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Golota NC, Fredin ZP, Banks DP, Preiss D, Bahri S, Patil P, Langford WK, Blackburn CL, Strand E, Michael B, Dastrup B, Nelson KA, Gershenfeld N, Griffin R. Diamond rotors. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107475. [PMID: 37224586 PMCID: PMC10504678 DOI: 10.1016/j.jmr.2023.107475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/26/2023]
Abstract
The resolution of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra remains bounded by the spinning frequency, which is limited by the material strength of MAS rotors. Since diamond is capable of withstanding 1.5-2.5x greater MAS frequencies, compared to state-of-the art zirconia, we fabricated rotors from single crystal diamond. When combined with bearings optimized for spinning with helium gas, diamond rotors could achieve the highest MAS frequencies to date. Furthermore, the excellent microwave transmission properties and thermal conductivity of diamond could improve sensitivity enhancements in dynamic nuclear polarization (DNP) experiments. The fabrication protocol we report involves novel laser micromachining and produced rotors that presently spin at ωr/2π = 111.000 ± 0.004 kHz, with stable spinning up to 124 kHz, using N2 gas as the driving fluid. We present the first proton-detected 13C/15N MAS spectra recorded using diamond rotors, a critical step towards studying currently inaccessible ex-vivo protein samples with MAS NMR. Previously, the high aspect ratio of MAS rotors (∼10:1) precluded fabrication of MAS rotors from diamond.
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Affiliation(s)
- Natalie C Golota
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zachary P Fredin
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel P Banks
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Preiss
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Salima Bahri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Prashant Patil
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William K Langford
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Camron L Blackburn
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Erik Strand
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian Michael
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Blake Dastrup
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Keith A Nelson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil Gershenfeld
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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2
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Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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3
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Xue K, Movellan KT, Zhang XC, Najbauer EE, Forster MC, Becker S, Andreas LB. Towards a native environment: structure and function of membrane proteins in lipid bilayers by NMR. Chem Sci 2021; 12:14332-14342. [PMID: 34880983 PMCID: PMC8580007 DOI: 10.1039/d1sc02813h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/07/2021] [Indexed: 01/17/2023] Open
Abstract
Solid-state NMR (ssNMR) is a versatile technique that can be used for the characterization of various materials, ranging from small molecules to biological samples, including membrane proteins. ssNMR can probe both the structure and dynamics of membrane proteins, revealing protein function in a near-native lipid bilayer environment. The main limitation of the method is spectral resolution and sensitivity, however recent developments in ssNMR hardware, including the commercialization of 28 T magnets (1.2 GHz proton frequency) and ultrafast MAS spinning (<100 kHz) promise to accelerate acquisition, while reducing sample requirement, both of which are critical to membrane protein studies. Here, we review recent advances in ssNMR methodology used for structure determination of membrane proteins in native and mimetic environments, as well as the study of protein functions such as protein dynamics, and interactions with ligands, lipids and cholesterol.
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Affiliation(s)
- Kai Xue
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Kumar Tekwani Movellan
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Xizhou Cecily Zhang
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Eszter E Najbauer
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Marcel C Forster
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Stefan Becker
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Loren B Andreas
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
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4
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Tong Q, Tan H, Li J, Xie H, Zhao Y, Chen Y, Yang J. Extensively sparse 13C labeling to simplify solid-state NMR 13C spectra of membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2021; 75:245-254. [PMID: 34148188 DOI: 10.1007/s10858-021-00372-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Solid-state Nuclear Magnetic Resonance (ssNMR) is an emerging technique to investigate the structures and dynamics of membrane proteins in an artificial or native membrane environment. However, the structural studies of proteins by ssNMR are usually prolonged or impeded by signal assignments, especially the assignments of signals for collection of distance restraints, because of serious overlapping of signals in 2D 13C-13C spectra. Sparse labeling of 13C spins is an effective approach to simplify the 13C spectra and facilitate the extractions of distance restraints. Here, we propose a new reverse labeling combination of six types of amino acid residues (Ile, Leu, Phe, Trp, Tyr and Lys), and show a clean reverse labeling effect on a model membrane protein E. coli aquaporin Z (AqpZ). We further combine this reverse labeling combination and alternate 13C-12C labeling, and demonstrate an enhanced dilution effect in 13C-13C spectra. In addition, the influences of reverse labeling on the labeling of the other types of residues are quantitatively analyzed in the two strategies (1, reverse labeling and 2, reverse labeling combining alternate 13C-12C labeling). The signal intensities of some other types of residues in 2D 13C-13C spectra are observed to be 20-50% weaker because of the unwanted reverse labeling. The extensively sparse 13C labeling proposed in this study is expected to be useful in the collection of distance restraints using 2D 13C-13C spectra of membrane proteins.
