains (TMDs). Asymmetric nucleotide-binding sites (NBSs) are present among several ABC subfamilies and their functional role remains elusive. Here we addressed this question using concomitant NO-NO, Mn2+ -NO, and Mn2+ -Mn2+ pulsed electron-electron double-resonance spectroscopy of TmrAB in a time-resolved manner. This type-IV ABC transporter undergoes a reversible transition in the presence of ATP with a significantly faster forward transition. The impaired degenerate NBS stably binds Mn2+ -ATP, and Mn2+ is preferentially released at the active consensus NBS. ATP hydrolysis at the consensus NBS considerably accelerates the reverse transition. Both NBSs fully open during each conformational cycle and the degenerate NBS may regulate the kinetics of this process.
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Affiliation(s)
- Michael Rudolph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Benesh Joseph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
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4
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Thangaratnarajah C, Nijland M, Borges-Araújo L, Jeucken A, Rheinberger J, Marrink SJ, Souza PCT, Paulino C, Slotboom DJ. Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nat Commun 2023; 14:4484. [PMID: 37491368 PMCID: PMC10368641 DOI: 10.1038/s41467-023-40266-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/20/2023] [Indexed: 07/27/2023] Open
Abstract
Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist of a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF module) Previous data indicate that the S-component topples within the membrane to alternately expose the binding site to either side of the membrane. In many ECF transporters, the substrate-free S-component can be expelled from the ECF module. Here we study this enigmatic expulsion step by cryogenic electron microscopy and reveal that ATP induces a concave-to-convex shape change of two long helices in the motor, thereby destroying the S-component's docking site and allowing for its dissociation. We show that adaptation of the membrane morphology to the conformational state of the motor may favour expulsion of the substrate-free S-component when ATP is bound and docking of the substrate-loaded S-component after hydrolysis. Our work provides a picture of bilayer-assisted chemo-mechanical coupling in the transport cycle of ECF transporters.
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Affiliation(s)
- Chancievan Thangaratnarajah
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Mark Nijland
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Aike Jeucken
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jan Rheinberger
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Siewert J Marrink
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Molecular Dynamics Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Cristina Paulino
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
| | - Dirk J Slotboom
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
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5
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Veit S, Paweletz LC, Günther Pomorski T. Determination of membrane protein orientation upon liposomal reconstitution down to the single vesicle level. Biol Chem 2023; 404:647-661. [PMID: 36857289 DOI: 10.1515/hsz-2022-0325] [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: 11/10/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023]
Abstract
Reconstitution of membrane proteins into liposomal membranes represents a key technique in enabling functional analysis under well-defined conditions. In this review, we provide a brief introduction to selected methods that have been developed to determine membrane protein orientation after reconstitution in liposomes, including approaches based on proteolytic digestion with proteases, site-specific labeling, fluorescence quenching and activity assays. In addition, we briefly highlight new strategies based on single vesicle analysis to address the problem of sample heterogeneity.
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Affiliation(s)
- Sarina Veit
- Department of Molecular Biochemistry , Faculty of Chemistry and Biochemistry , NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Laura Charlotte Paweletz
- Department of Molecular Biochemistry , Faculty of Chemistry and Biochemistry , NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Thomas Günther Pomorski
- Department of Molecular Biochemistry , Faculty of Chemistry and Biochemistry , NC 7/174, Ruhr University Bochum, Universitätsstraße 150, D-44780 Bochum, Germany
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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6
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Bilsing FL, Anlauf MT, Hachani E, Khosa S, Schmitt L. ABC Transporters in Bacterial Nanomachineries. Int J Mol Sci 2023; 24:ijms24076227. [PMID: 37047196 PMCID: PMC10094684 DOI: 10.3390/ijms24076227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Members of the superfamily of ABC transporters are found in all domains of life. Most of these primary active transporters act as isolated entities and export or import their substrates in an ATP-dependent manner across biological membranes. However, some ABC transporters are also part of larger protein complexes, so-called nanomachineries that catalyze the vectorial transport of their substrates. Here, we will focus on four bacterial examples of such nanomachineries: the Mac system providing drug resistance, the Lpt system catalyzing vectorial LPS transport, the Mla system responsible for phospholipid transport, and the Lol system, which is required for lipoprotein transport to the outer membrane of Gram-negative bacteria. For all four systems, we tried to summarize the existing data and provide a structure-function analysis highlighting the mechanistical aspect of the coupling of ATP hydrolysis to substrate translocation.
