1
|
Circularized fluorescent nanodiscs for probing protein-lipid interactions. Commun Biol 2022; 5:507. [PMID: 35618817 PMCID: PMC9135701 DOI: 10.1038/s42003-022-03443-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/03/2022] [Indexed: 12/29/2022] Open
Abstract
Protein–lipid interactions are vital for numerous transmembrane signaling pathways. However, simple tools to characterize these interactions remain scarce and are much needed to advance our understanding of signal transduction across lipid bilayers. To tackle this challenge, we herein engineer nanodisc as a robust fluorescent sensor for reporting membrane biochemical reactions. We circularize nanodiscs via split GFP and thereby create an intensity-based fluorescent sensor (isenND) for detecting membrane binding and remodeling events. We show that isenND responds robustly and specifically to the action of a diverse array of membrane-interacting proteins and peptides, ranging from synaptotagmin and synuclein involved in neurotransmission to viral fusion peptides of HIV-1 and SARS-CoV-2. Together, isenND can serve as a versatile biochemical reagent useful for basic and translational research of membrane biology. A fluorescent probe for detecting membrane protein binding and remodeling events is presented, which relies on split-GFP technology to generate circularized nanodiscs useful in membrane protein biophysics and structural biology.
Collapse
|
2
|
Zhang S, Ren Q, Novick SJ, Strutzenberg TS, Griffin PR, Bao H. One-step construction of circularized nanodiscs using SpyCatcher-SpyTag. Nat Commun 2021; 12:5451. [PMID: 34521837 PMCID: PMC8440770 DOI: 10.1038/s41467-021-25737-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/26/2021] [Indexed: 02/07/2023] Open
Abstract
Circularized nandiscs (cNDs) exhibit superb monodispersity and have the potential to transform functional and structural studies of membrane proteins. In particular, cNDs can stabilize large patches of lipid bilayers for the reconstitution of complex membrane biochemical reactions, enabling the capture of crucial intermediates involved in synaptic transmission and viral entry. However, previous methods for building cNDs require multiple steps and suffer from low yields. We herein introduce a simple, one-step approach to ease the construction of cNDs using the SpyCatcher-SpyTag technology. This approach increases the yield of cNDs by over 10-fold and is able to rapidly generates cNDs with diameters ranging from 11 to over 100 nm. We demonstrate the utility of these cNDs for mechanistic interrogations of vesicle fusion and protein-lipid interactions that are unattainable using small nanodiscs. Together, the remarkable performance of SpyCatcher-SpyTag in nanodisc circularization paves the way for the use of cNDs in membrane biochemistry and structural biology.
Collapse
Affiliation(s)
- Shanwen Zhang
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida, USA
| | - Qian Ren
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida, USA
| | - Scott J Novick
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida, USA
| | | | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida, USA.
| | - Huan Bao
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida, USA.
| |
Collapse
|
3
|
Abreu B, Cruz C, Oliveira ASF, Soares CM. ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK 2E importer. Sci Rep 2021; 11:10591. [PMID: 34012037 PMCID: PMC8134467 DOI: 10.1038/s41598-021-89556-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 04/27/2021] [Indexed: 02/03/2023] Open
Abstract
ATP binding cassette (ABC) transporters employ ATP hydrolysis to harness substrate translocation across membranes. The Escherichia coli MalFGK2E maltose importer is an example of a type I ABC importer and a model system for this class of ABC transporters. The MalFGK2E importer is responsible for the intake of malto-oligossacharides in E.coli. Despite being extensively studied, little is known about the effect of ATP hydrolysis and nucleotide exit on substrate transport. In this work, we studied this phenomenon using extensive molecular dynamics simulations (MD) along with potential of mean force calculations of maltose transport across the pore, in the pre-hydrolysis, post-hydrolysis and nucleotide-free states. We concluded that ATP hydrolysis and nucleotide exit trigger conformational changes that result in the decrease of energetic barriers to maltose translocation towards the cytoplasm, with a concomitant increase of the energy barrier in the periplasmic side of the pore, contributing for the irreversibility of the process. We also identified key residues that aid in positioning and orientation of maltose, as well as a novel binding pocket for maltose in MalG. Additionally, ATP hydrolysis leads to conformations similar to the nucleotide-free state. This study shows the contribution of ATP hydrolysis and nucleotide exit in the transport cycle, shedding light on ABC type I importer mechanisms.