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Affiliation(s)
- Qiong Tong
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China
| | - Huan Tan
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Jianping Li
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Yongxiang Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Yanke Chen
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, People's Republic of China.
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5
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Buslaev P, Mustafin K, Gushchin I. Principal component analysis highlights the influence of temperature, curvature and cholesterol on conformational dynamics of lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183253. [PMID: 32142820 DOI: 10.1016/j.bbamem.2020.183253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/14/2020] [Accepted: 02/27/2020] [Indexed: 01/06/2023]
Abstract
Membrane lipids are inherently highly dynamic molecules. Currently, it is difficult to probe the structures of individual lipids experimentally at the timescales corresponding to atomic motions, and consequently molecular dynamics simulations are used widely. In our previous work, we have introduced the principal component analysis (PCA) as a convenient framework for comprehensive quantitative description of lipid motions. Here, we present a newly developed open source script, PCAlipids, which automates the analysis and allows us to refine the approach and test its limitations. We use PCAlipids to determine the influence of temperature, cholesterol and curvature on individual lipids, and show that the most prominent lipid tail scissoring motion is strongly affected by these factors and allows tracking of phase transition. Addition of cholesterol affects the conformations and selectively changes the dynamics of lipid molecules, impacting the large-amplitude motions. Introduction of curvature biases the conformational ensembles towards more extended structures. We hope that the developed approach will be useful for understanding the molecular basis of different processes occurring in lipid membrane systems and will stimulate development of complementary experimental techniques probing the conformations of individual lipid molecules.
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Affiliation(s)
- P Buslaev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - K Mustafin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - I Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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6
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Jirasko V, Lakomek N, Penzel S, Fogeron M, Bartenschlager R, Meier BH, Böckmann A. Proton-Detected Solid-State NMR of the Cell-Free Synthesized α-Helical Transmembrane Protein NS4B from Hepatitis C Virus. Chembiochem 2020; 21:1453-1460. [PMID: 31850615 PMCID: PMC7318649 DOI: 10.1002/cbic.201900765] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Indexed: 01/01/2023]
Abstract
Proton-detected 100 kHz magic-angle-spinning (MAS) solid-state NMR is an emerging analysis method for proteins with only hundreds of microgram quantities, and thus allows structural investigation of eukaryotic membrane proteins. This is the case for the cell-free synthesized hepatitis C virus (HCV) nonstructural membrane protein 4B (NS4B). We demonstrate NS4B sample optimization using fast reconstitution schemes that enable lipid-environment screening directly by NMR. 2D spectra and relaxation properties guide the choice of the best sample preparation to record 2D 1 H-detected 1 H,15 N and 3D 1 H,13 C,15 N correlation experiments with linewidths and sensitivity suitable to initiate sequential assignments. Amino-acid-selectively labeled NS4B can be readily obtained using cell-free synthesis, opening the door to combinatorial labeling approaches which should enable structural studies.