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7
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Chen ZP, Xu D, Wang L, Mao YX, Li Y, Cheng MT, Zhou CZ, Hou WT, Chen Y. Structural basis of substrate recognition and translocation by human very long-chain fatty acid transporter ABCD1. Nat Commun 2022; 13:3299. [PMID: 35676282 PMCID: PMC9177597 DOI: 10.1038/s41467-022-30974-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/26/2022] [Indexed: 11/08/2022] Open
Abstract
Human ABC transporter ABCD1 transports very long-chain fatty acids from cytosol to peroxisome for β-oxidation, dysfunction of which usually causes the X-linked adrenoleukodystrophy (X-ALD). Here, we report three cryogenic electron microscopy structures of ABCD1: the apo-form, substrate- and ATP-bound forms. Distinct from what was seen in the previously reported ABC transporters, the two symmetric molecules of behenoyl coenzyme A (C22:0-CoA) cooperatively bind to the transmembrane domains (TMDs). For each C22:0-CoA, the hydrophilic 3'-phospho-ADP moiety of CoA portion inserts into one TMD, with the succeeding pantothenate and cysteamine moiety crossing the inter-domain cavity, whereas the hydrophobic fatty acyl chain extends to the opposite TMD. Structural analysis combined with biochemical assays illustrates snapshots of ABCD1-mediated substrate transport cycle. It advances our understanding on the selective oxidation of fatty acids and molecular pathology of X-ALD.
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Affiliation(s)
- Zhi-Peng Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Da Xu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Liang Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Yao-Xu Mao
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Yang Li
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Meng-Ting Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Wen-Tao Hou
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Yuxing Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
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8
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Shaltiel IA, Datta S, Lecomte L, Hassler M, Kschonsak M, Bravo S, Stober C, Ormanns J, Eustermann S, Haering CH. A hold-and-feed mechanism drives directional DNA loop extrusion by condensin. Science 2022; 376:1087-1094. [PMID: 35653469 DOI: 10.1126/science.abm4012] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes structure genomes by extruding DNA loops, but the molecular mechanism that underlies their activity has remained unknown. We show that the active condensin complex entraps the bases of a DNA loop transiently in two separate chambers. Single-molecule imaging and cryo-electron microscopy suggest a putative power-stroke movement at the first chamber that feeds DNA into the SMC-kleisin ring upon adenosine triphosphate binding, whereas the second chamber holds on upstream of the same DNA double helix. Unlocking the strict separation of "motor" and "anchor" chambers turns condensin from a one-sided into a bidirectional DNA loop extruder. We conclude that the orientation of two topologically bound DNA segments during the SMC reaction cycle determines the directionality of DNA loop extrusion.
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Affiliation(s)
- Indra A Shaltiel
- Department of Biochemistry and Cell Biology, Julius Maximilian University of Würzburg, 97074 Würzburg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Sumanjit Datta
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Léa Lecomte
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Markus Hassler
- Department of Biochemistry and Cell Biology, Julius Maximilian University of Würzburg, 97074 Würzburg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Marc Kschonsak
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Sol Bravo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Catherine Stober
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jenny Ormanns
- Department of Biochemistry and Cell Biology, Julius Maximilian University of Würzburg, 97074 Würzburg, Germany
| | | | - Christian H Haering
- Department of Biochemistry and Cell Biology, Julius Maximilian University of Würzburg, 97074 Würzburg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.,Structural and Computational Biology Unit, EMBL, 69117 Heidelberg, Germany
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9
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Metalloprotein-Specific or Critical Amino Acid Residues: Perspectives on Plant-Precise Detoxification and Recognition Mechanisms under Cadmium Stress. Int J Mol Sci 2022; 23:ijms23031734. [PMID: 35163656 PMCID: PMC8836122 DOI: 10.3390/ijms23031734] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 12/15/2022] Open
Abstract
Cadmium (Cd) pollution in cultivated land is caused by irresistible geological factors and human activities; intense diffusion and migration have seriously affected the safety of food crops. Plants have evolved mechanisms to control excessive influx of Cd in the environment, such as directional transport, chelation and detoxification. This is done by some specific metalloproteins, whose key amino acid motifs have been investigated by scientists one by one. The application of powerful cell biology, crystal structure science, and molecular probe targeted labeling technology has identified a series of protein families involved in the influx, transport and detoxification of the heavy metal Cd. This review summarizes them as influx proteins (NRAMP, ZIP), chelating proteins (MT, PDF), vacuolar proteins (CAX, ABCC, MTP), long-distance transport proteins (OPT, HMA) and efflux proteins (PCR, ABCG). We selected representative proteins from each family, and compared their amino acid sequence, motif structure, subcellular location, tissue specific distribution and other characteristics of differences and common points, so as to summarize the key residues of the Cd binding target. Then, we explain its special mechanism of action from the molecular structure. In conclusion, this review is expected to provide a reference for the exploration of key amino acid targets of Cd, and lay a foundation for the intelligent design and breeding of crops with high/low Cd accumulation.