Collapse
Affiliation(s)
- Bárbara Abreu
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Carlos Cruz
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - A. Sofia F. Oliveira
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal ,grid.5337.20000 0004 1936 7603School of Biochemistry and Centre for Computational Chemistry, University of Bristol, Bristol, UK
| | - Cláudio M. Soares
- grid.10772.330000000121511713ITQB NOVA, Instituto de Tecnologia Química E Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| |
Collapse
|
4
|
Bao H. Developing Nanodisc-ID for label-free characterizations of membrane proteins. Commun Biol 2021; 4:514. [PMID: 33931748 PMCID: PMC8087782 DOI: 10.1038/s42003-021-02043-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Membrane proteins (MPs) influence all aspects of life, such as tumorigenesis, immune response, and neural transmission. However, characterization of MPs is challenging, as it often needs highly specialized techniques inaccessible to many labs. We herein introduce nanodisc-ID that enables quantitative analysis of membrane proteins using a gel electrophoresis readout. By leveraging the power of nanodiscs and proximity labeling, nanodisc-ID serves both as scaffolds for encasing biochemical reactions and as sensitive reagents for detecting membrane protein-lipid and protein-protein interactions. We demonstrate this label-free and low-cost tool by characterizing a wide range of integral and peripheral membrane proteins from prokaryotes and eukaryotes.
Collapse
Affiliation(s)
- Huan Bao
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA.
| |
Collapse
|
5
|
Hiller RM, von Kügelgen J, Bao H, Van Hoa FD, Cytrynbaum EN. A Mathematical Model for the Kinetics of the MalFGK[Formula: see text] Maltose Transporter. Bull Math Biol 2020; 82:62. [PMID: 32415547 DOI: 10.1007/s11538-020-00737-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 04/15/2020] [Indexed: 11/28/2022]
Abstract
The MalFGK[Formula: see text] transporter regulates the movement of maltose across the inner membrane of E. coli and serves as a model system for bacterial ATP binding cassette (ABC) importers. Despite the wealth of biochemical and structural data available, a general model describing the various translocation pathways is still lacking. In this study, we formulate a mathematical model with the goal of determining the transporter reaction pathway, specifically looking at the order of binding events and conformation changes by which transport proceeds. Fitting our mathematical model to equilibrium binding data, we estimate the unknown equilibrium parameters of the system, several of which are key determinants of the transport process. Using these estimates along with steady-state ATPase rate data, we determine which of several possible reaction pathways is dominant, as a function of five underdetermined kinetic parameter values. Because neither experimental measurements nor estimates of certain kinetic rate constants are available, the problem of deciding which of the reaction pathways is responsible for transport remains unsolved. However, using the mathematical framework developed here, a firmer conclusion regarding the dominant reaction pathway as a function of MalE and maltose concentration could be drawn once these unknown kinetic parameters are determined.
Collapse
Affiliation(s)
- Rebecca M Hiller
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | | | - Huan Bao
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Franck Duong Van Hoa
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
| | - Eric N Cytrynbaum
- Department of Mathematics, University of British Columbia, Vancouver, Canada.
