1
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Novischi SYP, Karoly-Lakatos A, Chok K, Bonifer C, Becker-Baldus J, Glaubitz C. Probing the allosteric NBD-TMD crosstalk in the ABC transporter MsbA by solid-state NMR. Commun Biol 2024; 7:43. [PMID: 38182790 PMCID: PMC10770068 DOI: 10.1038/s42003-023-05617-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 11/21/2023] [Indexed: 01/07/2024] Open
Abstract
The ABC transporter MsbA plays a critical role in Gram-negative bacteria in the regulation of the outer membrane by translocating core-LPS across the inner membrane. Additionally, a broad substrate specificity for lipophilic drugs has been shown. The allosteric interplay between substrate binding in the transmembrane domains and ATP binding and turnover in the nucleotide-binding domains must be mediated via the NBD/TMD interface. Previous studies suggested the involvement of two intracellular loops called coupling helix 1 and 2 (CH1, CH2). Here, we demonstrate by solid-state NMR spectroscopy that substantial chemical shift changes within both CH1 and CH2 occur upon substrate binding, in the ATP hydrolysis transition state, and upon inhibitor binding. CH2 is domain-swapped within the MsbA structure, and it is noteworthy that substrate binding induces a larger response in CH2 compared to CH1. Our data demonstrate that CH1 and CH2 undergo structural changes as part of the TMD-NBD cross-talk.
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Affiliation(s)
- S Y Phoebe Novischi
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Andrea Karoly-Lakatos
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Kerby Chok
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Christian Bonifer
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany.
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2
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Rudolph M, Tampé R, Joseph B. Time-Resolved Mn 2+ -NO and NO-NO Distance Measurements Reveal That Catalytic Asymmetry Regulates Alternating Access in an ABC Transporter. Angew Chem Int Ed Engl 2023; 62:e202307091. [PMID: 37459565 DOI: 10.1002/anie.202307091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
ATP-binding cassette (ABC) transporters shuttle diverse substrates across biological membranes. Transport is often achieved through a transition between an inward-facing (IF) and an outward-facing (OF) conformation of the transmembrane domains (TMDs). Asymmetric nucleotide-binding sites (NBSs) are present among several ABC subfamilies and their functional role remains elusive. Here we addressed this question using concomitant NO-NO, Mn2+ -NO, and Mn2+ -Mn2+ pulsed electron-electron double-resonance spectroscopy of TmrAB in a time-resolved manner. This type-IV ABC transporter undergoes a reversible transition in the presence of ATP with a significantly faster forward transition. The impaired degenerate NBS stably binds Mn2+ -ATP, and Mn2+ is preferentially released at the active consensus NBS. ATP hydrolysis at the consensus NBS considerably accelerates the reverse transition. Both NBSs fully open during each conformational cycle and the degenerate NBS may regulate the kinetics of this process.
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Affiliation(s)
- Michael Rudolph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Benesh Joseph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
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3
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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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4
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Mann D, Labudda K, Zimmermann S, Vocke KU, Gasper R, Kötting C, Hofmann E. ATP binding and ATP hydrolysis in full-length MsbA monitored via time-resolved Fourier transform infrared spectroscopy. Biol Chem 2023:hsz-2023-0122. [PMID: 37185095 DOI: 10.1515/hsz-2023-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
The essential Escherichia coli ATPase MsbA is a lipid flippase that serves as a prototype for multi drug resistant ABC transporters. Its physiological function is the transport of lipopolisaccharides to build up the outer membranes of gram negative bacteria. Although several structural and biochemical studies of MsbA have been conducted previously, a detailed picture of the dynamic processes that link ATP hydrolysis to allocrit transport remains elusive. We report here for the first time time-resolved Fourier transform infrared (FTIR) spectroscopic measurements of the ATP binding and ATP hydrolysis reaction of full-length MsbA and determined reaction rates at 288 K of k 1 = 0.49 ± 0.28 s-1 and k 2 = 0.014 ± 0.003 s-1, respectively. We further verified these rates with photocaged NPEcgAppNHp where only nucleotide binding was observable and the negative mutant MsbA-H537A that showed slow hydrolysis (k 2 < 2 × 10-4 s-1). Besides single turnover kinetics, FTIR measurements also deliver IR signatures of all educts, products and the protein. ADP remains protein-bound after ATP hydrolysis. In addition, the spectral changes observed for the two variants MsbA-S378A and MsbA-S482A correlated with the loss of hydrogen bonding to the γ-phosphate of ATP. This study paves the way for FTIR-spectroscopic investigations of allocrite transport in full-length MsbA.