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10
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Pourhassan N Z, Smits SHJ, Ahn JH, Schmitt L. Biotechnological applications of type 1 secretion systems. Biotechnol Adv 2021; 53:107864. [PMID: 34767962 DOI: 10.1016/j.biotechadv.2021.107864] [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: 06/18/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 02/06/2023]
Abstract
Bacteria have evolved a diverse range of secretion systems to export different substrates across their cell envelope. Although secretion of proteins into the extracellular space could offer advantages for recombinant protein production, the low secretion titers of the secretion systems for some heterologous proteins remain a clear drawback of their utility at commercial scales. Therefore, a potential use of most of secretion systems as production platforms at large scales are still limited. To overcome this limitation, remarkable efforts have been made toward improving the secretion efficiency of different bacterial secretion systems in recent years. Here, we review the progress with respect to biotechnological applications of type I secretion system (T1SS) of Gram-negative bacteria. We will also focus on the applicability of T1SS for the secretion of heterologous proteins as well as vaccine development. Last but not least, we explore the employed engineering strategies that have enhanced the secretion efficiencies of T1SS. Attention is also paid to directed evolution approaches that may offer a more versatile approach to optimize secretion efficiency of T1SS.
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Affiliation(s)
- Zohreh Pourhassan N
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Jung Hoon Ahn
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, South Korea
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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11
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Li D, Chu W, Sheng X, Li W. Optimization of Membrane Protein TmrA Purification Procedure Guided by Analytical Ultracentrifugation. MEMBRANES 2021; 11:membranes11100780. [PMID: 34677546 PMCID: PMC8537081 DOI: 10.3390/membranes11100780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022]
Abstract
Membrane proteins are involved in various cellular processes. However, purification of membrane proteins has long been a challenging task, as membrane protein stability in detergent is the bottleneck for purification and subsequent analyses. Therefore, the optimization of detergent conditions is critical for the preparation of membrane proteins. Here, we utilize analytical ultracentrifugation (AUC) to examine the effects of different detergents (OG, Triton X-100, DDM), detergent concentrations, and detergent supplementation on the behavior of membrane protein TmrA. Our results suggest that DDM is more suitable for the purification of TmrA compared with OG and TritonX-100; a high concentration of DDM yields a more homogeneous protein aggregation state; supplementing TmrA purified with a low DDM concentration with DDM maintains the protein homogeneity and aggregation state, and may serve as a practical and cost-effective strategy for membrane protein purification.
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Affiliation(s)
- Dongdong Li
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Wendan Chu
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Xinlei Sheng
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
- Correspondence: (X.S.); (W.L.); Tel.: +86-1062782031 (W.L.)
| | - Wenqi Li
- Institute of Biomedicine, Tsinghua University, Beijing 100084, China; (D.L.); (W.C.)
- National Protein Science Facility, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
- Correspondence: (X.S.); (W.L.); Tel.: +86-1062782031 (W.L.)
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12
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Scortecci JF, Molday LL, Curtis SB, Garces FA, Panwar P, Van Petegem F, Molday RS. Cryo-EM structures of the ABCA4 importer reveal mechanisms underlying substrate binding and Stargardt disease. Nat Commun 2021; 12:5902. [PMID: 34625547 PMCID: PMC8501128 DOI: 10.1038/s41467-021-26161-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/20/2021] [Indexed: 12/04/2022] Open
Abstract
ABCA4 is an ATP-binding cassette (ABC) transporter that flips N-retinylidene-phosphatidylethanolamine (N-Ret-PE) from the lumen to the cytoplasmic leaflet of photoreceptor membranes. Loss-of-function mutations cause Stargardt disease (STGD1), a macular dystrophy associated with severe vision loss. To define the mechanisms underlying substrate binding and STGD1, we determine the cryo-EM structure of ABCA4 in its substrate-free and bound states. The two structures are similar and delineate an elongated protein with the two transmembrane domains (TMD) forming an outward facing conformation, extended and twisted exocytoplasmic domains (ECD), and closely opposed nucleotide binding domains. N-Ret-PE is wedged between the two TMDs and a loop from ECD1 within the lumen leaflet consistent with a lateral access mechanism and is stabilized through hydrophobic and ionic interactions with residues from the TMDs and ECDs. Our studies provide a framework for further elucidating the molecular mechanism associated with lipid transport and disease and developing promising disease interventions.
