1
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Badiee SA, Isu UH, Khodadadi E, Moradi M. The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs. MEMBRANES 2023; 13:568. [PMID: 37367772 DOI: 10.3390/membranes13060568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023]
Abstract
Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug resistance, which subsequently leads to the failure of therapeutic interventions and hinders successful treatments. One key mechanism by which multidrug resistance (MDR) proteins carry out their transport function is through alternating access. This mechanism involves intricate conformational changes that enable the binding and transport of substrates across cellular membranes. In this extensive review, we provide an overview of ABC transporters, including their classifications and structural similarities. We focus specifically on well-known mammalian multidrug resistance proteins such as MRP1 and Pgp (MDR1), as well as bacterial counterparts such as Sav1866 and lipid flippase MsbA. By exploring the structural and functional features of these MDR proteins, we shed light on the roles of their nucleotide-binding domains (NBDs) and transmembrane domains (TMDs) in the transport process. Notably, while the structures of NBDs in prokaryotic ABC proteins, such as Sav1866, MsbA, and mammalian Pgp, are identical, MRP1 exhibits distinct characteristics in its NBDs. Our review also emphasizes the importance of two ATP molecules for the formation of an interface between the two binding sites of NBD domains across all these transporters. ATP hydrolysis occurs following substrate transport and is vital for recycling the transporters in subsequent cycles of substrate transportation. Specifically, among the studied transporters, only NBD2 in MRP1 possesses the ability to hydrolyze ATP, while both NBDs of Pgp, Sav1866, and MsbA are capable of carrying out this reaction. Furthermore, we highlight recent advancements in the study of MDR proteins and the alternating access mechanism. We discuss the experimental and computational approaches utilized to investigate the structure and dynamics of MDR proteins, providing valuable insights into their conformational changes and substrate transport. This review not only contributes to an enhanced understanding of multidrug resistance proteins but also holds immense potential for guiding future research and facilitating the development of effective strategies to overcome multidrug resistance, thus improving therapeutic interventions.
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Affiliation(s)
- Shadi A Badiee
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ugochi H Isu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ehsaneh Khodadadi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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2
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Saha S, Ratrey P, Mishra A. Association of Lasioglossin-III Antimicrobial Peptide with Model Lipid Bilayers. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922020178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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3
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Structural dynamics of ABC transporters: molecular simulation studies. Biochem Soc Trans 2021; 49:405-414. [PMID: 33634827 DOI: 10.1042/bst20200710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/31/2022]
Abstract
The biological activities of living organisms involve various inputs and outputs. The ATP-driven substances (biomolecules) responsible for these kinds of activities through membrane (i.e. uptake and efflux of substrates) include ATP-binding cassette (ABC) transporters, some of which play important roles in multidrug resistance. The basic architecture of ABC transporters comprises transmembrane domains (TMDs) and nucleotide-binding domains (NBDs). The functional dynamics (substrate transport) of ABC transporters are realized by concerted motions, such as NBD dimerization, mechanical transmission via coupling helices (CHs), and the translocation of substrates through TMDs, which are induced by the binding and/or hydrolysis of ATP molecules and substrates. In this mini-review, we briefly discuss recent progresses in the structural dynamics as revealed by molecular simulation studies at all-atom (AA), coarse-grained (CG), and quantum mechanics/molecular mechanics (QM/MM) levels.
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4
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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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5
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Zhao ZJ, Gao XY, Zeng JC, Zhang SL, Meng XM, Shen YJ, Sheng XH. Theoretical Insights into the Cotransport Mechanism of GSH with Anticancer Drugs by MRP1. J Phys Chem B 2020; 124:9803-9811. [DOI: 10.1021/acs.jpcb.0c06662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Zi-Jing Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Xin-Ying Gao
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Jia-Cheng Zeng
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
| | - Shao-Long Zhang
- College of Physics and Electronics, Shandong Normal University, 88 Wenhuadonglu, Jinan, Shandong 250014, China
| | - Xian-Mai Meng
- College of Physics and Electronics, Shandong Normal University, 88 Wenhuadonglu, Jinan, Shandong 250014, China
| | - Yan-Jun Shen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Shandong University Qilu Hospital, Jinan, Shandong 250012, China
| | - Xie-Huang Sheng
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, China
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6
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Acar B, Rose J, Aykac Fas B, Ben-Tal N, Lewinson O, Haliloglu T. Distinct Allosteric Networks Underlie Mechanistic Speciation of ABC Transporters. Structure 2020; 28:651-663.e5. [DOI: 10.1016/j.str.2020.03.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/20/2020] [Accepted: 03/27/2020] [Indexed: 02/08/2023]
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7
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Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
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8
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Holland IB. Rise and rise of the ABC transporter families. Res Microbiol 2019; 170:304-320. [PMID: 31442613 DOI: 10.1016/j.resmic.2019.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/30/2019] [Accepted: 08/13/2019] [Indexed: 01/15/2023]
Abstract
This review will inevitably be influenced by my personal experience and personal view of the progression of this amazing family of proteins. This has generated a huge literature in over nearly five decades, some ideas have bloomed and faded while others have persisted, other contributions simply become redundant, overtaken by better techniques. At the outset, the pioneers had no idea of the magnitude of the topic they were working on, then a very rough idea of the significance emerged and, progressively, the picture becomes sharper and finally extraordinary. I have tried to produce at least an outline of that progression. My apologies for the also inevitable omissions, especially relating to the mass of biochemical and spectroscopy and genetical studies. I decided to prioritise structural biology because structures when successful are definitive and of course provide a 'visual' image. However, I tried to limit the structural aspects to the proteins that reflected the main advances.
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Affiliation(s)
- I Barry Holland
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Sud, Orsay, France.