| |
Collapse
|
6
|
Mächtel R, Narducci A, Griffith DA, Cordes T, Orelle C. An integrated transport mechanism of the maltose ABC importer. Res Microbiol 2019; 170:321-337. [PMID: 31560984 PMCID: PMC6906923 DOI: 10.1016/j.resmic.2019.09.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/10/2019] [Accepted: 09/13/2019] [Indexed: 12/27/2022]
Abstract
ATP-binding cassette (ABC) transporters use the energy of ATP hydrolysis to transport a large diversity of molecules actively across biological membranes. A combination of biochemical, biophysical, and structural studies has established the maltose transporter MalFGK2 as one of the best characterized proteins of the ABC family. MalF and MalG are the transmembrane domains, and two MalKs form a homodimer of nucleotide-binding domains. A periplasmic maltose-binding protein (MalE) delivers maltose and other maltodextrins to the transporter, and triggers its ATPase activity. Substrate import occurs in a unidirectional manner by ATP-driven conformational changes in MalK2 that allow alternating access of the substrate-binding site in MalF to each side of the membrane. In this review, we present an integrated molecular mechanism of the transport process considering all currently available information. Furthermore, we summarize remaining inconsistencies and outline possible future routes to decipher the full mechanistic details of transport by MalEFGK2 complex and that of related importer systems.
Collapse
Affiliation(s)
- Rebecca Mächtel
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Douglas A Griffith
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany.
| | - Cédric Orelle
- Université de Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 7 passage du Vercors, 69367 Lyon, France.
| |
Collapse
|
7
|
Hsu WL, Furuta T, Sakurai M. The mechanism of nucleotide-binding domain dimerization in the intact maltose transporter as studied by all-atom molecular dynamics simulations. Proteins 2017; 86:237-247. [PMID: 29194754 DOI: 10.1002/prot.25433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/09/2017] [Accepted: 11/27/2017] [Indexed: 11/12/2022]
Abstract
The Escherichia coli maltose transporter MalFGK2 -E belongs to the protein superfamily of ATP-binding cassette (ABC) transporters. This protein is composed of heterodimeric transmembrane domains (TMDs) MalF and MalG, and the homodimeric nucleotide-binding domains (NBDs) MalK2 . In addition to the TMDs and NBDs, the periplasmic maltose binding protein MalE captures maltose and shuttle it to the transporter. In this study, we performed all-atom molecular dynamics (MD) simulations on the maltose transporter and found that both the binding of MalE to the periplasmic side of the TMDs and binding of ATP to the MalK2 are necessary to facilitate the conformational change from the inward-facing state to the occluded state, in which MalK2 is completely dimerized. MalE binding suppressed the fluctuation of the TMDs and MalF periplasmic region (MalF-P2), and thus prevented the incorrect arrangement of the MalF C-terminal (TM8) helix. Without MalE binding, the MalF TM8 helix showed a tendency to intrude into the substrate translocation pathway, hindering the closure of the MalK2 . This observation is consistent with previous mutagenesis experimental results on MalF and provides a new point of view regarding the understanding of the substrate translocation mechanism of the maltose transporter.
Collapse
Affiliation(s)
- Wei-Lin Hsu
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Midori-ku, Yokohama, Japan
| |
Collapse
|
8
|
Fabre L, Bao H, Innes J, Duong F, Rouiller I. Negative Stain Single-particle EM of the Maltose Transporter in Nanodiscs Reveals Asymmetric Closure of MalK 2 and Catalytic Roles of ATP, MalE, and Maltose. J Biol Chem 2017; 292:5457-5464. [PMID: 28188291 DOI: 10.1074/jbc.m116.757898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 02/08/2017] [Indexed: 12/26/2022] Open
Abstract
The Escherichia coli MalE-MalFGK2 complex is one of the best characterized members of the large and ubiquitous family of ATP-binding cassette (ABC) transporters. It is composed of a membrane-spanning heterodimer, MalF-MalG; a homodimeric ATPase, MalK2; and a periplasmic maltose receptor, MalE. Opening and closure of MalK2 is coupled to conformational changes in MalF-MalG and the alternate exposition of the substrate-binding site to either side of the membrane. To further define this alternate access mechanism and the impact of ATP, MalE, and maltose on the conformation of the transporter during the transport cycle, we have reconstituted MalFGK2 in nanodiscs and analyzed its conformations under 10 different biochemical conditions using negative stain single-particle EM. EM map results (at 15-25 Å resolution) indicate that binding of ATP to MalK2 promotes an asymmetric, semi-closed conformation in accordance with the low ATPase activity of MalFGK2 In the presence of MalE, the MalK dimer becomes fully closed, gaining the ability to hydrolyze ATP. In the presence of ADP or maltose, MalE·MalFGK2 remains essentially in a semi-closed symmetric conformation, indicating that release of these ligands is required for the return to the initial state. Taken together, this structural information provides a rationale for the stimulation of MalK ATPase activity by MalE as well as by maltose.