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Affiliation(s)
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Susan B Curtis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Fabian A Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Pankaj Panwar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, Canada.
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13
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Padariya M, Kote S, Mayordomo M, Dapic I, Alfaro J, Hupp T, Fahraeus R, Kalathiya U. Structural determinants of peptide-dependent TAP1-TAP2 transit passage targeted by viral proteins and altered by cancer-associated mutations. Comput Struct Biotechnol J 2021; 19:5072-5091. [PMID: 34589184 PMCID: PMC8453138 DOI: 10.1016/j.csbj.2021.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023] Open
Abstract
The TAP1-TAP2 complex transports antigenic peptide substrates into the endoplasmic reticulum (ER). In ER, the peptides are further processed and loaded on the major histocompatibility class (MHC) I molecules by the peptide loading complex (PLC). The TAP transporters are linked with the PLC; a target for cancers and viral immune evasion. But the mechanisms whereby the cancer-derived mutations in TAP1-TAP2 or viral factors targeting the PLC, interfere peptide transport are only emerging. This study describes that transit of peptides through TAP can take place via two different channels (4 or 8 helices) depending on peptide length and sequence. Molecular dynamics and binding affinity predictions of peptide-transporters demonstrated that smaller peptides (8-10 mers; e.g. AAGIGILTV, SIINFEKL) can transport quickly through the transport tunnel compared to longer peptides (15-mer; e.g. ENPVVHFFKNIVTPR). In line with a regulated and selective peptide transport by TAPs, the immunopeptidome upon IFN-γ treatment in melanoma cells induced the shorter length (9-mer) peptide presentation over MHC-I that exhibit a relatively weak binding affinity with TAP. A conserved distance between N and C terminus residues of the studied peptides in the transport tunnel were reported. Furthermore, by adversely interacting with the TAP transport passage or affecting TAPNBD domains tilt movement, the viral proteins and cancer-derived mutations in TAP1-TAP2 may induce allosteric effects in TAP that block conformation of the tunnel (closed towards ER lumen). Interestingly, some cancer-associated mutations (e.g. TAP1R372Q and TAP2R373H) can specifically interfere with selective transport channels (i.e. for longer-peptides). These results provide a model for how viruses and cancer-associated mutations targeting TAP interfaces can affect MHC-I antigen presentation, and how the IFN-γ pathway alters MHC-I antigen presentation via the kinetics of peptide transport.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Marcos Mayordomo
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
| | - Javier Alfaro
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland EH4 2XR, United Kingdom
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland EH4 2XR, United Kingdom
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- Department of Medical Biosciences, Building 6M, Umeå University, 901 85 Umeå, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zlutykopec 7, 65653 Brno, Czech Republic
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdansk, Poland
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14
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Davies JS, Currie MJ, Wright JD, Newton-Vesty MC, North RA, Mace PD, Allison JR, Dobson RCJ. Selective Nutrient Transport in Bacteria: Multicomponent Transporter Systems Reign Supreme. Front Mol Biosci 2021; 8:699222. [PMID: 34268334 PMCID: PMC8276074 DOI: 10.3389/fmolb.2021.699222] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
Multicomponent transporters are used by bacteria to transport a wide range of nutrients. These systems use a substrate-binding protein to bind the nutrient with high affinity and then deliver it to a membrane-bound transporter for uptake. Nutrient uptake pathways are linked to the colonisation potential and pathogenicity of bacteria in humans and may be candidates for antimicrobial targeting. Here we review current research into bacterial multicomponent transport systems, with an emphasis on the interaction at the membrane, as well as new perspectives on the role of lipids and higher oligomers in these complex systems.