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9
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Hirano R, Yabuchi T, Sakurai M, Furuta T. Development of an ATP force field for coarse-grained simulation of ATPases and its application to the maltose transporter. J Comput Chem 2019; 40:2096-2102. [PMID: 31090948 DOI: 10.1002/jcc.25861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/28/2019] [Accepted: 05/01/2019] [Indexed: 01/30/2023]
Abstract
The biological functions of ATPases, such as myosin, kinesin, and ABC transporter, are due to large conformational motions driven by energy obtained from ATP. Elucidation of the mechanisms underlying these ATP-driven movements is one of the greatest challenges in computational chemistry. It has been shown that the MARTINI coarse-grained method is a promising tool for the investigation of large conformational motions in various proteins. However, this method has not yet been applied to ATPases because of the lack of a force field for the ATP molecule. Here, we developed force field parameters for the ATP molecule and conducted simulations using these parameters for the subunits (MalK2 ) and the full-length structure (MalFGK2 -E) of a maltose transporter. It was found for both targets that the dimerization of the nucleotide binding domains (NBDs) is induced upon ATP binding. Moreover, for the full-length transporter, the conformational transition from the pre-translocation state to the outward-facing state was observed and was accompanied by an initial transport motion of the substrate. It is expected that coarse-grained simulations utilizing the parameters for the ATP molecule developed here will serve as a powerful tool for investigating other ATPases as well. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Ryosuke Hirano
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Tsubasa Yabuchi
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
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10
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Ladefoged LK, Zeppelin T, Schiøtt B. Molecular modeling of neurological membrane proteins − from binding sites to synapses. Neurosci Lett 2019; 700:38-49. [DOI: 10.1016/j.neulet.2018.05.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 01/07/2023]
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11
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Lacabanne D, Orelle C, Lecoq L, Kunert B, Chuilon C, Wiegand T, Ravaud S, Jault JM, Meier BH, Böckmann A. Flexible-to-rigid transition is central for substrate transport in the ABC transporter BmrA from Bacillus subtilis. Commun Biol 2019; 2:149. [PMID: 31044174 PMCID: PMC6488656 DOI: 10.1038/s42003-019-0390-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/15/2019] [Indexed: 01/15/2023] Open
Abstract
ATP-binding-cassette (ABC) transporters are molecular pumps that translocate molecules across the cell membrane by switching between inward-facing and outward-facing states. To obtain a detailed understanding of their mechanism remains a challenge to structural biology, as these proteins are notoriously difficult to study at the molecular level in their active, membrane-inserted form. Here we use solid-state NMR to investigate the multidrug ABC transporter BmrA reconstituted in lipids. We identify the chemical-shift differences between the inward-facing, and outward-facing state induced by ATP:Mg2+:Vi addition. Analysis of an X-loop mutant, for which we show that ATPase and transport activities are uncoupled, reveals an incomplete transition to the outward-facing state upon ATP:Mg2+:Vi addition, notably lacking the decrease in dynamics of a defined set of residues observed in wild-type BmrA. This suggests that this stiffening is required for an efficient transmission of the conformational changes to allow proper transport of substrate by the pump.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Britta Kunert
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Claire Chuilon
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stéphanie Ravaud
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
| | - Beat H. Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7, passage de Vercors, 69367 Lyon, France
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12
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Immadisetty K, Hettige J, Moradi M. Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter. ACS CENTRAL SCIENCE 2019; 5:43-56. [PMID: 30693324 PMCID: PMC6346382 DOI: 10.1021/acscentsci.8b00480] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 06/09/2023]
Abstract
By undergoing conformational changes, active membrane transporters alternate between an inward-facing (IF) and an outward-facing (OF) state to transport their substrates across cellular membrane. The conformational landscape of membrane transporters, however, could be influenced by their environment, and the dependence of the alternating access mechanism on the lipid composition has not been understood at the molecular level. We have performed an extensive set of microsecond-level all-atom molecular dynamics (MD) simulations on bacterial ATP binding cassette (ABC) exporter Sav1866 in six different phosphocholine (PC) and phosphoethanolamine (PE) lipid membrane environments. This study mainly focuses on the energetically downhill OF-to-IF conformational transition of Sav1866 upon the ATP hydrolysis. We observe that the transporter undergoes large-scale conformational changes in the PE environment, particularly in the POPE lipids, resulting in an IF-occluded conformation, a transition that does not occur when the transporter is embedded in any of the PC lipid bilayers. We propose that the PE lipids facilitate the closing of the protein on the periplasmic side due to their highly polar headgroups that mediate the interaction of the two transmembrane (TM) bundles by a network of lipid-lipid and lipid-protein hydrogen bonds. POPE lipids in particular facilitate the closure of periplasmic gate by promoting a hinge formation in TM helices and an interbundle salt bridge formation. This study explains how the alternating access mechanism and the flippase activity in ABC exporters could be lipid-dependent.
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13
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Rahman SJ, Kaur P. Conformational changes in a multidrug resistance ABC transporter DrrAB: Fluorescence-based approaches to study substrate binding. Arch Biochem Biophys 2018; 658:31-45. [PMID: 30243711 DOI: 10.1016/j.abb.2018.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/30/2018] [Accepted: 09/19/2018] [Indexed: 01/12/2023]
Abstract
Bacterial multidrug transporter DrrAB exhibits overlapping substrate specificity with mammalian P-glycoprotein. DrrA hydrolyzes ATP, and the energy is transduced to carrier DrrB resulting in export of drugs. Previous studies suggested that DrrB contains a large and flexible drug-binding pocket made of aromatic residues contributed by several transmembrane helices with different drugs binding to both specific and shared residues in this pocket. However, direct binding of drugs to DrrAB or the mechanism of substrate-induced conformational changes between DrrA and DrrB has so far not been investigated. We used two fluorescence-based approaches to determine substrate binding to purified DrrAB. Our analysis shows that DrrB binds drugs with variable affinities and contains multiple drug binding sites. This work also provides evidence for two asymmetric nucleotide binding sites in DrrA with strikingly different binding affinities. Using targeted fluorescence labeling, we provide clear evidence of long-range conformational changes occurring between DrrA and DrrB. It is proposed that the transduction pathway from the nucleotide-binding DrrA subunit to the substrate binding DrrB subunit includes Q-loop and CREEM motifs in DrrA and EAA-like motif in DrrB. This study lays a solid groundwork for examining roles of various conserved regions of DrrA and DrrB in transduction of conformational changes.
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Affiliation(s)
- Sadia J Rahman
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States.
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14
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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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15
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Szöllősi D, Szakács G, Chiba P, Stockner T. Dissecting the Forces that Dominate Dimerization of the Nucleotide Binding Domains of ABCB1. Biophys J 2018; 114:331-342. [PMID: 29401431 PMCID: PMC5984967 DOI: 10.1016/j.bpj.2017.11.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/11/2017] [Accepted: 11/14/2017] [Indexed: 01/10/2023] Open
Abstract
P-glycoprotein, also known as multidrug resistance protein 1 or ABCB1, can export a wide range of chemically unrelated compounds, including chemotherapeutic drugs. ABCB1 consists of two transmembrane domains that form the substrate binding and translocation domain, and of two cytoplasmic nucleotide binding domains (NBDs) that energize substrate transport by ATP binding and hydrolysis. ATP binding triggers dimerization of the NBDs, which switches the transporter from an inward facing to an outward facing transmembrane domain conformation. We performed MD simulations to study the dynamic behavior of the NBD dimer in the presence or absence of nucleotides. In the apo configuration, the NBDs were overall attractive to each other as shown in the potential of mean force profile, but the energy well was shallow and broad. In contrast, a sharp and deep energy minimum (∼-42 kJ/mol) was found in the presence of ATP, leading to a well-defined conformation. Motif interaction network analyses revealed that ATP stabilizes the NBD dimer by serving as the central hub for interdomain connections. Simulations showed that forces promoting dimerization are multilayered, dominated by electrostatic interactions between the nucleotide and conserved amino acids of the signature sequence and the Walker A motif. In addition, direct and water-bridged hydrogen bonds between NBDs provided conformation-defining interactions. Importantly, we characterized a largely unrecognized but essential contribution from hydrophobic interactions between the adenine moiety of the nucleotides and a hydrophobic surface of the X-loop to the stabilization of the nucleotide-bound NBD dimer. These hydrophobic interactions lead to a sharp energy minimum, thereby conformationally restricting the nucleotide-bound state.