Collapse
Affiliation(s)
- Lucien Fabre
- From the Department of Anatomy and Cell Biology, Groupe de Recherche Axé sur la Structure des Protéines, Groupe d'Étude des Protéines Membranaires, McGill University, Montreal, Quebec H3A 2B2, Canada and
| | - Huan Bao
- the Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - James Innes
- From the Department of Anatomy and Cell Biology, Groupe de Recherche Axé sur la Structure des Protéines, Groupe d'Étude des Protéines Membranaires, McGill University, Montreal, Quebec H3A 2B2, Canada and
| | - Franck Duong
- the Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Isabelle Rouiller
- From the Department of Anatomy and Cell Biology, Groupe de Recherche Axé sur la Structure des Protéines, Groupe d'Étude des Protéines Membranaires, McGill University, Montreal, Quebec H3A 2B2, Canada and
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Lv X, Liu H, Chen H, Gong H. Coupling between ATP hydrolysis and protein conformational change in maltose transporter. Proteins 2016; 85:207-220. [PMID: 27616441 DOI: 10.1002/prot.25160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/29/2016] [Accepted: 09/02/2016] [Indexed: 11/12/2022]
Abstract
As the intracellular part of maltose transporter, MalK dimer utilizes the energy of ATP hydrolysis to drive protein conformational change, which then facilitates substrate transport. Free energy evaluation of the complete conformational change before and after ATP hydrolysis is helpful to elucidate the mechanism of chemical-to-mechanical energy conversion in MalK dimer, but is lacking in previous studies. In this work, we used molecular dynamics simulations to investigate the structural transition of MalK dimer among closed, semi-open and open states. We observed spontaneous structural transition from closed to open state in the ADP-bound system and partial closure of MalK dimer from the semi-open state in the ATP-bound system. Subsequently, we calculated the reaction pathways connecting the closed and open states for the ATP- and ADP-bound systems and evaluated the free energy profiles along the paths. Our results suggested that the closed state is stable in the presence of ATP but is markedly destabilized when ATP is hydrolyzed to ADP, which thus explains the coupling between ATP hydrolysis and protein conformational change of MalK dimer in thermodynamics. Proteins 2017; 85:207-220. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Xiaoying Lv
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hao Liu
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial metabolism, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Haifeng Chen
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial metabolism, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| |
Collapse
|
11
|
Naoe Y, Nakamura N, Doi A, Sawabe M, Nakamura H, Shiro Y, Sugimoto H. Crystal structure of bacterial haem importer complex in the inward-facing conformation. Nat Commun 2016; 7:13411. [PMID: 27830695 PMCID: PMC5136619 DOI: 10.1038/ncomms13411] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/30/2016] [Indexed: 11/29/2022] Open
Abstract
Pathogenic bacteria remove iron from the haem of host tissues and use it as a catalytic center of many enzymes. Haem uptake by pathogenic bacteria is facilitated by the membrane-integrated haem importer, which belongs to the type II ATP-binding cassette (ABC) transporter. Here we present crystal structures of Burkholderia cenocepacia haem importer BhuUV complexed with the periplasmic haem-binding protein BhuT and in the absence of BhuT. The transmembrane helices of these structures show an inward-facing conformation, in which the cytoplasmic gate of the haem translocation pathway is completely open. Since this conformation is found in both the haem- and nucleotide-free form, the structure of BhuUV-T provides the post-translocation state and the missing piece in the transport cycle of the type II importer. Structural comparison with the outward-facing conformation reported for the haem importer ortholog HmuUV from Yersenia pestis gives mechanistic insights into conformational transitions and haem secretion during the haem transport cycle. Pathogenic bacteria acquire iron from heme cofactors imported by ABC heme transporters. Here the authors present crystal structures of Burkholderia cenocepacia heme importer BhuUV with and without the heme-binding protein BhuT, gathering mechanistic insight into the catalytic cycle of heme import.