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Affiliation(s)
- James S Davies
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael J Currie
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Joshua D Wright
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Michael C Newton-Vesty
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Rachel A North
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Jane R Allison
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, Digital Life Institute, University of Auckland, Auckland, New Zealand
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
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15
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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16
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Stefan E, Obexer R, Hofmann S, Vu Huu K, Huang Y, Morgner N, Suga H, Tampé R. De novo macrocyclic peptides dissect energy coupling of a heterodimeric ABC transporter by multimode allosteric inhibition. eLife 2021; 10:67732. [PMID: 33929325 PMCID: PMC8116058 DOI: 10.7554/elife.67732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/29/2021] [Indexed: 12/16/2022] Open
Abstract
ATP-binding cassette (ABC) transporters constitute the largest family of primary active transporters involved in a multitude of physiological processes and human diseases. Despite considerable efforts, it remains unclear how ABC transporters harness the chemical energy of ATP to drive substrate transport across cell membranes. Here, by random nonstandard peptide integrated discovery (RaPID), we leveraged combinatorial macrocyclic peptides that target a heterodimeric ABC transport complex and explore fundamental principles of the substrate translocation cycle. High-affinity peptidic macrocycles bind conformationally selective and display potent multimode inhibitory effects. The macrocycles block the transporter either before or after unidirectional substrate export along a single conformational switch induced by ATP binding. Our study reveals mechanistic principles of ATP binding, conformational switching, and energy transduction for substrate transport of ABC export systems. We highlight the potential of de novo macrocycles as effective inhibitors for membrane proteins implicated in multidrug resistance, providing avenues for the next generation of pharmaceuticals.
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Affiliation(s)
- Erich Stefan
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Richard Obexer
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Susanne Hofmann
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Khanh Vu Huu
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Yichao Huang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
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17
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Diederichs T, Tampé R. Single Cell-like Systems Reveal Active Unidirectional and Light-Controlled Transport by Nanomachineries. ACS NANO 2021; 15:6747-6755. [PMID: 33724767 PMCID: PMC8157534 DOI: 10.1021/acsnano.0c10139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cellular life depends on transport and communication across membranes, which is emphasized by the fact that membrane proteins are prime drug targets. The cell-like environment of membrane proteins has gained increasing attention based on its important role in function and regulation. As a versatile scaffold for bottom-up synthetic biology and nanoscience, giant liposomes represent minimalistic models of living cells. Nevertheless, the incorporation of fragile multiprotein membrane complexes still remains a major challenge. Here, we report on an approach for the functional reconstitution of membrane assemblies exemplified by human and bacterial ATP-binding cassette (ABC) transporters. We reveal that these nanomachineries transport substrates unidirectionally against a steep concentration gradient. Active substrate transport can be spatiotemporally resolved in single cell-like compartments by light, enabling real-time tracking of substrate export and import in individual liposomes. This approach will help to construct delicate artificial cell-like systems.
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Affiliation(s)
- Tim Diederichs
- Institute of Biochemistry, Biocenter,
Goethe-University Frankfurt, Max-von Laue-Straße 9,
60438 Frankfurt a.M., Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter,
Goethe-University Frankfurt, Max-von Laue-Straße 9,
60438 Frankfurt a.M., Germany
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18
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Souabni H, Batista Dos Santos W, Cece Q, Catoire LJ, Puvanendran D, Bavro VN, Picard M. Quantitative real-time analysis of the efflux by the MacAB-TolC tripartite efflux pump clarifies the role of ATP hydrolysis within mechanotransmission mechanism. Commun Biol 2021; 4:493. [PMID: 33888866 PMCID: PMC8062640 DOI: 10.1038/s42003-021-01997-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Tripartite efflux pumps built around ATP-binding cassette (ABC) transporters are membrane protein machineries that perform vectorial export of a large variety of drugs and virulence factors from Gram negative bacteria, using ATP-hydrolysis as energy source. Determining the number of ATP molecules consumed per transport cycle is essential to understanding the efficiency of substrate transport. Using a reconstituted pump in a membrane mimic environment, we show that MacAB-TolC from Escherichia coli couples substrate transport to ATP-hydrolysis with high efficiency. Contrary to the predictions of the currently prevailing "molecular bellows" model of MacB-operation, which assigns the power stroke to the ATP-binding by the nucleotide binding domains of the transporter, by utilizing a novel assay, we report clear synchronization of the substrate transfer with ATP-hydrolysis, suggesting that at least some of the power stroke for the substrate efflux is provided by ATP-hydrolysis. Our findings narrow down the window for energy consumption step that results in substrate transition into the TolC-channel, expanding the current understanding of the efflux cycle of the MacB-based tripartite assemblies. Based on that we propose a modified model of the MacB cycle within the context of tripartite complex assembly.