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Affiliation(s)
- Vlastimil Jirasko
- ETH ZürichPhysical ChemistryVladimir-Prelog Weg 28093ZürichSwitzerland
| | | | - Susanne Penzel
- ETH ZürichPhysical ChemistryVladimir-Prelog Weg 28093ZürichSwitzerland
| | - Marie‐Laure Fogeron
- Institut de Biologie et Chimie des ProteinesMMSBLabex EcofectUMR 5086 CNRSUniversité de Lyon7 passage du Vercors69367LyonFrance
| | - Ralf Bartenschlager
- Department of Infectious DiseasesMolecular VirologyHeidelberg UniversityIm Neuenheimer Feld 34569120HeidelbergGermany
- Division of Virus-Associated Carcinogenesis (Germany)Cancer Research Center (DKFZ)Im Neuenheimer Feld 24269120HeidelbergGermany
| | - Beat H. Meier
- ETH ZürichPhysical ChemistryVladimir-Prelog Weg 28093ZürichSwitzerland
| | - Anja Böckmann
- Institut de Biologie et Chimie des ProteinesMMSBLabex EcofectUMR 5086 CNRSUniversité de Lyon7 passage du Vercors69367LyonFrance
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7
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Hoffmann J, Ruta J, Shi C, Hendriks K, Chevelkov V, Franks WT, Oschkinat H, Giller K, Becker S, Lange A. Protein resonance assignment by BSH-CP-based 3D solid-state NMR experiments: A practical guide. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:445-465. [PMID: 31691361 DOI: 10.1002/mrc.4945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/05/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Solid-state NMR (ssNMR) spectroscopy has evolved into a powerful method to obtain structural information and to study the dynamics of proteins at atomic resolution and under physiological conditions. The method is especially well suited to investigate insoluble and noncrystalline proteins that cannot be investigated easily by X-ray crystallography or solution NMR. To allow for detailed analysis of ssNMR data, the assignment of resonances to the protein atoms is essential. For this purpose, a set of three-dimensional (3D) spectra needs to be acquired. Band-selective homo-nuclear cross-polarization (BSH-CP) is an effective method for magnetization transfer between carbonyl carbon (CO) and alpha carbon (CA) atoms, which is an important transfer step in multidimensional ssNMR experiments. This tutorial describes the detailed procedure for the chemical shift assignment of the backbone atoms of 13 C-15 N-labeled proteins by BSH-CP-based 13 C-detected ssNMR experiments. A set of six 3D experiments is used for unambiguous assignment of the protein backbone as well as certain side-chain resonances. The tutorial especially addresses scientists with little experience in the field of ssNMR and provides all the necessary information for protein assignment in an efficient, time-saving approach.
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Affiliation(s)
- Jutta Hoffmann
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Julia Ruta
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Kitty Hendriks
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - W Trent Franks
- Department of NMR-supported Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Hartmut Oschkinat
- Department of NMR-supported Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Karin Giller
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
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8
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein–RNA Complex by Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
- Group of NMR-based Structural ChemistryHelmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
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9
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2020; 59:6866-6873. [PMID: 32023357 PMCID: PMC7187219 DOI: 10.1002/anie.201915465] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Indexed: 12/17/2022]
Abstract
Solid‐state NMR (ssNMR) is applicable to high molecular‐weight (MW) protein assemblies in a non‐amorphous precipitate. The technique yields atomic resolution structural information on both soluble and insoluble particles without limitations of MW or requirement of crystals. Herein, we propose and demonstrate an approach that yields the structure of protein–RNA complexes (RNP) solely from ssNMR data. Instead of using low‐sensitivity magnetization transfer steps between heteronuclei of the protein and the RNA, we measure paramagnetic relaxation enhancement effects elicited on the RNA by a paramagnetic tag coupled to the protein. We demonstrate that this data, together with chemical‐shift‐perturbation data, yields an accurate structure of an RNP complex, starting from the bound structures of its components. The possibility of characterizing protein–RNA interactions by ssNMR may enable applications to large RNP complexes, whose structures are not accessible by other methods.