Collapse
Affiliation(s)
- Youichi Naoe
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Nozomi Nakamura
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.,Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan
| | - Akihiro Doi
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Mia Sawabe
- Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan
| | - Hiro Nakamura
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Yoshitsugu Shiro
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.,Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan
| | - Hiroshi Sugimoto
- Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.,Department of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigohri, Akoh, Hyogo 678-1297, Japan
| |
Collapse
|
12
|
Carlson ML, Bao H, Duong F. Formation of a Chloride-conducting State in the Maltose ATP-binding Cassette (ABC) Transporter. J Biol Chem 2016; 291:12119-25. [PMID: 27059961 DOI: 10.1074/jbc.m115.711622] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Indexed: 11/06/2022] Open
Abstract
ATP-binding cassette transporters use an alternating access mechanism to move substrates across cellular membranes. This mode of transport ensures the selective passage of molecules while preserving membrane impermeability. The crystal structures of MalFGK2, inward- and outward-facing, show that the transporter is sealed against ions and small molecules. It has yet to be determined whether membrane impermeability is maintained when MalFGK2 cycles between these two conformations. Through the use of a mutant that resides in intermediate conformations close to the transition state, we demonstrate that not only is chloride conductance occurring, but also to a degree large enough to compromise cell viability. Introduction of mutations in the periplasmic gate lead to the formation of a channel that is quasi-permanently open. MalFGK2 must therefore stay away from these ion-conducting conformations to preserve the membrane barrier; otherwise, a few mutations that increase access to the ion-conducting states are enough to convert an ATP-binding cassette transporter into a channel.
Collapse
Affiliation(s)
- Michael L Carlson
- From the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Huan Bao
- From the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Franck Duong
- From the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
13
|
Alvarez FJD, Orelle C, Huang Y, Bajaj R, Everly RM, Klug CS, Davidson AL. Full engagement of liganded maltose-binding protein stabilizes a semi-open ATP-binding cassette dimer in the maltose transporter. Mol Microbiol 2015; 98:878-94. [PMID: 26268698 DOI: 10.1111/mmi.13165] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 01/31/2023]
Abstract
MalFGK2 is an ATP-binding cassette (ABC) transporter that mediates the uptake of maltose/maltodextrins into Escherichia coli. A periplasmic maltose-binding protein (MBP) delivers maltose to the transmembrane subunits (MalFG) and stimulates the ATPase activity of the cytoplasmic nucleotide-binding subunits (MalK dimer). This MBP-stimulated ATPase activity is independent of maltose for purified transporter in detergent micelles. However, when the transporter is reconstituted in membrane bilayers, only the liganded form of MBP efficiently stimulates its activity. To investigate the mechanism of maltose stimulation, electron paramagnetic resonance spectroscopy was used to study the interactions between the transporter and MBP in nanodiscs and in detergent. We found that full engagement of both lobes of maltose-bound MBP unto MalFGK2 is facilitated by nucleotides and stabilizes a semi-open MalK dimer. Maltose-bound MBP promotes the transition to the semi-open state of MalK when the transporter is in the membrane, whereas such regulation does not require maltose in detergent. We suggest that stabilization of the semi-open MalK2 conformation by maltose-bound MBP is key to the coupling of maltose transport to ATP hydrolysis in vivo, because it facilitates the progression of the MalK dimer from the open to the semi-open conformation, from which it can proceed to hydrolyze ATP.