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Affiliation(s)
- Hager Souabni
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS UMR 7099, Université de Paris, Paris, France
- Fondation Edmond de Rothschild pour le développement de la recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France
| | - William Batista Dos Santos
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS UMR 7099, Université de Paris, Paris, France
- Fondation Edmond de Rothschild pour le développement de la recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France
| | - Quentin Cece
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS UMR 7099, Université de Paris, Paris, France
- Fondation Edmond de Rothschild pour le développement de la recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France
| | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS UMR 7099, Université de Paris, Paris, France
- Fondation Edmond de Rothschild pour le développement de la recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France
| | - Dhenesh Puvanendran
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS UMR 7099, Université de Paris, Paris, France
- Fondation Edmond de Rothschild pour le développement de la recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | | | - Martin Picard
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS UMR 7099, Université de Paris, Paris, France.
- Fondation Edmond de Rothschild pour le développement de la recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France.
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19
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Thomas C, Tampé R. MHC I assembly and peptide editing - chaperones, clients, and molecular plasticity in immunity. Curr Opin Immunol 2021; 70:48-56. [PMID: 33689959 DOI: 10.1016/j.coi.2021.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/07/2021] [Indexed: 11/24/2022]
Abstract
Peptides presented on MHC I molecules allow the immune system to detect diseased cells. The displayed peptides typically stem from proteasomal degradation of cytoplasmic proteins and are translocated into the ER lumen where they are trimmed and loaded onto MHC I. Peptide translocation is carried out by the transporter associated with antigen processing, which forms the central building block of a dynamic assembly called the peptide-loading complex (PLC). By coordinating peptide transfer with MHC I loading and peptide optimization, the PLC is a linchpin in the adaptive immune system. Peptide loading and optimization is catalyzed by the PLC component tapasin and the PLC-independent TAPBPR, two MHC I-dedicated enzymes chaperoning empty or suboptimally loaded MHC I and selecting stable peptide-MHC I complexes in a process called peptide editing or proofreading. Recent structural and functional studies of peptide editing have dramatically improved our understanding of this pivotal event in antigen processing/presentation. This review is dedicated to Vincenzo Cerundolo (1959-2020) for his pioneering work in the field of antigen processing/presentation.
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Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
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20
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Shukla S, Baumgart T. Enzymatic trans-bilayer lipid transport: Mechanisms, efficiencies, slippage, and membrane curvature. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183534. [PMID: 33340491 PMCID: PMC8351443 DOI: 10.1016/j.bbamem.2020.183534] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
The eukaryotic plasma membrane's lipid composition is found to be ubiquitously asymmetric comparing inner and outer leaflets. This membrane lipid asymmetry plays a crucial role in diverse cellular processes critical for cell survival. A specialized set of transmembrane proteins called translocases, or flippases, have evolved to maintain this membrane lipid asymmetry in an energy-dependent manner. One potential consequence of local variations in membrane lipid asymmetry is membrane remodeling, which is essential for cellular processes such as intracellular trafficking. Recently, there has been a surge in the identification and characterization of flippases, which has significantly advanced the understanding of their functional mechanisms. Furthermore, there are intriguing possibilities for a coupling between membrane curvature and flippase activity. In this review we highlight studies that link membrane shape and remodeling to differential stresses generated by the activity of lipid flippases with an emphasis on data obtained through model membrane systems. We review the common mechanistic models of flippase-mediated lipid flipping and discuss common techniques used to test lipid flippase activity. We then compare the existing data on lipid translocation rates by flippases and conclude with potential future directions for this field.
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Affiliation(s)
- Sankalp Shukla
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States.