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Affiliation(s)
- Daniel Mann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Forschungszentrum Jülich GmbH, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons / ER-C-3: Structural Biology, D-52425 Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute for Biological Information Processing / IBI-6 Cellular Structural Biology, D-52425 Jülich, Germany
| | - Kristin Labudda
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Sophie Zimmermann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Kai Ulrich Vocke
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Raphael Gasper
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Max Planck Institute of Molecular Physiology, Crystallography and Biophysics Facility, D-44227 Dortmund, Germany
| | - Carsten Kötting
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Eckhard Hofmann
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
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5
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Lacabanne D, Wiegand T, Di Cesare M, Orelle C, Ernst M, Jault JM, Meier BH, Böckmann A. Solid-State NMR Reveals Asymmetric ATP Hydrolysis in the Multidrug ABC Transporter BmrA. J Am Chem Soc 2022; 144:12431-12442. [PMID: 35776907 PMCID: PMC9284561 DOI: 10.1021/jacs.2c04287] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
The detailed mechanism
of ATP hydrolysis in ATP-binding cassette
(ABC) transporters is still not fully understood. Here, we employed 31P solid-state NMR to probe the conformational changes and
dynamics during the catalytic cycle by locking the multidrug ABC transporter
BmrA in prehydrolytic, transition, and posthydrolytic states, using
a combination of mutants and ATP analogues. The 31P spectra
reveal that ATP binds strongly in the prehydrolytic state to both
ATP-binding sites as inferred from the analysis of the nonhydrolytic
E504A mutant. In the transition state of wild-type BmrA, the symmetry
of the dimer is broken and only a single site is tightly bound to
ADP:Mg2+:vanadate, while the second site is more ‘open’
allowing exchange with the nucleotides in the solvent. In the posthydrolytic
state, weak binding, as characterized by chemical exchange with free
ADP and by asymmetric 31P–31P two-dimensional
(2D) correlation spectra, is observed for both sites. Revisiting the 13C spectra in light of these findings confirms the conformational
nonequivalence of the two nucleotide-binding sites in the transition
state. Our results show that following ATP binding, the symmetry of
the ATP-binding sites of BmrA is lost in the ATP-hydrolysis step,
but is then recovered in the posthydrolytic ADP-bound state.
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Affiliation(s)
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Margot Di Cesare
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR5086 CNRS/University of Lyon, 7, passage du Vercors, 69367 Lyon, France
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6
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Kehlenbeck DM, Traore DAK, Josts I, Sander S, Moulin M, Haertlein M, Prevost S, Forsyth VT, Tidow H. Cryo-EM structure of MsbA in saposin-lipid nanoparticles (Salipro) provides insights into nucleotide coordination. FEBS J 2022; 289:2959-2970. [PMID: 34921499 DOI: 10.1111/febs.16327] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/05/2021] [Accepted: 12/16/2021] [Indexed: 01/28/2023]
Abstract
The ATP-binding cassette transporter MsbA is a lipid flippase, translocating lipid A, glycolipids, and lipopolysaccharides from the inner to the outer leaflet of the inner membrane of Gram-negative bacteria. It has been used as a model system for time-resolved structural studies as several MsbA structures in different states and reconstitution systems (detergent/nanodiscs/peptidiscs) are available. However, due to the limited resolution of the available structures, detailed structural information on the bound nucleotides has remained elusive. Here, we have reconstituted MsbA in saposin A-lipoprotein nanoparticles (Salipro) and determined the structure of ADP-vanadate-bound MsbA by single-particle cryo-electron microscopy to 3.5 Å resolution. This procedure has resulted in significantly improved resolution and enabled us to model all side chains and visualise detailed ADP-vanadate interactions in the nucleotide-binding domains. The approach may be applicable to other dynamic membrane proteins.