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Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany.,Group of NMR-based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
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10
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Zhang R, Nishiyama Y, Ramamoorthy A. Exploiting heterogeneous time scale of dynamics to enhance 2D HETCOR solid-state NMR sensitivity. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 309:106615. [PMID: 31669793 DOI: 10.1016/j.jmr.2019.106615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/11/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
Multidimensional solid-state NMR spectroscopy plays a significant role in offering atomic-level insights into molecular systems. In particular, heteronuclear chemical shift correlation (HETCOR) experiments could provide local chemical and structural information in terms of spatial heteronuclear proximity and through-bond connectivity. In solid state, the transfer of magnetization between heteronuclei, a key step in HETCOR experiments, is usually achieved using cross-polarization (CP) or insensitive nuclei enhanced by polarization transfer (INEPT) depending on the sample characteristics and magic-angle-spinning (MAS) frequency. But, for a multiphase system constituting molecular components that differ in their time scales of mobilities, CP efficiency is pretty low for mobile components because of the averaging of heteronuclear dipolar couplings whereas INEPT is inefficient for immobile components due to the short T2 and can yield through-space connectivity due to strong proton spin diffusion for immobile components especially under moderate spinning speeds. Herein, in this study we present two 2D pulse sequences that enable the sequential acquisition of 13C/1H HETCOR NMR spectra for the rigid and mobile components by taking full advantage of the abundant proton magnetization in a single experiment with barely increasing the overall experimental time. In particular, the 13C-detected HETCOR experiment could be applied under slow MAS conditions, where a multiple-pulse sequence is typically employed to enhance 1H spectral resolution in the indirect dimension. In contrast, the 1H-detected HETCOR experiment should be applied under ultrafast MAS, where CP and heteronuclear nuclear Overhauser effect (NOE) polarization transfer are combined to enhance 13C signal intensities for mobile components. These pulse sequences are experimentally demonstrated on two model systems to obtain 2D 13C/1H chemical shift correlation spectra of rigid and mobile components independently and separately. These pulse sequences can be used for dynamics based spectral editing and resonance assignments. Therefore, we believe the proposed 2D HETCOR NMR pulse sequences will be beneficial for the structural studies of heterogeneous systems containing molecular components that differ in their time scale of motions for understanding the interplay of structures and properties.
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Affiliation(s)
- Rongchun Zhang
- Biophysics and Department of Chemistry, Biomedical Engineering, Maromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Yusuke Nishiyama
- NMR Science and Development Division, RIKEN SPring-8 Center, Nanocrystallography Unit, RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Maromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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11
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Mori T, Sugita Y. Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation. J Chem Theory Comput 2019; 16:711-724. [DOI: 10.1021/acs.jctc.9b00783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
- RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Center for Biosystems Dynamics Research, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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12
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Wang S, Gopinath T, Veglia G. Improving the quality of oriented membrane protein spectra using heat-compensated separated local field experiments. JOURNAL OF BIOMOLECULAR NMR 2019; 73:617-624. [PMID: 31463642 PMCID: PMC6861693 DOI: 10.1007/s10858-019-00273-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/21/2019] [Indexed: 05/03/2023]
Abstract
Oriented sample solid-state NMR (OS-ssNMR) spectroscopy is a powerful technique to determine the topology of membrane proteins in oriented lipid bilayers. Separated local field (SLF) experiments are central to this technique as they provide first-order orientational restraints, i.e., dipolar couplings and anisotropic chemical shifts. Despite the use of low-E (or E-free) probes, the heat generated during the execution of 2D and 3D SLF pulse sequences causes sizeable line-shape distortions. Here, we propose a new heat-compensated SE-SAMPI4 (hcSE-SAMPI4) pulse sequence that holds the temperature constant for the duration of the experiment. This modification of the SE-SAMPI4 results in sharper and more intense resonances without line-shape distortions. The spectral improvements are even more apparent when paramagnetic relaxation agents are used to speed up data collection. We tested the hcSE-SAMPI4 pulse sequence on a single-span membrane protein, sarcolipin (SLN), reconstituted in magnetically aligned lipid bicelles. In addition to eliminating peak distortions, the hcSE-SAMPI4 experiment increased the average signal-to-noise ratio by 20% with respect to the original SE-SAMPI4.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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Jaroniec CP. Two decades of progress in structural and dynamic studies of amyloids by solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:42-47. [PMID: 31311708 PMCID: PMC6703944 DOI: 10.1016/j.jmr.2019.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 06/22/2019] [Accepted: 07/08/2019] [Indexed: 05/09/2023]