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Affiliation(s)
- Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Gergely Szakács
- Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Peter Chiba
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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16
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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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17
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Jafari M, Mehrnejad F, Aghdami R, Chaparzadeh N, Razaghi Moghadam Kashani Z, Doustdar F. Identification of the Crucial Residues in the Early Insertion of Pardaxin into Different Phospholipid Bilayers. J Chem Inf Model 2017; 57:929-941. [DOI: 10.1021/acs.jcim.6b00693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Majid Jafari
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 14395-1561, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran
| | - Raheleh Aghdami
- Department of Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz 53714-161, Iran
| | - Nader Chaparzadeh
- Department of Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz 53714-161, Iran
| | - Zahra Razaghi Moghadam Kashani
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Farahnoosh Doustdar
- Department of Microbiology, Faculty of
Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
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18
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Xu Y, Seelig A, Bernèche S. Unidirectional Transport Mechanism in an ATP Dependent Exporter. ACS CENTRAL SCIENCE 2017; 3:250-258. [PMID: 28386603 PMCID: PMC5364450 DOI: 10.1021/acscentsci.7b00068] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Indexed: 05/25/2023]
Abstract
ATP-binding cassette (ABC) transporters use the energy of ATP binding and hydrolysis to move a large variety of compounds across biological membranes. P-glycoprotein, involved in multidrug resistance, is the most investigated eukaryotic family member. Although a large number of biochemical and structural approaches have provided important information, the conformational dynamics underlying the coupling between ATP binding/hydrolysis and allocrite transport remains elusive. To tackle this issue, we performed molecular dynamic simulations for different nucleotide occupancy states of Sav1866, a prokaryotic P-glycoprotein homologue. The simulations reveal an outward-closed conformation of the transmembrane domain that is stabilized by the binding of two ATP molecules. The hydrolysis of a single ATP leads the X-loop, a key motif of the ATP binding cassette, to interfere with the transmembrane domain and favor its outward-open conformation. Our findings provide a structural basis for the unidirectionality of transport in ABC exporters and suggest a ratio of one ATP hydrolyzed per transport cycle.
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Affiliation(s)
- Yanyan Xu
- SIB
Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Anna Seelig
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Simon Bernèche
- SIB
Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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19
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Weng J, Gu S, Gao X, Huang X, Wang W. Maltose-binding protein effectively stabilizes the partially closed conformation of the ATP-binding cassette transporter MalFGK2. Phys Chem Chem Phys 2017; 19:9366-9373. [DOI: 10.1039/c6cp07943a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Maltose transporter MalFGK2is a type-I importer in the ATP-binding cassette (ABC) transporter superfamily.
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Affiliation(s)
- Jingwei Weng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- Department of Chemistry, and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
| | - Shuo Gu
- Department of Chemistry
- Institute for Advance Study and School of Science
- The Hong Kong University of Science and Technology
- Kowloon
- China
| | - Xin Gao
- Computer, Electrical and Mathematical Sciences and Engineering Division
- King Abdullah University of Science and Technology
- Thuwal
- Saudi Arabia
| | - Xuhui Huang
- Department of Chemistry
- Institute for Advance Study and School of Science
- The Hong Kong University of Science and Technology
- Kowloon
- China
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials
- Department of Chemistry, and Institutes of Biomedical Sciences
- Fudan University
- Shanghai
- P. R. China
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20
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Pan C, Weng J, Wang W. Conformational Dynamics and Protein-Substrate Interaction of ABC Transporter BtuCD at the Occluded State Revealed by Molecular Dynamics Simulations. Biochemistry 2016; 55:6897-6907. [PMID: 27951660 DOI: 10.1021/acs.biochem.6b00386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ATP-binding cassette (ABC) transporters are ubiquitous in all three kingdoms of life and are implicated in many clinically relevant physiological processes. They couple the energy released by ATP hydrolysis to facilitate substrate translocation across cell membranes. The crystal structures of type II ABC importers have revealed their unique transmembrane domain architecture consisting of 10 transmembrane helices and their structurally conserved nucleotide-binding domains among all ABC transporters. However, molecular details of the interactions between the importers and their substrate remain largely elusive. Taking vitamin B12 importer BtuCD as an exemplar of type II importers, we investigated the dynamics of its occluded state and the detailed protein-substrate interactions using molecular dynamics simulation. Our trajectories show that the importer accommodates the substrate through a nonspecific binding mode as the substrate undergoes evident vertical and tilt motions inside the translocation cavity. Extensive hydrogen bond and hydrophobic interactions were observed between the substrate and the importer; however, most of these interactions are weak, with <38% occurrence. The presence of substrate leads to enlargement of the translocation cavity, especially at its cytoplasmic end, which may activate cytoplasmic regions and probably facilitate the transportation. The perturbations caused by periplasmic binding protein and nucleotides were also investigated. The study provides deeper insight into the translocation mechanism of BtuCD.
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Affiliation(s)
- Chao Pan
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University , Shanghai, P. R. China
| | - Jingwei Weng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University , Shanghai, P. R. China
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University , Shanghai, P. R. China
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21
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Furuta T, Sato Y, Sakurai M. Structural Dynamics of the Heterodimeric ABC Transporter TM287/288 Induced by ATP and Substrate Binding. Biochemistry 2016; 55:6730-6738. [PMID: 27933796 DOI: 10.1021/acs.biochem.6b00947] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
TM287/288 is a heterodimeric ATP-binding cassette (ABC) transporter, which harnesses the energy of ATP binding and hydrolysis at the nucleotide-binding domains (NBDs) to transport a wide variety of molecules through the transmembrane domains (TMDs) by alternating inward- and outward-facing conformations. Here, we conducted multiple 100 ns molecular dynamics simulations of TM287/288 in different ATP- and substrate-bound states to elucidate the effects of ATP and substrate binding. As a result, the binding of two ATP molecules to the NBDs induced the formation of the consensus ATP-binding pocket (ABP2) or the NBD dimerization, whereas these processes did not occur in the presence of a single ATP molecule or when the protein was in its apo state. Moreover, binding of the substrate to the TMDs enhanced the formation of ABP2 through allosteric TMD-NBD communication. Furthermore, in the apo state, α-helical subdomains of the NBDs approached each other, acquiring a conformation with core half-pockets exposed to the solvent, appropriate for ATP binding. We propose a "core-exposed" model for this novel conformation found in the apo state of ABC transporters. These findings provide important insights into the structural dynamics of ABC transporters.
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Affiliation(s)
- Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yukiko Sato
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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22
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Pan C, Weng J, Wang W. ATP Hydrolysis Induced Conformational Changes in the Vitamin B12 Transporter BtuCD Revealed by MD Simulations. PLoS One 2016; 11:e0166980. [PMID: 27870912 PMCID: PMC5117765 DOI: 10.1371/journal.pone.0166980] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 11/07/2016] [Indexed: 12/17/2022] Open
Abstract
ATP binding cassette (ABC) transporters utilize the energy of ATP hydrolysis to uni-directionally transport substrates across cell membrane. ATP hydrolysis occurs at the nucleotide-binding domain (NBD) dimer interface of ABC transporters, whereas substrate translocation takes place at the translocation pathway between the transmembrane domains (TMDs), which is more than 30 angstroms away from the NBD dimer interface. This raises the question of how the hydrolysis energy released at NBDs is "transmitted" to trigger the conformational changes at TMDs. Using molecular dynamics (MD) simulations, we studied the post-hydrolysis state of the vitamin B12 importer BtuCD. Totally 3-μs MD trajectories demonstrate a predominantly asymmetric arrangement of the NBD dimer interface, with the ADP-bound site disrupted and the ATP-bound site preserved in most of the trajectories. TMDs response to ATP hydrolysis by separation of the L-loops and opening of the cytoplasmic gate II, indicating that hydrolysis of one ATP could facilitate substrate translocation by opening the cytoplasmic end of translocation pathway. It was also found that motions of the L-loops and the cytoplasmic gate II are coupled with each other through a contiguous interaction network involving a conserved Asn83 on the extended stretch preceding TM3 helix plus the cytoplasmic end of TM2/6/7 helix bundle. These findings entail a TMD-NBD communication mechanism for type II ABC importers.