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Affiliation(s)
- Dominique-Maurice Kehlenbeck
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany.,Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France
| | - Daouda A K Traore
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France.,Faculty of Natural Sciences, Keele University, UK.,Faculté des Sciences et Techniques, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Inokentijs Josts
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Simon Sander
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Martine Moulin
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France
| | - Sylvain Prevost
- Large Scale Structures Group, Institut Laue-Langevin, Grenoble, France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France.,Faculty of Natural Sciences, Keele University, UK
| | - Henning Tidow
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany
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7
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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8
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Pérez Carrillo VH, Rose-Sperling D, Tran MA, Wiedemann C, Hellmich UA. Backbone NMR assignment of the nucleotide binding domain of the Bacillus subtilis ABC multidrug transporter BmrA in the post-hydrolysis state. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:81-86. [PMID: 34988902 PMCID: PMC9068644 DOI: 10.1007/s12104-021-10063-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 05/11/2023]
Abstract
ATP binding cassette (ABC) proteins are present in all phyla of life and form one of the largest protein families. The Bacillus subtilis ABC transporter BmrA is a functional homodimer that can extrude many different harmful compounds out of the cell. Each BmrA monomer is composed of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). While the TMDs of ABC transporters are sequentially diverse, the highly conserved NBDs harbor distinctive conserved motifs that enable nucleotide binding and hydrolysis, interdomain communication and that mark a protein as a member of the ABC superfamily. In the catalytic cycle of an ABC transporter, the NBDs function as the molecular motor that fuels substrate translocation across the membrane via the TMDs and are thus pivotal for the entire transport process. For a better understanding of the structural and dynamic consequences of nucleotide interactions within the NBD at atomic resolution, we determined the 1H, 13C and 15N backbone chemical shift assignments of the 259 amino acid wildtype BmrA-NBD in its post-hydrolytic, ADP-bound state.
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Affiliation(s)
- Victor Hugo Pérez Carrillo
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Dania Rose-Sperling
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Mai Anh Tran
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Christoph Wiedemann
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, 07743, Jena, Germany.
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9
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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10
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MsbA: an ABC transporter paradigm. Biochem Soc Trans 2021; 49:2917-2927. [PMID: 34821931 DOI: 10.1042/bst20211030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
ATP-binding cassette (ABC) transporters play an important role in various cellular processes. They display a similar architecture and share a mechanism which couples ATP hydrolysis to substrate transport. However, in the light of current data and recent experimental progress, this protein superfamily appears as multifaceted as their broad substrate range. Among the prokaryotic ABC transporters, MsbA can serve as a paradigm for research in this field. It is located in the inner membrane of Gram-negative bacteria and functions as a floppase for the lipopolysaccharide (LPS) precursor core-LPS, which is involved in the biogenesis of the bacterial outer membrane. While MsbA shows high similarity to eukaryotic ABC transporters, its expression in Gram-negative bacteria makes it conveniently accessible for many experimental approaches from spectroscopy to 3D structure determination. As an essential protein for bacterial membrane integrity, MsbA has also become an attractive target for the development of novel antibiotics. Furthermore, it serves as a model for multidrug efflux pumps. Here we provide an overview of recent findings and their relevance to the field, highlight the potential of methods such as solid-state NMR and EPR spectroscopy and provide a perspective for future work.
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11
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Frozen motion: how cryo-EM changes the way we look at ABC transporters. Trends Biochem Sci 2021; 47:136-148. [PMID: 34930672 DOI: 10.1016/j.tibs.2021.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/18/2022]
Abstract
ATP-binding cassette (ABC) transporters are widely present molecular machines that transfer substrates across the cell membrane. ABC transporters are involved in numerous physiological processes and are often clinical targets. Structural biology is fundamental to obtain the molecular details underlying ABC transporter function and suggest approaches to modulate it. Until recently, X-ray crystallography has been the only method capable of providing high-resolution structures of ABC transporters. However, modern cryo-electron microscopy (cryo-EM) opens entirely new ways of studying these dynamic membrane proteins. Cryo-EM enables analyses of targets that resist X-ray crystallography, challenging multicomponent complexes, and the exploration of conformational dynamics. These unique capacities have turned cryo-EM into the dominant technique for structural studies of membrane proteins, including ABC transporters.