Abstract
In this perspective article I briefly highlight the rapid progress made over the past two decades in atomic level structural and dynamic studies of amyloids, which are representative of non-crystalline biomacromolecular assemblies, by magic-angle spinning solid-state NMR spectroscopy. Given new and continuing developments in solid-state NMR instrumentation and methodology, ongoing research in this area promises to contribute to an improved understanding of amyloid structure, polymorphism, interactions, assembly mechanisms, and biological function and toxicity.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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14
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Öster C, Hendriks K, Kopec W, Chevelkov V, Shi C, Michl D, Lange S, Sun H, de Groot BL, Lange A. The conduction pathway of potassium channels is water free under physiological conditions. SCIENCE ADVANCES 2019; 5:eaaw6756. [PMID: 31392272 PMCID: PMC6669007 DOI: 10.1126/sciadv.aaw6756] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
Ion conduction through potassium channels is a fundamental process of life. On the basis of crystallographic data, it was originally proposed that potassium ions and water molecules are transported through the selectivity filter in an alternating arrangement, suggesting a "water-mediated" knock-on mechanism. Later on, this view was challenged by results from molecular dynamics simulations that revealed a "direct" knock-on mechanism where ions are in direct contact. Using solid-state nuclear magnetic resonance techniques tailored to characterize the interaction between water molecules and the ion channel, we show here that the selectivity filter of a potassium channel is free of water under physiological conditions. Our results are fully consistent with the direct knock-on mechanism of ion conduction but contradict the previously proposed water-mediated knock-on mechanism.
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Affiliation(s)
- Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Kitty Hendriks
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Wojciech Kopec
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Dagmar Michl
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Han Sun
- Section Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Bert L. de Groot
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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15
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Zhang R, Duong NT, Nishiyama Y. Resolution enhancement and proton proximity probed by 3D TQ/DQ/SQ proton NMR spectroscopy under ultrafast magic-angle-spinning beyond 70 kHz. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 304:78-86. [PMID: 31146121 DOI: 10.1016/j.jmr.2019.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/15/2019] [Accepted: 05/18/2019] [Indexed: 06/09/2023]
Abstract
Proton nuclear magnetic resonance (NMR) in solid state has gained significant attention in recent years due to the remarkable resolution and sensitivity enhancement afforded by ultrafast magic-angle-spinning (MAS). In spite of the substantial suppression of 1H-1H dipolar couplings, the proton spectral resolution is still poor compared to that of 13C or 15N NMR, rendering it challenging for the structural and conformational analysis of complex chemicals or biological solids. Herein, by utilizing the benefits of double-quantum (DQ) and triple-quantum (TQ) coherences, we propose a 3D single-channel pulse sequence that correlates proton triple-quantum/double-quantum/single-quantum (TQ/DQ/SQ) chemical shifts. In addition to the two-spin proximity information, this 3D TQ/DQ/SQ pulse sequence enables more reliable extraction of three-spin proximity information compared to the regular 2D TQ/SQ correlation experiment, which could aid in revealing the proton network in solids. Furthermore, the TQ/DQ slice taken at a specific SQ chemical shift only reveals the local correlations to the corresponding SQ chemical shift, and thus it enables accurate assignments of the proton peaks along the TQ and DQ dimensions and simplifies the interpretation of proton spectra especially for dense proton networks. The high performance of this 3D pulse sequence is well demonstrated on small compounds, L-alanine and a tripeptide, N-formyl-L-methionyl-L-leucyl-L-phenylalanine (MLF). We expect that this new methodology can inspire the development of multidimensional solid-state NMR pulse sequences using the merits of TQ and DQ coherences and enable high-throughput investigations of complex solids using abundant protons.