Collapse
Affiliation(s)
| | - Cédric Orelle
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yan Huang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ruchika Bajaj
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - R Michael Everly
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Candice S Klug
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Amy L Davidson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
14
|
Bao H, Dalal K, Cytrynbaum E, Duong F. Sequential Action of MalE and Maltose Allows Coupling ATP Hydrolysis to Translocation in the MalFGK2 Transporter. J Biol Chem 2015; 290:25452-60. [PMID: 26338707 DOI: 10.1074/jbc.m115.671826] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Indexed: 01/05/2023] Open
Abstract
ATP-binding cassette (ABC) transporters have evolved an ATP-dependent alternating-access mechanism to transport substrates across membranes. Despite important progress, especially in their structural analysis, it is still unknown how the substrate stimulates ATP hydrolysis, the hallmark of ABC transporters. In this study, we measure the ATP turnover cycle of MalFGK2 in steady and pre-steady state conditions. We show that (i) the basal ATPase activity of MalFGK2 is very low because the cleavage of ATP is rate-limiting, (ii) the binding of open-state MalE to the transporter induces ATP cleavage but leaves release of Pi limiting, and (iii) the additional presence of maltose stimulates release of Pi, and therefore increases the overall ATP turnover cycle. We conclude that open-state MalE stabilizes MalFGK2 in the outward-facing conformation until maltose triggers return to the inward-facing state for substrate and Pi release. This concerted action explains why ATPase activity of MalFGK2 depends on maltose, and why MalE is essential for transport.
Collapse
Affiliation(s)
- Huan Bao
- From the Departments of Biochemistry and Molecular Biology and
| | - Kush Dalal
- From the Departments of Biochemistry and Molecular Biology and
| | - Eric Cytrynbaum
- Mathematics, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | - Franck Duong
- From the Departments of Biochemistry and Molecular Biology and
| |
Collapse
|
15
|
Hsu WL, Furuta T, Sakurai M. Analysis of the Free Energy Landscapes for the Opening-Closing Dynamics of the Maltose Transporter ATPase MalK2 Using Enhanced-Sampling Molecular Dynamics Simulation. J Phys Chem B 2015; 119:9717-25. [PMID: 26158224 DOI: 10.1021/acs.jpcb.5b05432] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein dynamics are considered significant for many physiological processes, such as metabolism, biomolecular recognition, and the regulation of several vital cellular processes. Due to their flexibility, proteins may stay in different substates with or without the existence of the cognate substrates. To describe these phenomena, two models have been proposed: the "induced fit" and the "conformational selection" mechanisms. In this study, we used MalK2, the subunits that mainly include the nucleotide-binding domains (NBDs) of the maltose transporter from Escherichia coli, as a target to understand the NBD dimerization mechanism. Accelerated and conventional molecular dynamics have been performed. The results revealed that Mg-ATP binding to MalK2 led to a significant change in the free energy profile and thus stabilized the closed conformation. On the contrary, when Mg-ATP was removed, the open conformation would be favored. The fact that ligand binding induces a drastic free energy change leads to a significant inference: MalK2 dimerization would occur through the induced-fit mechanism rather than the conformational selection mechanism. This study sheds new light on the NBD dimerization mechanism and would be of wide applicability to other ABC transporters.
Collapse
Affiliation(s)
- Wei-Lin Hsu
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| |
Collapse
|
16
|
Bosdriesz E, Magnúsdóttir S, Bruggeman FJ, Teusink B, Molenaar D. Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate. FEBS J 2015; 282:2394-407. [PMID: 25846030 DOI: 10.1111/febs.13289] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/17/2015] [Accepted: 03/20/2015] [Indexed: 11/27/2022]
Abstract
Microorganisms rely on binding-protein assisted, active transport systems to scavenge for scarce nutrients. Several advantages of using binding proteins in such uptake systems have been proposed. However, a systematic, rigorous and quantitative analysis of the function of binding proteins is lacking. By combining knowledge of selection pressure and physiochemical constraints, we derive kinetic, thermodynamic, and stoichiometric properties of binding-protein dependent transport systems that enable a maximal import activity per amount of transporter. Under the hypothesis that this maximal specific activity of the transport complex is the selection objective, binding protein concentrations should exceed the concentration of both the scarce nutrient and the transporter. This increases the encounter rate of transporter with loaded binding protein at low substrate concentrations, thereby enhancing the affinity and specific uptake rate. These predictions are experimentally testable, and a number of observations confirm them.