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12
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Baeta T, Giandoreggio-Barranco K, Ayala I, Moura ECCM, Sperandeo P, Polissi A, Simorre JP, Laguri C. The lipopolysaccharide-transporter complex LptB 2FG also displays adenylate kinase activity in vitro dependent on the binding partners LptC/LptA. J Biol Chem 2021; 297:101313. [PMID: 34673027 PMCID: PMC8633020 DOI: 10.1016/j.jbc.2021.101313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 02/02/2023] Open
Abstract
Lipopolysaccharide (LPS) is an essential glycolipid that covers the surface of gram-negative bacteria. The transport of LPS involves a dedicated seven-protein transporter system called the lipopolysaccharide transport system (Lpt) machinery that physically spans the entire cell envelope. The LptB2FG complex is an ABC transporter that hydrolyzes ATP to extract LPS from the inner membrane for transport to the outer membrane. Here, we extracted LptB2FG directly from the inner membrane with its original lipid environment using styrene-maleic acid polymers. We found that styrene-maleic acid polymers–LptB2FG in nanodiscs display not only ATPase activity but also a previously uncharacterized adenylate kinase (AK) activity, as it catalyzed phosphotransfer between two ADP molecules to generate ATP and AMP. The ATPase and AK activities of LptB2FG were both stimulated by the interaction on the periplasmic side with the periplasmic LPS transport proteins LptC and LptA and inhibited by the presence of the LptC transmembrane helix. We determined that the isolated ATPase module (LptB) had weak AK activity in the absence of transmembrane proteins LptF and LptG, and one mutation in LptB that weakens its affinity for ADP led to AK activity similar to that of fully assembled complex. Thus, we conclude that LptB2FG is capable of producing ATP from ADP, depending on the assembly of the Lpt bridge, and that this AK activity might be important to ensure efficient LPS transport in the fully assembled Lpt system.
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Affiliation(s)
- Tiago Baeta
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Isabel Ayala
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Elisabete C C M Moura
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Paola Sperandeo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Alessandra Polissi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | | | - Cedric Laguri
- Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.
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13
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He G, Tian W, Qin L, Meng L, Wu D, Huang Y, Li D, Zhao D, He T. Identification of novel heavy metal detoxification proteins in Solanum tuberosum: Insights to improve food security protection from metal ion stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146197. [PMID: 33744586 DOI: 10.1016/j.scitotenv.2021.146197] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/07/2021] [Accepted: 02/25/2021] [Indexed: 05/22/2023]
Abstract
With increasingly serious environmental pollution problems, research has focused on identifying functional genes within plants that can help ensure food security and soil governance. In particular, plants seem to have been able to evolve specific functional genes to respond to environmental changes by losing partial gene functions, thereby representing a novel adaptation mechanism. Herein, a new category of functional genes was identified and investigated, providing new directions for understanding heavy metal detoxification mechanisms. Interestingly, this category of proteins appears to exhibit specific complexing functions for heavy metals. Further, a new approach was established to evaluate ATP-binding cassette (ABC) transporter family functions using microRNA targeted inhibition. Moreover, mutant and functional genes were identified for future research targets. Expression profiling under five heavy metal stress treatments provided an important framework to further study defense responses of plants to metal exposure. In conclusion, the new insights identified here provide a theoretical basis and reference to better understand the mechanisms of heavy metal tolerance in potato plants. Further, these new data provide additional directions and foundations for mining gene resources for heavy metal tolerance genes to improve safe, green crop production and plant treatment of heavy metal soil pollution.
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Affiliation(s)
- Guandi He
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang 550025, China.
| | - Weijun Tian
- Agricultural College, Guizhou University, Guiyang 550025, China.
| | - Lijun Qin
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang 550025, China.
| | - Lulu Meng
- Agricultural College, Guizhou University, Guiyang 550025, China.
| | - Danxia Wu
- Agricultural College, Guizhou University, Guiyang 550025, China.
| | - Yun Huang
- Agricultural College, Guizhou University, Guiyang 550025, China.
| | - Dandan Li
- Agricultural College, Guizhou University, Guiyang 550025, China.
| | - Degang Zhao
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering and College of Life Sciences, Guizhou University, Guiyang 550025, China; Guizhou Academy of Agricultural Science, Guiyang 550025, China.
| | - Tengbing He
- Agricultural College, Guizhou University, Guiyang 550025, China; Institute of New Rural Development of Guizhou University, Guiyang 550025, China.
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14
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Hendriks K, Öster C, Shi C, Sun H, Lange A. Sodium Ions Do Not Stabilize the Selectivity Filter of a Potassium Channel. J Mol Biol 2021; 433:167091. [PMID: 34090923 DOI: 10.1016/j.jmb.2021.167091] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/12/2021] [Accepted: 05/27/2021] [Indexed: 11/28/2022]
Abstract
Ion conduction is an essential function for electrical activity in all organisms. The non-selective ion channel NaK was previously shown to adopt two stable conformations of the selectivity filter. Here, we present solid-state NMR measurements of NaK demonstrating a population shift between these conformations induced by changing the ions in the sample while the overall structure of NaK is not affected. We show that two K+-selective mutants (NaK2K and NaK2K-Y66F) suffer a complete loss of selectivity filter stability under Na+ conditions, but do not collapse into a defined structure. Widespread chemical shift perturbations are seen between the Na+ and K+ states of the K+-selective mutants in the region of the pore helix indicating structural changes. We conclude that the stronger link between the selectivity filter and the pore helix in the K+-selective mutants, compared to the non-selective wild-type NaK channel, reduces the ion-dependent conformational flexibility of the selectivity filter.