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Affiliation(s)
- Rongchun Zhang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, PR China.
| | - Nghia Tuan Duong
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Yusuke Nishiyama
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
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16
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Gopinath T, Wang S, Lee J, Aihara H, Veglia G. Hybridization of TEDOR and NCX MAS solid-state NMR experiments for simultaneous acquisition of heteronuclear correlation spectra and distance measurements. JOURNAL OF BIOMOLECULAR NMR 2019; 73:141-153. [PMID: 30805819 PMCID: PMC6526076 DOI: 10.1007/s10858-019-00237-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/12/2019] [Indexed: 05/05/2023]
Abstract
Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is a major technique for the characterization of the structural dynamics of biopolymers at atomic resolution. However, the intrinsic low sensitivity of this technique poses significant limitations to its routine application in structural biology. Here we achieve substantial savings in experimental time using a new subclass of Polarization Optimized Experiments (POEs) that concatenate TEDOR and SPECIFIC-CP transfers into a single pulse sequence. Specifically, we designed new 2D and 3D experiments (2D TEDOR-NCX, 3D TEDOR-NCOCX, and 3D TEDOR-NCACX) to obtain distance measurements and heteronuclear chemical shift correlations for resonance assignments using only one experiment. We successfully tested these experiments on N-Acetyl-Val-Leu dipeptide, microcrystalline U-13C,15N ubiquitin, and single- and multi-span membrane proteins reconstituted in lipid membranes. These pulse sequences can be implemented on any ssNMR spectrometer equipped with standard solid-state hardware using only one receiver. Since these new POEs speed up data acquisition considerably, we anticipate their broad application to fibrillar, microcrystalline, and membrane-bound proteins.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - John Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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17
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Pinto C, Mance D, Julien M, Daniels M, Weingarth M, Baldus M. Studying assembly of the BAM complex in native membranes by cellular solid-state NMR spectroscopy. J Struct Biol 2019; 206:1-11. [DOI: 10.1016/j.jsb.2017.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 12/31/2022]
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18
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Han R, Yang Y, Wang S. Longitudinal Relaxation Optimization Enhances 1 H-Detected HSQC in Solid-State NMR Spectroscopy on Challenging Biological Systems. Chemistry 2019; 25:4115-4122. [PMID: 30632195 DOI: 10.1002/chem.201805327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Indexed: 11/10/2022]
Abstract
Solid-state (SS) NMR spectroscopy is a powerful technique for studying challenging biological systems, but it often suffers from low sensitivity. A longitudinal relaxation optimization scheme to enhance the signal sensitivity of HSQC experiments in SSNMR spectroscopy is reported. Under the proposed scheme, the 1 H spins of 1 H-X (15 N or 13 C) are selected for signal acquisition, whereas other vast 1 H spins are flipped back to the axis of the static magnetic field to accelerate the spin recovery of the observed 1 H spins, resulting in enhanced sensitivity. Three biological systems are used to evaluate this strategy, including a seven-transmembrane protein, an RNA, and a whole-cell sample. For all three samples, the proposed scheme largely shortens the effective 1 H longitudinal relaxation time and results in a 1.3-2.5-fold gain in sensitivity. The selected systems are representative of challenging biological systems for observation by means of SSNMR spectroscopy; thus indicating the general applicability of this method, which is particularly important for biological samples with a short lifetime or with limited sample quantities.