Collapse
Affiliation(s)
- Evert Bosdriesz
- Systems Bioinformatics, VU University, Amsterdam, The Netherlands
| | | | | | - Bas Teusink
- Systems Bioinformatics, VU University, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Systems Bioinformatics, VU University, Amsterdam, The Netherlands
| |
Collapse
|
17
|
Active transporters as enzymes: an energetic framework applied to major facilitator superfamily and ABC importer systems. Biochem J 2015; 467:193-9. [DOI: 10.1042/bj20140675] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Active membrane transporters are dynamic molecular machines that catalyse transport across a membrane by coupling solute movement to a source of energy such as ATP or a secondary ion gradient. A central question for many active transporters concerns the mechanism by which transport is coupled to a source of energy. The transport process and associated energetic coupling involve conformational changes in the transporter. For efficient transport, the conformational changes must be tightly regulated and they must link energy use to movement of the substrate across the membrane. The present review discusses active transport using the well-established energetic framework for enzyme-mediated catalysis. In particular, membrane transport systems can be viewed as ensembles consisting of low-energy and high-energy conformations. The transport process involves binding interactions that selectively stabilize the higher energy conformations, and in this way promote conformational changes in the system that are coupled to decreases in free energy and substrate translocation. The major facilitator superfamily of secondary active transporters is used to illustrate these ideas, which are then be expanded to primary active transport mediated by ABC (ATP-binding cassette) import systems, with a focus on the well-studied maltose transporter.
Collapse
|
18
|
Gouridis G, Schuurman-Wolters GK, Ploetz E, Husada F, Vietrov R, de Boer M, Cordes T, Poolman B. Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ. Nat Struct Mol Biol 2014; 22:57-64. [DOI: 10.1038/nsmb.2929] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/06/2014] [Indexed: 11/09/2022]
|
19
|
Abstract
ATP-binding cassette (ABC) transporters form a large superfamily of ATP-dependent protein complexes that mediate transport of a vast array of substrates across membranes. The 14 currently available structures of ABC transporters have greatly advanced insight into the transport mechanism and revealed a tremendous structural diversity. Whereas the domains that hydrolyze ATP are structurally related in all ABC transporters, the membrane-embedded domains, where the substrates are translocated, adopt four different unrelated folds. Here, we review the structural characteristics of ABC transporters and discuss the implications of this structural diversity for mechanistic diversity.
Collapse
Affiliation(s)
- Josy ter Beek
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | | | | |
Collapse
|
20
|
Bao H, Duong F. Nucleotide-free MalK drives the transition of the maltose transporter to the inward-facing conformation. J Biol Chem 2014; 289:9844-51. [PMID: 24526688 DOI: 10.1074/jbc.m113.545525] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The complex MalFGK2 hydrolyzes ATP and alternates between inward- and outward-facing conformations during maltose transport. It has been shown that ATP promotes closure of MalK2 and opening of MalFG toward the periplasm. Yet, why the transporter rests in a conformation facing the cytosol in the absence of nucleotide and how it returns to this state after hydrolysis of ATP is unknown. The membrane domain MalFG may be naturally stable in the inward-facing conformation, or the ABC domain may catalyze the transition. We address this question by analyzing the conformation of MalFG in nanodiscs and in proteoliposomes. We find that MalFG alone exists in an intermediate state until MalK binds and converts the membrane domain to the inward-facing state. We also find that MalK, if overly-bound to MalFG, blocks the transition of the transporter, whereas suppressor mutations that weaken this association restore transport. MalK therefore exploits hydrolysis of ATP to reverse the conformation of MalFG to the inward-facing conformation, a step essential for release of maltose in the cytosol.