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Affiliation(s)
- Chao Pan
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Jingwei Weng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
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23
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Abstract
P-glycoprotein (P-gp) is an ATP-binding cassette transporter that exports a huge range of compounds out of cells and is thus one of the key proteins in conferring multi-drug resistance in cancer. Understanding how it achieves such a broad specificity and the series of conformational changes that allow export to occur form major, on-going, research objectives around the world. Much of our knowledge to date has been derived from mutagenesis and assay data. However, in recent years, there has also been great progress in structural biology and although the structure of human P-gp has not yet been solved, there are now a handful of related structures on which homology models can be built to aid in the interpretation of the vast amount of experimental data that currently exists. Many models for P-gp have been built with this aim, but the situation is complicated by the apparent flexibility of the system and by the fact that although many potential templates exist, there is large variation in the conformational state in which they have been crystallized. In this review, we summarize how homology modelling has been used in the past, how models are typically selected and finally illustrate how MD simulations can be used as a means to give more confidence about models that have been generated via this approach.
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24
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Schindler BD, Kaatz GW. Multidrug efflux pumps of Gram-positive bacteria. Drug Resist Updat 2016; 27:1-13. [DOI: 10.1016/j.drup.2016.04.003] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/28/2016] [Accepted: 04/22/2016] [Indexed: 11/16/2022]
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25
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Prieß M, Schäfer LV. Release of Entropic Spring Reveals Conformational Coupling Mechanism in the ABC Transporter BtuCD-F. Biophys J 2016; 110:2407-2418. [PMID: 27276259 PMCID: PMC4906252 DOI: 10.1016/j.bpj.2016.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/30/2016] [Accepted: 04/20/2016] [Indexed: 01/14/2023] Open
Abstract
Substrate translocation by ATP-binding cassette (ABC) transporters involves coupling of ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) to conformational changes in the transmembrane domains. We used molecular dynamics simulations to investigate the atomic-level mechanism of conformational coupling in the ABC transporter BtuCD-F, which imports vitamin B12 across the inner membrane of Escherichia coli. Our simulations show how an engineered disulfide bond across the NBD dimer interface reduces conformational fluctuations and hence configurational entropy. As a result, the disulfide bond is under substantial mechanical stress. Releasing this entropic spring, as is the case in the wild-type transporter, combined with analyzing the pairwise forces between individual residues, unravels the coupling mechanism. The identified pathways along which force is propagated from the NBDs via the coupling helix to the transmembrane domains are composed of highly conserved residues, underlining their functional relevance. This study not only reveals the details of conformational coupling in BtuCD-F, it also provides a promising approach to other long-range conformational couplings, e.g., in ABC exporters or other ATP-driven molecular machines.
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Affiliation(s)
- Marten Prieß
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany.
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26
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Grouleff J, Søndergaard S, Koldsø H, Schiøtt B. Properties of an inward-facing state of LeuT: conformational stability and substrate release. Biophys J 2016; 108:1390-1399. [PMID: 25809252 DOI: 10.1016/j.bpj.2015.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 01/12/2023] Open
Abstract
The leucine transporter (LeuT) is a bacterial homolog of the human monoamine transporters, which are important pharmaceutical targets. There are no high-resolution structures of the human transporters available; however, LeuT has been crystallized in several different conformational states. Recently, an inward-facing conformation of LeuT was solved revealing an unexpectedly large movement of transmembrane helix 1a (TM1a). We have performed molecular dynamics simulations of the mutated and wild-type transporter, with and without the cocrystallized Fab antibody fragment, to investigate the properties of this inward-facing conformation in relation to transport by LeuT within the membrane environment. In all of the simulations, local conformational changes with respect to the crystal structure are consistently observed, especially in TM1a. Umbrella sampling revealed a soft potential for TM1a tilting. Furthermore, simulations of inward-facing LeuT with Na(+) ions and substrate bound suggest that one of the Na(+) ion binding sites is fully disrupted. Release of alanine and the second Na(+) ion is also observed, giving insight into the final stage of the translocation process in atomistic detail.
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Affiliation(s)
- Julie Grouleff
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Siri Søndergaard
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Heidi Koldsø
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures and Interdisciplinary Nanoscience Center, Department of Chemistry, Aarhus University, Aarhus, Denmark.
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27
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Liu H, Li D, Li Y, Hou T. Atomistic molecular dynamics simulations of ATP-binding cassette transporters. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hui Liu
- College of Pharmaceutical Sciences; Zhejiang University; Hangzhou China
| | - Dan Li
- College of Pharmaceutical Sciences; Zhejiang University; Hangzhou China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM); Soochow University; Suzhou China
| | - Tingjun Hou
- College of Pharmaceutical Sciences; Zhejiang University; Hangzhou China
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28
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Corradi V, Vergani P, Tieleman DP. Cystic Fibrosis Transmembrane Conductance Regulator (CFTR): CLOSED AND OPEN STATE CHANNEL MODELS. J Biol Chem 2015; 290:22891-906. [PMID: 26229102 PMCID: PMC4645605 DOI: 10.1074/jbc.m115.665125] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 01/06/2023] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a member of the ATP-binding cassette (ABC) transporter superfamily. CFTR controls the flow of anions through the apical membrane of epithelia. Dysfunctional CFTR causes the common lethal genetic disease cystic fibrosis. Transitions between open and closed states of CFTR are regulated by ATP binding and hydrolysis on the cytosolic nucleotide binding domains, which are coupled with the transmembrane (TM) domains forming the pathway for anion permeation. Lack of structural data hampers a global understanding of CFTR and thus the development of "rational" approaches directly targeting defective CFTR. In this work, we explored possible conformational states of the CFTR gating cycle by means of homology modeling. As templates, we used structures of homologous ABC transporters, namely TM(287-288), ABC-B10, McjD, and Sav1866. In the light of published experimental results, structural analysis of the transmembrane cavity suggests that the TM(287-288)-based CFTR model could correspond to a commonly occupied closed state, whereas the McjD-based model could represent an open state. The models capture the important role played by Phe-337 as a filter/gating residue and provide structural information on the conformational transition from closed to open channel.