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21
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Millan CR, Francis M, Khandelwal NK, Thompson VF, Thaker TM, Tomasiak TM. A Conserved Motif in Intracellular Loop 1 Stabilizes the Outward-Facing Conformation of TmrAB. J Mol Biol 2021; 433:166834. [PMID: 33524413 DOI: 10.1016/j.jmb.2021.166834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/05/2023]
Abstract
The ATP binding cassette (ABC) family of transporters moves small molecules (lipids, sugars, peptides, drugs, nutrients) across membranes in nearly all organisms. Transport activity requires conformational switching between inward-facing and outward-facing states driven by ATP-dependent dimerization of two nucleotide binding domains (NBDs). The mechanism that connects ATP binding and hydrolysis in the NBDs to conformational changes in a substrate binding site in the transmembrane domains (TMDs) is currently an outstanding question. Here we use sequence coevolution analyses together with biochemical characterization to investigate the role of a highly conserved region in intracellular loop 1 we define as the GRD motif in coordinating domain rearrangements in the heterodimeric peptide exporter from Thermus thermophilus, TmrAB. Mutations in the GRD motif alter ATPase activity as well as transport. Disulfide crosslinking, evolutionary trace, and evolutionary coupling analysis reveal that these effects are likely due to the destabilization of a network in which the GRD motif in TmrA bridges residues of the Q-loop, X-loop, and ABC motif in the NBDs to residues in the TmrAB peptide substrate binding site, thus providing an avenue for conformational coupling. We further find that disruption of this network in TmrA versus TmrB has different functional consequences, hinting at an intrinsic asymmetry in heterodimeric ABC transporters extending beyond that of the NBDs. These results support a mechanism in which the GRD motifs help coordinate a transition to an outward open conformation, and each half of the transporter likely plays a different role in the conformational cycle of TmrAB.
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Affiliation(s)
- Cinthia R Millan
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | - Martina Francis
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | | | - Valery F Thompson
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | - Tarjani M Thaker
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
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22
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Stockner T, Gradisch R, Schmitt L. The role of the degenerate nucleotide binding site in type I ABC exporters. FEBS Lett 2020; 594:3815-3838. [PMID: 33179257 PMCID: PMC7756269 DOI: 10.1002/1873-3468.13997] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/26/2020] [Accepted: 10/15/2020] [Indexed: 12/18/2022]
Abstract
ATP‐binding cassette (ABC) transporters are fascinating molecular machines that are capable of transporting a large variety of chemically diverse compounds. The energy required for translocation is derived from binding and hydrolysis of ATP. All ABC transporters share a basic architecture and are composed of two transmembrane domains and two nucleotide binding domains (NBDs). The latter harbor all conserved sequence motifs that hallmark the ABC transporter superfamily. The NBDs form the nucleotide binding sites (NBSs) in their interface. Transporters with two active NBSs are called canonical transporters, while ABC exporters from eukaryotic organisms, including humans, frequently have a degenerate NBS1 containing noncanonical residues that strongly impair ATP hydrolysis. Here, we summarize current knowledge on degenerate ABC transporters. By integrating structural information with biophysical and biochemical evidence of asymmetric function, we develop a model for the transport cycle of degenerate ABC transporters. We will elaborate on the unclear functional advantages of a degenerate NBS.
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Affiliation(s)
- Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Ralph Gradisch
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
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23
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Srikant S. Evolutionary history of ATP-binding cassette proteins. FEBS Lett 2020; 594:3882-3897. [PMID: 33145769 DOI: 10.1002/1873-3468.13985] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/01/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
ATP-binding cassette (ABC) proteins are found in every sequenced genome and evolved deep in the phylogenetic tree of life. ABC proteins form one of the largest homologous protein families, with most being involved in substrate transport across biological membranes, and a few cytoplasmic members regulating in essential processes like translation. The predominant ABC protein classification scheme is derived from human members, but the increasing number of fully sequenced genomes permits to reevaluate this paradigm in the light of the evolutionary history the ABC-protein superfamily. As we study the diversity of substrates, mechanisms, and physiological roles of ABC proteins, knowledge of the evolutionary relationships highlights similarities and differences that can be attributed to specific branches in protein divergence. While alignments and trees built on natural sequence variation account for the evolutionary divergence of ABC proteins, high-throughput experiments and next-generation sequencing creating experimental sequence variation are instrumental in identifying functional constraints. The combination of natural and experimentally produced sequence variation allows a broader and more rational study of the function and physiological roles of ABC proteins.
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Affiliation(s)
- Sriram Srikant
- Department of Biology, Massachusetts Institute of Technology
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24
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Lewinson O, Orelle C, Seeger MA. Structures of ABC transporters: handle with care. FEBS Lett 2020; 594:3799-3814. [PMID: 33098660 PMCID: PMC7756565 DOI: 10.1002/1873-3468.13966] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/22/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
In the past two decades, the ATP‐binding cassette (ABC) transporters' field has undergone a structural revolution. The importance of structural biology to the development of the field of ABC transporters cannot be overstated, as the ensemble of structures not only revealed the architecture of ABC transporters but also shaped our mechanistic view of these remarkable molecular machines. Nevertheless, we advocate that the mechanistic interpretation of the structures is not trivial and should be carried out with prudence. Herein, we bring several examples of structures of ABC transporters that merit re‐interpretation via careful comparison to experimental data. We propose that it is of the upmost importance to place new structures within the context of the available experimental data.