Collapse
Affiliation(s)
- Huan Bao
- From the Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | | |
Collapse
|
21
|
Fulyani F, Schuurman-Wolters GK, Zagar AV, Guskov A, Slotboom DJ, Poolman B. Functional diversity of tandem substrate-binding domains in ABC transporters from pathogenic bacteria. Structure 2013; 21:1879-88. [PMID: 23994008 DOI: 10.1016/j.str.2013.07.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/05/2013] [Accepted: 07/23/2013] [Indexed: 11/17/2022]
Abstract
The ATP-binding cassette (ABC) transporter GlnPQ is an essential uptake system for amino acids in gram-positive pathogens and related nonpathogenic bacteria. The transporter has tandem substrate-binding domains (SBDs) fused to each transmembrane domain, giving rise to four SBDs per functional transporter complex. We have determined the crystal structures and ligand-binding properties of the SBDs of GlnPQ from Enterococcus faecalis, Streptococcus pneumoniae, and Lactococcus lactis. The tandem SBDs differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. The combined structural, functional, and thermodynamic analysis revealed the roles of individual residues in determining the substrate affinity. We succeeded in converting a low-affinity SBD into a high-affinity receptor and vice versa. Our data indicate that a small number of residues that reside in the binding pocket constitute the major affinity determinants of the SBDs.
Collapse
Affiliation(s)
- Faizah Fulyani
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | | | | | | | | | | |
Collapse
|
22
|
Bao H, Duong F. Phosphatidylglycerol directs binding and inhibitory action of EIIAGlc protein on the maltose transporter. J Biol Chem 2013; 288:23666-74. [PMID: 23821551 DOI: 10.1074/jbc.m113.489567] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The signal-transducing protein EIIA(Glc) belongs to the phosphoenolpyruvate carbohydrate phosphotransferase system. In its dephosphorylated state, EIIA(Glc) is a negative regulator for several permeases, including the maltose transporter MalFGK2. How EIIA(Glc) is targeted to the membrane, how it interacts with the transporter, and how it inhibits sugar uptake remain obscure. We show here that acidic phospholipids together with the N-terminal tail of EIIA(Glc) are essential for the high affinity binding of the protein to the transporter. Using protein docking prediction and chemical cross-linking, we demonstrate that EIIA(Glc) binds to the MalK dimer, interacting with both the nucleotide-binding and the C-terminal regulatory domains. Dissection of the ATPase cycle reveals that EIIA(Glc) does not affect the binding of ATP but rather inhibits the capacity of MalK to cleave ATP. We propose a mechanism of maltose transport inhibition by this central amphitropic regulatory protein.
Collapse
Affiliation(s)
- Huan Bao
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada
| | | |
Collapse
|
23
|
Bao H, Dalal K, Wang V, Rouiller I, Duong F. The maltose ABC transporter: action of membrane lipids on the transporter stability, coupling and ATPase activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1723-30. [PMID: 23562402 DOI: 10.1016/j.bbamem.2013.03.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/13/2013] [Accepted: 03/25/2013] [Indexed: 01/25/2023]
Abstract
The coupling between ATP hydrolysis and substrate transport remains a key question in the understanding of ABC-mediated transport. We show using the MalFGK2 complex reconstituted into nanodiscs, that membrane lipids participate directly to the coupling reaction by stabilizing the transporter in a low energy conformation. When surrounded by short acyl chain phospholipids, the transporter is unstable and hydrolyzes large amounts of ATP without inducing maltose. The presence of long acyl chain phospholipids stabilizes the conformational dynamics of the transporter, reduces its ATPase activity and restores dependence on maltose. Membrane lipids therefore play an essential allosteric function, they restrict the transporter ATPase activity to increase coupling to the substrate. In support to the notion, we show that increasing the conformational dynamics of MalFGK2 with mutations in MalF increases the transporter ATPase activity but decreases the maltose transport efficiency.
Collapse
Affiliation(s)
- Huan Bao
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, Canada
| | | | | | | | | |
Collapse
|