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Affiliation(s)
- Valentina Corradi
- From the Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada and
| | - Paola Vergani
- Research Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - D Peter Tieleman
- From the Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta T2N 1N4, Canada and
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29
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Yang Z, Niu X, Zhang H, Wang S, Zhao X, Huang X. Conformational changes in MetNI: steered molecular dynamic studies of the methionine ABC transporter with and without substrates. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.910599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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30
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Ferreira RJ, Ferreira MJU, dos Santos DJVA. Reversing cancer multidrug resistance: insights into the efflux by ABC transports fromin silicostudies. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1196] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ricardo J. Ferreira
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia; Universidade de Lisboa; Lisboa Portugal
| | - Maria-José U. Ferreira
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia; Universidade de Lisboa; Lisboa Portugal
| | - Daniel J. V. A. dos Santos
- Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia; Universidade de Lisboa; Lisboa Portugal
- REQUIMTE, Department of Chemistry & Biochemistry, Faculty of Sciences; University of Porto; Porto Portugal
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31
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LaRusch J, Jung J, General IJ, Lewis MD, Park HW, Brand RE, Gelrud A, Anderson MA, Banks PA, Conwell D, Lawrence C, Romagnuolo J, Baillie J, Alkaade S, Cote G, Gardner TB, Amann ST, Slivka A, Sandhu B, Aloe A, Kienholz ML, Yadav D, Barmada MM, Bahar I, Lee MG, Whitcomb DC. Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis. PLoS Genet 2014; 10:e1004376. [PMID: 25033378 PMCID: PMC4102440 DOI: 10.1371/journal.pgen.1004376] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 03/10/2014] [Indexed: 02/07/2023] Open
Abstract
CFTR is a dynamically regulated anion channel. Intracellular WNK1-SPAK activation causes CFTR to change permeability and conductance characteristics from a chloride-preferring to bicarbonate-preferring channel through unknown mechanisms. Two severe CFTR mutations (CFTRsev) cause complete loss of CFTR function and result in cystic fibrosis (CF), a severe genetic disorder affecting sweat glands, nasal sinuses, lungs, pancreas, liver, intestines, and male reproductive system. We hypothesize that those CFTR mutations that disrupt the WNK1-SPAK activation mechanisms cause a selective, bicarbonate defect in channel function (CFTRBD) affecting organs that utilize CFTR for bicarbonate secretion (e.g. the pancreas, nasal sinus, vas deferens) but do not cause typical CF. To understand the structural and functional requirements of the CFTR bicarbonate-preferring channel, we (a) screened 984 well-phenotyped pancreatitis cases for candidate CFTRBD mutations from among 81 previously described CFTR variants; (b) conducted electrophysiology studies on clones of variants found in pancreatitis but not CF; (c) computationally constructed a new, complete structural model of CFTR for molecular dynamics simulation of wild-type and mutant variants; and (d) tested the newly defined CFTRBD variants for disease in non-pancreas organs utilizing CFTR for bicarbonate secretion. Nine variants (CFTR R74Q, R75Q, R117H, R170H, L967S, L997F, D1152H, S1235R, and D1270N) not associated with typical CF were associated with pancreatitis (OR 1.5, p = 0.002). Clones expressed in HEK 293T cells had normal chloride but not bicarbonate permeability and conductance with WNK1-SPAK activation. Molecular dynamics simulations suggest physical restriction of the CFTR channel and altered dynamic channel regulation. Comparing pancreatitis patients and controls, CFTRBD increased risk for rhinosinusitis (OR 2.3, p<0.005) and male infertility (OR 395, p<<0.0001). WNK1-SPAK pathway-activated increases in CFTR bicarbonate permeability are altered by CFTRBD variants through multiple mechanisms. CFTRBD variants are associated with clinically significant disorders of the pancreas, sinuses, and male reproductive system.
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Affiliation(s)
- Jessica LaRusch
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jinsei Jung
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Ignacio J. General
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michele D. Lewis
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, United States of America
| | - Hyun Woo Park
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Randall E. Brand
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Andres Gelrud
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michelle A. Anderson
- Department of Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peter A. Banks
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Darwin Conwell
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Christopher Lawrence
- Digestive Disease Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Joseph Romagnuolo
- Digestive Disease Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - John Baillie
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Samer Alkaade
- Department of Internal Medicine, St. Louis University School of Medicine, St Louis, Missouri, United States of America
| | - Gregory Cote
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Timothy B. Gardner
- Dartmouth-Hitchcock Medical Center, Hanover, New Hampshire, United States of America
| | - Stephen T. Amann
- North Mississippi Medical Center, Tupelo, Mississippi, United States of America
| | - Adam Slivka
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bimaljit Sandhu
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University Medical Center, Richmond, Virginia, United States of America
| | - Amy Aloe
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michelle L. Kienholz
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dhiraj Yadav
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - M. Michael Barmada
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ivet Bahar
- Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Min Goo Lee
- Department of Pharmacology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - David C. Whitcomb
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Cell Biology and Molecular Physiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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32
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Furuta T, Yamaguchi T, Kato H, Sakurai M. Analysis of the structural and functional roles of coupling helices in the ATP-binding cassette transporter MsbA through enzyme assays and molecular dynamics simulations. Biochemistry 2014; 53:4261-72. [PMID: 24937232 DOI: 10.1021/bi500255j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
ATP-binding cassette (ABC) transporters are constructed from some common structural units: the highly conserved nucleotide-binding domains (NBDs), which work as a nucleotide-dependent engine for driving substrate transport, the diverse transmembrane domains (TMDs), which create the translocation pathway, and the coupling helices (CHs), which are located at the NBD-TMD interface. Although the CHs are believed to be essential for NBD-TMD communication, their roles remain unclear. In this study, we performed enzyme assays and molecular dynamics (MD) simulations of the ABC transporter MsbA and two MsbA mutants in which the amino acid residues of one of the CHs were mutated to alanines: (i) wild type (Wt), (ii) CH1 mutant (Mt1), and (iii) CH2 mutant (Mt2). The experiments show that the CH2 mutation decreases the ATPase activity (kcat) compared with that of the Wt (a decrease of 32%), and a nearly equal degree of decrease in the ATP binding affinity (Km) was observed for both Mt1 and Mt2. The MD simulations successfully accounted for several structural and dynamical origins for these experimental observations. In addition, on the basis of collective motion and morphing analyses, we propose that the reverse-rotational motions and noddinglike motions between the NBDs and TMDs are indispensable for the conformational transition between the inward- and outward-facing conformations. In particular, CH2 is significantly important for the occurrence of the noddinglike motion. These findings provide important insights into the structure-function relationship of ABC transporters.
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Affiliation(s)
- Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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33
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Islami M, Mehrnejad F, Doustdar F, Alimohammadi M, Khadem-Maaref M, Mir-Derikvand M, Taghdir M. Study of orientation and penetration of LAH4 into lipid bilayer membranes: pH and composition dependence. Chem Biol Drug Des 2014; 84:242-52. [PMID: 24581146 DOI: 10.1111/cbdd.12311] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 11/29/2022]
Abstract
LAH4 is an antimicrobial peptide that is believed to possess both antibiotic and DNA delivery capabilities. It is one of a number of membrane-active peptides that show increased affinity toward anionic lipids. Herein, we have performed molecular dynamics simulations to compare LAH4 effects on anionic palmitoyl-oleoyl-phosphatidylglycerol bilayer, which approximate a prokaryotic membrane environment and zwitterionic palmitoyl-oleoyl-phosphatidylcholine bilayer, which approximate a eukaryotic membrane environment. One particular interest in this work is to study how different kinds of lipid bilayers respond to the attraction of LAH4. Remarkably, our data have shown that the depth of peptide penetration strongly depends on membrane composition and pH. At acidic pH, LAH4 has exhibited a high tendency to interact strongly with and be adsorbed on anionic membrane. We have also shown that electrostatic interactions between His11 and the phosphor atoms of bilayers should have a significant impact on the penetration of LAH4. These results provide insights into the interactions of LAH4 and lipid bilayers at the atomic level, which is useful to understand cell selectivity and mechanism of the peptide action.