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Affiliation(s)
- Oded Lewinson
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Cédric Orelle
- CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), University of Lyon, Lyon, France
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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25
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Barth K, Rudolph M, Diederichs T, Prisner TF, Tampé R, Joseph B. Thermodynamic Basis for Conformational Coupling in an ATP-Binding Cassette Exporter. J Phys Chem Lett 2020; 11:7946-7953. [PMID: 32818376 DOI: 10.1021/acs.jpclett.0c01876] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
ATP-binding cassette (ABC) transporters constitute one of the largest protein superfamilies, and they mediate the transport of diverse substrates across the membrane. The molecular mechanism for transducing the energy from ATP binding and hydrolysis into the conformational changes remains elusive. Here, we determined the thermodynamics underlying the ATP-induced global conformational switching for the ABC exporter TmrAB using temperature-resolved pulsed electron-electron double resonance (PELDOR or DEER) spectroscopy. We show that a strong entropy-enthalpy compensation mechanism enables the closure of the nucleotide-binding domains (NBDs) over a wide temperature range. This is mechanically coupled with an outward opening of the transmembrane domains (TMDs) accompanied by an entropy gain. The conserved catalytic glutamate plays a key role in the overall energetics. Our results reveal the thermodynamic basis for the chemomechanical energy coupling in an ABC exporter and present a new strategy to explore the energetics of similar membrane protein complexes.
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Affiliation(s)
- Katja Barth
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany
- Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Michael Rudolph
- Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany
| | - Tim Diederichs
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany
- Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Benesh Joseph
- Centre of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany
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A structural framework for unidirectional transport by a bacterial ABC exporter. Proc Natl Acad Sci U S A 2020; 117:19228-19236. [PMID: 32703810 PMCID: PMC7430982 DOI: 10.1073/pnas.2006526117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A specific ATP-binding cassette (ABC) transporter is generally viewed to function as either an exporter or an importer, but in principle ABC transporters can transport substrates in both directions across the membrane. Structural studies of the prokaryotic ABC exporter NaAtm1 demonstrate that progression through the transport cycle is accompanied by changes in transmembrane helix 6 (TM6) that modulate the binding cavity for transported substrate. Significantly, kinking of TM6 in a post-ATP hydrolysis state stabilized by MgADPVO4 eliminates the substrate-binding cavity. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport. The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from Novosphingobium aromaticivorans (NaAtm1) can export glutathione derivatives and confer protection against heavy-metal toxicity. To establish the structural framework underlying the NaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single-particle cryo-electron microscopy in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As NaAtm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione-binding site and the associated substrate-binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO4 eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provide an elegant and conceptually simple mechanism for enforcing the export directionality of transport by NaAtm1. One of the disulfide crosslinked NaAtm1 variants characterized in this work retains significant glutathione transport activity, suggesting that ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide-binding domains in the inward-facing conformation.
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Göddeke H, Schäfer LV. Capturing Substrate Translocation in an ABC Exporter at the Atomic Level. J Am Chem Soc 2020; 142:12791-12801. [PMID: 32578427 DOI: 10.1021/jacs.0c05502] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
ATP-binding cassette (ABC) transporters chemomechanically couple ATP binding and hydrolysis to large-scale conformational changes, ultimately leading to substrate translocation across biological membranes. Despite recent progress in the structure determination of substrate-bound ABC exporters, the inherently dynamic mechanism of substrate transport remains unclear at the atomic level. In this work, we capture substrate translocation in the heterodimeric ABC exporter TM287/288 from the hyperthermophilic bacterium Thermotoga maritima using all-atom molecular dynamics (MD) simulations. Unguided multimicrosecond simulations at 375 K show how the drugs daunorubicin and verapamil, which were initially docked into the ABC transporter, get translocated through the exporter by following its large-scale alternating access conformational transitions between an inward-facing (IF) and an outward-facing (OF) conformation. Triggered by the affinity difference due to differential solvation of the binding cavity in the IF and OF conformations, the substrates unbind from the OF transporter and partition into the lipid bilayer. While daunorubicin is stably inserted into the outer leaflet of the bilayer, verapamil dynamically flip flops between the bilayer leaflets, possibly rendering its net transport futile.
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Affiliation(s)
- Hendrik Göddeke
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
| | - Lars V Schäfer
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44780 Bochum, Germany
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