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Affiliation(s)
- Kitty Hendriks
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Han Sun
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany.
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15
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Fogeron ML, Lecoq L, Cole L, Harbers M, Böckmann A. Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. Front Mol Biosci 2021; 8:639587. [PMID: 33842544 PMCID: PMC8027086 DOI: 10.3389/fmolb.2021.639587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.
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Affiliation(s)
- Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
| | - Matthias Harbers
- CellFree Sciences, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, Lyon, France
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16
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Solid-state NMR approaches to investigate large enzymes in complex with substrates and inhibitors. Biochem Soc Trans 2020; 49:131-144. [PMID: 33367567 DOI: 10.1042/bst20200099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022]
Abstract
Enzyme catalysis is omnipresent in the cell. The mechanisms by which highly evolved protein folds enable rapid and specific chemical transformation of substrates belong to the marvels of structural biology. Targeting of enzymes with inhibitors has immediate application in drug discovery, from chemotherapeutics over antibiotics to antivirals. NMR spectroscopy combines multiple assets for the investigation of enzyme function. The non-invasive technique can probe enzyme structure and dynamics and map interactions with substrates, cofactors and inhibitors at the atomic level. With experiments performed at close to native conditions, catalytic transformations can be monitored in real time, giving access to kinetic parameters. The power of NMR in the solid state, in contrast with solution, lies in the absence of fundamental size limitations, which is crucial for enzymes that are either membrane-embedded or assemble into large soluble complexes exceeding hundreds of kilodaltons in molecular weight. Here we review recent progress in solid-state NMR methodology, which has taken big leaps in the past years due to steady improvements in hardware design, notably magic angle spinning, and connect it to parallel biochemical advances that enable isotope labelling of increasingly complex enzymes. We first discuss general concepts and requirements of the method and then highlight the state-of-the-art in sample preparation, structure determination, dynamics and interaction studies. We focus on examples where solid-state NMR has been instrumental in elucidating enzyme mechanism, alone or in integrative studies.
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17
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Rydzek S, Shein M, Bielytskyi P, Schütz AK. Observation of a Transient Reaction Intermediate Illuminates the Mechanochemical Cycle of the AAA-ATPase p97. J Am Chem Soc 2020; 142:14472-14480. [DOI: 10.1021/jacs.0c03180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Simon Rydzek
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Mikhail Shein
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Pavlo Bielytskyi
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Anne K. Schütz
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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18
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Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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19
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Wiegand T, Lacabanne D, Torosyan A, Boudet J, Cadalbert R, Allain FHT, Meier BH, Böckmann A. Sedimentation Yields Long-Term Stable Protein Samples as Shown by Solid-State NMR. Front Mol Biosci 2020; 7:17. [PMID: 32154263 PMCID: PMC7047159 DOI: 10.3389/fmolb.2020.00017] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/30/2020] [Indexed: 01/02/2023] Open
Abstract
Today, the sedimentation of proteins into a magic-angle spinning (MAS) rotor gives access to fast and reliable sample preparation for solid-state Nuclear Magnetic Resonance (NMR), and this has allowed for the investigation of a variety of non-crystalline protein samples. High protein concentrations on the order of 400 mg/mL can be achieved, meaning that around 50–60% of the NMR rotor content is protein; the rest is a buffer solution, which includes counter ions to compensate for the charge of the protein. We have demonstrated herein the long-term stability of four sedimented proteins and complexes thereof with nucleotides, comprising a bacterial DnaB helicase, an ABC transporter, an archaeal primase, and an RNA polymerase subunit. Solid-state NMR spectra recorded directly after sample filling and up to 5 years later indicated no spectral differences and no loss in signal intensity, allowing us to conclude that protein sediments in the rotor can be stable over many years. We have illustrated, using an example of an ABC transporter, that not only the structure is maintained, but that the protein is still functional after long-term storage in the sedimented state.