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Affiliation(s)
- Matin Islami
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, 53714-161, Iran
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Asymmetric perturbations of signalling oligomers. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:153-69. [PMID: 24650570 DOI: 10.1016/j.pbiomolbio.2014.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 01/06/2023]
Abstract
This review focuses on rapid and reversible noncovalent interactions for symmetric oligomers of signalling proteins. Symmetry mismatch, transient symmetry breaking and asymmetric perturbations via chemical (ligand binding) and physical (electric or mechanic) effects can initiate the signalling events. Advanced biophysical methods can reveal not only structural symmetries of stable membrane-bound signalling proteins but also asymmetric functional transition states. Relevant techniques amenable to distinguish between symmetric and asymmetric architectures are discussed including those with the capability of capturing low-populated transient conformational states. Typical examples of signalling proteins are overviewed for symmetry breaking in dimers (GPCRs, growth factor receptors, transcription factors); trimers (acid-sensing ion channels); tetramers (voltage-gated cation channels, ionotropic glutamate receptor, CNG and CHN channels); pentameric ligand-gated and mechanosensitive channels; higher order oligomers (gap junction channel, chaperonins, proteasome, virus capsid); as well as primary and secondary transporters. In conclusion, asymmetric perturbations seem to play important functional roles in a broad range of communicating networks.
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A Microscopic View of the Mechanisms of Active Transport Across the Cellular Membrane. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63378-1.00004-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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36
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Rahmanpour A, Ghahremanpour MM, Mehrnejad F, Moghaddam ME. Interaction of Piscidin-1 with zwitterionic versus anionic membranes: a comparative molecular dynamics study. J Biomol Struct Dyn 2013; 31:1393-403. [DOI: 10.1080/07391102.2012.737295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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Mechanistic picture for conformational transition of a membrane transporter at atomic resolution. Proc Natl Acad Sci U S A 2013; 110:18916-21. [PMID: 24191018 DOI: 10.1073/pnas.1313202110] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During their transport cycle, ATP-binding cassette (ABC) transporters undergo large-scale conformational changes between inward- and outward-facing states. Using an approach based on designing system-specific reaction coordinates and using nonequilibrium work relations, we have performed extensive all-atom molecular dynamics simulations in the presence of explicit membrane/solvent to sample a large number of mechanistically distinct pathways for the conformational transition of MsbA, a bacterial ABC exporter whose structure has been solved in multiple functional states. The computational approach developed here is based on (i) extensive exploration of system-specific biasing protocols (e.g., using collective variables designed based on available low-resolution crystal structures) and (ii) using nonequilibrium work relations for comparing the relevance of the transition pathways. The most relevant transition pathway identified using this approach involves several distinct stages reflecting the complex nature of the structural changes associated with the function of the protein. The opening of the cytoplasmic gate during the outward- to inward-facing transition of apo MsbA is found to be disfavored when the periplasmic gate is open and facilitated by a twisting motion of the nucleotide-binding domains that involves a dramatic change in their relative orientation. These results highlight the cooperativity between the transmembrane and the nucleotide-binding domains in the conformational transition of ABC exporters. The approach introduced here provides a framework to study large-scale conformational changes of other membrane transporters whose computational investigation at an atomic resolution may not be currently feasible using conventional methods.
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Underhaug J, Koldsø H, Runager K, Nielsen JT, Sørensen CS, Kristensen T, Otzen DE, Karring H, Malmendal A, Schiøtt B, Enghild JJ, Nielsen NC. Mutation in transforming growth factor beta induced protein associated with granular corneal dystrophy type 1 reduces the proteolytic susceptibility through local structural stabilization. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2812-22. [PMID: 24129074 DOI: 10.1016/j.bbapap.2013.10.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/30/2013] [Accepted: 10/06/2013] [Indexed: 10/26/2022]
Abstract
Hereditary mutations in the transforming growth factor beta induced (TGFBI) gene cause phenotypically distinct corneal dystrophies characterized by protein deposition in cornea. We show here that the Arg555Trp mutant of the fourth fasciclin 1 (FAS1-4) domain of the protein (TGFBIp/keratoepithelin/βig-h3), associated with granular corneal dystrophy type 1, is significantly less susceptible to proteolysis by thermolysin and trypsin than the WT domain. High-resolution liquid-state NMR of the WT and Arg555Trp mutant FAS1-4 domains revealed very similar structures except for the region around position 555. The Arg555Trp substitution causes Trp555 to be buried in an otherwise empty hydrophobic cavity of the FAS1-4 domain. The first thermolysin cleavage in the core of the FAS1-4 domain occurs on the N-terminal side of Leu558 adjacent to the Arg555 mutation. MD simulations indicated that the C-terminal end of helix α3' containing this cleavage site is less flexible in the mutant domain, explaining the observed proteolytic resistance. This structural change also alters the electrostatic properties, which may explain increased propensity of the mutant to aggregate in vitro with 2,2,2-trifluoroethanol. Based on our results we propose that the Arg555Trp mutation disrupts the normal degradation/turnover of corneal TGFBIp, leading to accumulation and increased propensity to aggregate through electrostatic interactions.
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Affiliation(s)
- Jarl Underhaug
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark; Department of Biomedicine, University of Bergen, Jonas Lies vei 91, NO-5009 Bergen, Norway
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Wang Z, Li S, Sun L, Fan J, Liu Z. Comparative analyses of lipoprotein lipase, hepatic lipase, and endothelial lipase, and their binding properties with known inhibitors. PLoS One 2013; 8:e72146. [PMID: 23991054 PMCID: PMC3749185 DOI: 10.1371/journal.pone.0072146] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 07/08/2013] [Indexed: 11/30/2022] Open
Abstract
The triglyceride lipase gene subfamily plays a central role in lipid and lipoprotein metabolism. There are three members of this subfamily: lipoprotein lipase, hepatic lipase, and endothelial lipase. Although these lipases are implicated in the pathophysiology of hyperlipidemia and atherosclerosis, their structures have not been fully solved. In the current study, we established homology models of these three lipases, and carried out analysis of their activity sites. In addition, we investigated the kinetic characteristics for the catalytic residues using a molecular dynamics simulation strategy. To elucidate the molecular interactions and determine potential key residues involved in the binding to lipase inhibitors, we analyzed the binding pockets and binding poses of known inhibitors of the three lipases. We identified the spatial consensus catalytic triad “Ser-Asp-His”, a characteristic motif in all three lipases. Furthermore, we found that the spatial characteristics of the binding pockets of the lipase molecules play a key role in ligand recognition, binding poses, and affinities. To the best of our knowledge, this is the first report that systematically builds homology models of all the triglyceride lipase gene subfamily members. Our data provide novel insights into the molecular structures of lipases and their structure-function relationship, and thus provides groundwork for functional probe design towards lipase-based therapeutic inhibitors for the treatment of hyperlipidemia and atherosclerosis.
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Affiliation(s)
- Ziyun Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, P. R. China
| | - Shen Li
- Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi, Japan
| | - Lidan Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, P. R. China
| | - Jianglin Fan
- Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi, Japan
- * E-mail: (ZML); (JLF)
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, P. R. China
- * E-mail: (ZML); (JLF)
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40
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Ma J, Biggin PC. Substrate versus inhibitor dynamics of P-glycoprotein. Proteins 2013; 81:1653-68. [PMID: 23670856 DOI: 10.1002/prot.24324] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/24/2013] [Accepted: 04/19/2013] [Indexed: 12/20/2022]
Abstract
By far the most studied multidrug resistance protein is P-glycoprotein. Despite recent structural data, key questions about its function remain. P-glycoprotein (P-gp) is flexible and undergoes large conformational changes as part of its function and in this respect, details not only of the export cycle, but also the recognition stage are currently lacking. Given the flexibility, molecular dynamics (MD) simulations provide an ideal tool to examine this aspect in detail. We have performed MD simulations to examine the behaviour of P-gp. In agreement with previous reports, we found that P-gp undergoes large conformational changes which tended to result in the nucleotide-binding domains coming closer together. In all simulations, the approach of the NBDs was asymmetrical in agreement with previous observations for other ABC transporter proteins. To validate the simulations, we make extensive comparison to previous cross-linking data. Our results show very good agreement with the available data. We then went on to compare the influence of inhibitor compounds bound with simulations of a substrate (daunorubicin) bound. Our results suggest that inhibitors may work by keeping the NBDs apart, thus preventing ATP-hydrolysis. On the other hand, repeat simulations of daunorubicin (substrate) in one particular binding pose suggest that the approach of the NBDs is not impaired and that the structure would be still be competent to perform ATP hydrolysis, thus providing a model for inhibition or substrate transport. Finally we compare the latter to earlier QSAR data to provide a model for the first part of substrate transport within P-gp.
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Affiliation(s)
- Jerome Ma
- Department of Biochemistry, Structural Bioinformatics and Computational Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
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41
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Koldsø H, Autzen HE, Grouleff J, Schiøtt B. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations. PLoS One 2013; 8:e63635. [PMID: 23776432 PMCID: PMC3680404 DOI: 10.1371/journal.pone.0063635] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/04/2013] [Indexed: 11/18/2022] Open
Abstract
The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.
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Affiliation(s)
- Heidi Koldsø
- The Center for Insoluble Protein Structures (inSPIN), Aarhus University, Aarhus, Denmark
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42
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Wen PC, Verhalen B, Wilkens S, Mchaourab HS, Tajkhorshid E. On the origin of large flexibility of P-glycoprotein in the inward-facing state. J Biol Chem 2013; 288:19211-20. [PMID: 23658020 PMCID: PMC3696692 DOI: 10.1074/jbc.m113.450114] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
P-glycoprotein (Pgp) is one of the most biomedically relevant transporters in the ATP binding
cassette (ABC) superfamily due to its involvement in developing multidrug resistance in cancer
cells. Employing molecular dynamics simulations and double electron-electron resonance spectroscopy,
we have investigated the structural dynamics of membrane-bound Pgp in the inward-facing state and
found that Pgp adopts an unexpectedly wide range of conformations, highlighted by the degree of
separation between the two nucleotide-binding domains (NBDs). The distance between the two NBDs in
the equilibrium simulations covers a range of at least 20 Å, including, both, more open and
more closed NBD configurations than the crystal structure. The double electron-electron resonance
measurements on spin-labeled Pgp mutants also show wide distributions covering both longer and
shorter distances than those observed in the crystal structure. Based on structural and sequence
analyses, we propose that the transmembrane domains of Pgp might be more flexible than other
structurally known ABC exporters. The structural flexibility of Pgp demonstrated here is not only in
close agreement with, but also helps rationalize, the reported high NBD fluctuations in several ABC
exporters and possibly represents a fundamental difference in the transport mechanism between ABC
exporters and ABC importers. In addition, during the simulations we have captured partial entrance
of a lipid molecule from the bilayer into the lumen of Pgp, reaching the putative drug binding site.
The location of the protruding lipid suggests a putative pathway for direct drug recruitment from
the membrane.
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Affiliation(s)
- Po-Chao Wen
- Center for Biophysics and Computational Biology, Department of Biochemistry, College of Medicine, and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illnois 61801, USA
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43
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Pajeva IK, Hanl M, Wiese M. Protein contacts and ligand binding in the inward-facing model of human P-glycoprotein. ChemMedChem 2013; 8:748-62. [PMID: 23564544 DOI: 10.1002/cmdc.201200491] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 02/26/2013] [Indexed: 01/24/2023]
Abstract
The primary aim of this work was to analyze the contacts between residues in the nucleotide binding domains (NBDs) and at the interface between the transmembrane domains (TMDs) and the NBDs in the inward-open homology model of human P-glycoprotein (P-gp). The analysis revealed communication nets through hydrogen bonding in the NBD and at the NBD-TMD interface of each half involving residues from the adenosine triphosphate (ATP) motifs and the coupling helices of the intracellular loops. Similar networks have been identified in P-gp conformations generated by molecular dynamics simulation. Differences have been recorded in the networking between both halves of P-gp. Many of the residue contacts have also been observed in the X-ray crystal structures of other ATP binding cassette (ABC) transporters, which confirms their validity. Next, possible binding pockets involving residues of importance for the TMD-NBD communication were identified. By studying these pockets, binding sites were suggested for rhodamine 123 (R-site) and prazosin (regulatory site) at the NBD-TMD interface that agreed with the experimental data on their location. Additionally, one more R-site in the protein cavity was proposed, in accordance with the available biochemical data. Together with the previously suggested Hoechst 33342 site (H-site), all sites were interpreted with respect to their effects on the protein ATPase activity, in correspondence with the experimental observations. Several residues involved in key contacts in the P-gp NBDs were proposed for further targeted mutagenesis experiments.
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Affiliation(s)
- Ilza K Pajeva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 105, 1113 Sofia, Bulgaria.
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44
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Shaikh S, Li J, Enkavi G, Wen PC, Huang Z, Tajkhorshid E. Visualizing functional motions of membrane transporters with molecular dynamics simulations. Biochemistry 2013; 52:569-87. [PMID: 23298176 PMCID: PMC3560430 DOI: 10.1021/bi301086x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 12/21/2012] [Indexed: 01/08/2023]
Abstract
Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.
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Affiliation(s)
- Saher
A. Shaikh
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jing Li
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Giray Enkavi
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Po-Chao Wen
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Zhijian Huang
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, Beckman Institute for Advanced
Science and Technology, and Center for Biophysics and Computational
Biology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
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45
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Doshi R, Ali A, Shi W, Freeman EV, Fagg LA, van Veen HW. Molecular disruption of the power stroke in the ATP-binding cassette transport protein MsbA. J Biol Chem 2013; 288:6801-13. [PMID: 23306205 DOI: 10.1074/jbc.m112.430074] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP-binding cassette transporters affect drug pharmacokinetics and are associated with inherited human diseases and impaired chemotherapeutic treatment of cancers and microbial infections. Current alternating access models for ATP-binding cassette exporter activity suggest that ATP binding at the two cytosolic nucleotide-binding domains provides a power stroke for the conformational switch of the two membrane domains from the inward-facing conformation to the outward-facing conformation. In outward-facing crystal structures of the bacterial homodimeric ATP-binding cassette transporters MsbA from gram-negative bacteria and Sav1866 from Staphylococcus aureus, two transmembrane helices (3 and 4) in the membrane domains have their cytoplasmic extensions in close proximity, forming a tetrahelix bundle interface. In biochemical experiments on MsbA from Escherichia coli, we show for the first time that a robust network of inter-monomer interactions in the tetrahelix bundle is crucial for the transmission of nucleotide-dependent conformational changes to the extracellular side of the membrane domains. Our observations are the first to suggest that modulation of tetrahelix bundle interactions in ATP-binding cassette exporters might offer a potent strategy to alter their transport activity.