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Affiliation(s)
| | | | | | - Julien Boudet
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zurich, Switzerland
| | | | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zürich, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université de Lyon, Labex Ecofect, Lyon, France
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20
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Kaur H, Grahl A, Hartmann JB, Hiller S. Sample Preparation and Technical Setup for NMR Spectroscopy with Integral Membrane Proteins. Methods Mol Biol 2020; 2127:373-396. [PMID: 32112334 DOI: 10.1007/978-1-0716-0373-4_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
NMR spectroscopy is a method of choice to characterize structure, function, and dynamics of integral membrane proteins at atomic resolution. Here, we describe protocols for sample preparation and characterization by NMR spectroscopy of two integral membrane proteins with different architecture, the α-helical membrane protein MsbA and the β-barrel membrane protein BamA. The protocols describe recombinant expression in E. coli, protein refolding, purification, and reconstitution in suitable membrane mimetics, as well as key setup steps for basic NMR experiments. These include experiments on protein samples in the solid state under magic angle spinning (MAS) conditions and experiments on protein samples in aqueous solution. Since MsbA and BamA are typical examples of their respective architectural classes, the protocols presented here can also serve as a reference for other integral membrane proteins.
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Affiliation(s)
- Hundeep Kaur
- Biozentrum, University of Basel, Basel, Switzerland
| | - Anne Grahl
- Biozentrum, University of Basel, Basel, Switzerland
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21
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Two closed ATP- and ADP-dependent conformations in yeast Hsp90 chaperone detected by Mn(II) EPR spectroscopic techniques. Proc Natl Acad Sci U S A 2019; 117:395-404. [PMID: 31862713 DOI: 10.1073/pnas.1916030116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hsp90 plays a central role in cell homeostasis by assisting folding and maturation of a large variety of clients. It is a homo-dimer, which functions via hydrolysis of ATP-coupled to conformational changes. Hsp90's conformational cycle in the absence of cochaperones is currently postulated as apo-Hsp90 being an ensemble of "open"/"closed" conformations. Upon ATP binding, Hsp90 adopts an active ATP-bound closed conformation where the N-terminal domains, which comprise the ATP binding site, are in close contact. However, there is no consensus regarding the conformation of the ADP-bound Hsp90, which is considered important for client release. In this work, we tracked the conformational states of yeast Hsp90 at various stages of ATP hydrolysis in frozen solutions employing electron paramagnetic resonance (EPR) techniques, particularly double electron-electron resonance (DEER) distance measurements. Using rigid Gd(III) spin labels, we found the C domains to be dimerized with same distance distribution at all hydrolysis states. Then, we substituted the ATPase Mg(II) cofactor with paramagnetic Mn(II) and followed the hydrolysis state using hyperfine spectroscopy and measured the inter-N-domain distance distributions via Mn(II)-Mn(II) DEER. The point character of the Mn(II) spin label allowed us resolve 2 different closed states: The ATP-bound (prehydrolysis) characterized by a distance distribution having a maximum of 4.3 nm, which broadened and shortened, shifting the mean to 3.8 nm at the ADP-bound state (posthydrolysis). This provides experimental evidence to a second closed conformational state of Hsp90 in solution, referred to as "compact." Finally, the so-called high-energy state, trapped by addition of vanadate, was found structurally similar to the posthydrolysis state.
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22
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Exploring Protein Structures by DNP-Enhanced Methyl Solid-State NMR Spectroscopy. J Am Chem Soc 2019; 141:19888-19901. [DOI: 10.1021/jacs.9b11195] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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23
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Elkins MR, Hong M. Elucidating ligand-bound structures of membrane proteins using solid-state NMR spectroscopy. Curr Opin Struct Biol 2019; 57:103-109. [PMID: 30903830 PMCID: PMC6697555 DOI: 10.1016/j.sbi.2019.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 01/08/2023]
Abstract
Magic-angle-spinning (MAS) solid-state NMR spectroscopy is a versatile technique to elucidate functionally important protein-ligand interactions in lipid membranes. Here, we review recent solid-state NMR studies of membrane protein interactions with cholesterol, lipids, transported substrates, and peptide ligands. These studies are conducted in synthetic or native lipid bilayers to provide an accurate environment for ligand binding. The solid-state NMR approaches include multinuclear detection to gain comprehensive structural information, distance measurements to locate ligand-binding sites, and dynamic nuclear polarization and 1H detection to enhance spectral sensitivity. These studies provide novel insights into the mechanisms of virus budding, virus entry into cells, transmembrane signaling, substrate transport, antibacterial action, and many other biological processes.
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Affiliation(s)
- Matthew R Elkins
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States.
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