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Affiliation(s)
- Rupak Doshi
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom
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46
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Kolaczkowski M, Sroda-Pomianek K, Kolaczkowska A, Michalak K. A conserved interdomain communication pathway of pseudosymmetrically distributed residues affects substrate specificity of the fungal multidrug transporter Cdr1p. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:479-90. [PMID: 23122779 DOI: 10.1016/j.bbamem.2012.10.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 09/19/2012] [Accepted: 10/21/2012] [Indexed: 11/19/2022]
Abstract
Understanding the communication pathways between remote sites in proteins is of key importance for understanding their function and mechanism of action. These remain largely unexplored among the pleiotropic drug resistance (PDR) representatives of the ubiquitous superfamily of ATP-binding cassette (ABC) transporters. To identify functionally coupled residues important for the polyspecific transport by the fungal ABC multidrug transporter Cdr1p a new selection strategy, towards increased resistance to a preferred substrate of the homologous Snq2p, was applied to a library of randomly generated mutants. The single amino acid substitutions, located pseudosymmetrically in each domain of the internally duplicated protein: the H-loop of the N-terminal nucleotide binding domain (NBD1) (C363R) and in the C-terminal NBD2 region preceding Walker A (V885G). The central regions of the first transmembrane helices 1 and 7 of both transmembrane domains were also affected by the G521S/D and A1208V substitutions respectively. Although the mutants were expressed at a similar level and located correctly to the plasma membrane, they selectively affected transport of multiple drugs, including azole antifungals. The synergistic effects of combined mutations on drug resistance, drug dependent ATPase activity and transport support the view inferred from the statistical coupling analysis (SCA) of aminoacid coevolution and mutational analysis of other ABC transporter families that these residues are an important part of the conserved, allosterically coupled interdomain communication network. Our results shed new light on the communication between the pseudosymmetrically arranged domains in a fungal PDR ABC transporter and reveal its profound influence on substrate specificity.
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Affiliation(s)
- Marcin Kolaczkowski
- Department of Biophysics, Wroclaw Medical University, PL-50-368 Wroclaw, Poland.
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47
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George AM, Jones PM. Perspectives on the structure-function of ABC transporters: the Switch and Constant Contact models. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 109:95-107. [PMID: 22765920 DOI: 10.1016/j.pbiomolbio.2012.06.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 06/14/2012] [Indexed: 12/20/2022]
Abstract
ABC transporters constitute one of the largest protein families across the kingdoms of archaea, eubacteria and eukarya. They couple ATP hydrolysis to vectorial translocation of diverse substrates across membranes. The ABC transporter architecture comprises two transmembrane domains and two cytosolic ATP-binding cassettes. During 2002-2012, nine prokaryotic ABC transporter structures and two eukaryotic structures have been solved to medium resolution. Despite a wealth of biochemical, biophysical, and structural data, fundamental questions remain regarding the coupling of ATP hydrolysis to unidirectional substrate translocation, and the mechanistic suite of steps involved. The mechanics of the ATP cassette dimer is defined most popularly by the 'Switch Model', which proposes that hydrolysis in each protomer is sequential, and that as the sites are freed of nucleotide, the protomers lose contact across a large solvent-filled gap of 20-30 Å; as captured in several X-ray solved structures. Our 'Constant Contact' model for the operational mechanics of ATP binding and hydrolysis in the ATP-binding cassettes is derived from the 'alternating sites' model, proposed in 1995, and which requires an intrinsic asymmetry in the ATP sites, but does not require the partner protomers to lose contact. Thus one of the most debated issues regarding the function of ABC transporters is whether the cooperative mechanics of ATP hydrolysis requires the ATP cassettes to separate or remain in constant contact and this dilemma is discussed at length in this review.
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Affiliation(s)
- Anthony M George
- School of Medical and Molecular Biosciences, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia.
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48
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Ward AB, Guvench O, Hills RD. Coarse grain lipid-protein molecular interactions and diffusion with MsbA flippase. Proteins 2012; 80:2178-90. [DOI: 10.1002/prot.24108] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/10/2012] [Accepted: 04/25/2012] [Indexed: 12/27/2022]
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49
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Mittal A, Böhm S, Grütter MG, Bordignon E, Seeger MA. Asymmetry in the homodimeric ABC transporter MsbA recognized by a DARPin. J Biol Chem 2012; 287:20395-406. [PMID: 22523072 DOI: 10.1074/jbc.m112.359794] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
ABC transporters harness the energy from ATP binding and hydrolysis to translocate substrates across the membrane. Binding of two ATP molecules at the nucleotide binding domains (NBDs) leads to the formation of an outward-facing state. The conformational changes required to reset the transporter to the inward-facing state are initiated by sequential hydrolysis of the bound nucleotides. In a homodimeric ABC exporter such as MsbA responsible for lipid A transport in Escherichia coli, sequential ATP hydrolysis implies the existence of an asymmetric conformation. Here we report the in vitro selection of a designed ankyrin repeat protein (DARPin) specifically binding to detergent-solubilized MsbA. Only one DARPin binds to the homodimeric transporter in the absence as well as in the presence of nucleotides, suggesting that it recognizes asymmetries in MsbA. DARPin binding increases the rate of ATP hydrolysis by a factor of two independent of the substrate-induced ATPase stimulation. Electron paramagnetic resonance (EPR) measurements are found to be in good agreement with the available crystal structures and reveal that DARPin binding does not affect the large nucleotide-driven conformational changes of MsbA. The binding epitope was mapped by cross-linking and EPR to the membrane-spanning part of the transmembrane domain (TMD). Using cross-linked DARPin-MsbA complexes, 8-azido-ATP was found to preferentially photolabel one chain of the homodimer, suggesting that the asymmetries captured by DARPin binding at the TMDs are propagated to the NBDs. This work demonstrates that in vitro selected binders are useful tools to study the mechanism of membrane proteins.
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Affiliation(s)
- Anshumali Mittal
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
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50
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Jones PM, George AM. Role of the D-loops in allosteric control of ATP hydrolysis in an ABC transporter. J Phys Chem A 2012; 116:3004-13. [PMID: 22369471 DOI: 10.1021/jp211139s] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
ABC transporters couple ATP hydrolysis to movement of substrates across cell membranes. They comprise two transmembrane domains and two cytosolic nucleotide-binding domains forming two active sites that hydrolyze ATP cooperatively. The mechanism of ATP hydrolysis is controversial and the structural dynamic basis of its allosteric control unknown. Here we report molecular dynamics simulations of the ATP/apo and ATP/ADP states of the bacterial ABC exporter Sav1866, in which the cytoplasmic region of the protein was simulated in explicit water for 150 ns. In the simulation of the ATP/apo state, we observed, for the first time, conformers of the active site with the canonical geometry for an in-line nucleophilic attack on the ATP γ-phosphate. The conserved glutamate immediately downstream of the Walker B motif is the catalytic base, forming a dyad with the H-loop histidine, whereas the Q-loop glutamine has an organizing role. Each D-loop provides a coordinating residue of the attacking water, and comparison with the simulation of the ATP/ADP state suggests that via their flexibility, the D-loops modulate formation of the hydrolysis-competent state. A global switch involving a coupling helix delineates the signal transmission route by which allosteric control of ATP hydrolysis in ABC transporters is mediated.
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Affiliation(s)
- Peter M Jones
- School of Medical and Molecular Biosciences, and iThree Institute, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia.
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