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Affiliation(s)
- Rong Han
- College of Chemistry and Molecular Engineering and Beijing NMR Center, Peking University, No. 5th, Yiheyuan Rd., Beijing, 100871, P.R. China
| | - Yufei Yang
- College of Chemistry and Molecular Engineering and Beijing NMR Center, Peking University, No. 5th, Yiheyuan Rd., Beijing, 100871, P.R. China
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center, Peking University, No. 5th, Yiheyuan Rd., Beijing, 100871, P.R. China.,Beijing National Laboratory for Molecular Sciences, Beijing, P.R. China
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19
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van Emmerik CL, van Ingen H. Unspinning chromatin: Revealing the dynamic nucleosome landscape by NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 110:1-19. [PMID: 30803691 DOI: 10.1016/j.pnmrs.2019.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 05/09/2023]
Abstract
NMR is an essential technique for obtaining information at atomic resolution on the structure, motions and interactions of biomolecules. Here, we review the contribution of NMR to our understanding of the fundamental unit of chromatin: the nucleosome. Nucleosomes compact the genome by wrapping the DNA around a protein core, the histone octamer, thereby protecting genomic integrity. Crucially, the imposed barrier also allows strict regulation of gene expression, DNA replication and DNA repair processes through an intricate system of histone and DNA modifications and a wide range of interactions between nucleosomes and chromatin factors. In this review, we describe how NMR has contributed to deciphering the molecular basis of nucleosome function. Starting from pioneering studies in the 1960s using natural abundance NMR studies, we focus on the progress in sample preparation and NMR methodology that has allowed high-resolution studies on the nucleosome and its subunits. We summarize the results and approaches of state-of-the-art NMR studies on nucleosomal DNA, histone complexes, nucleosomes and nucleosomal arrays. These studies highlight the particular strength of NMR in studying nucleosome dynamics and nucleosome-protein interactions. Finally, we look ahead to exciting new possibilities that will be afforded by on-going developments in solution and solid-state NMR. By increasing both the depth and breadth of nucleosome NMR studies, it will be possible to offer a unique perspective on the dynamic landscape of nucleosomes and its interacting proteins.
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Affiliation(s)
- Clara L van Emmerik
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
| | - Hugo van Ingen
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
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20
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Movellan KT, Najbauer EE, Pratihar S, Salvi M, Giller K, Becker S, Andreas LB. Alpha protons as NMR probes in deuterated proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:81-91. [PMID: 30762170 PMCID: PMC6441447 DOI: 10.1007/s10858-019-00230-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 01/28/2019] [Indexed: 05/08/2023]
Abstract
We describe a new labeling method that allows for full protonation at the backbone Hα position, maintaining protein side chains with a high level of deuteration. We refer to the method as alpha proton exchange by transamination (α-PET) since it relies on transaminase activity demonstrated here using Escherichia coli expression. We show that α-PET labeling is particularly useful in improving structural characterization of solid proteins by introduction of an additional proton reporter, while eliminating many strong dipolar couplings. The approach benefits from the high sensitivity associated with 1.3 mm samples, more abundant information including Hα resonances, and the narrow proton linewidths encountered for highly deuterated proteins. The labeling strategy solves amide proton exchange problems commonly encountered for membrane proteins when using perdeuteration and backexchange protocols, allowing access to alpha and all amide protons including those in exchange-protected regions. The incorporation of Hα protons provides new insights, as the close Hα-Hα and Hα-HN contacts present in β-sheets become accessible, improving the chance to determine the protein structure as compared with HN-HN contacts alone. Protonation of the Hα position higher than 90% is achieved for Ile, Leu, Phe, Tyr, Met, Val, Ala, Gln, Asn, Thr, Ser, Glu, Asp even though LAAO is only active at this degree for Ile, Leu, Phe, Tyr, Trp, Met. Additionally, the glycine methylene carbon is labeled preferentially with a single deuteron, allowing stereospecific assignment of glycine alpha protons. In solution, we show that the high deuteration level dramatically reduces R2 relaxation rates, which is beneficial for the study of large proteins and protein dynamics. We demonstrate the method using two model systems, as well as a 32 kDa membrane protein, hVDAC1, showing the applicability of the method to study membrane proteins.
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Affiliation(s)
- Kumar Tekwani Movellan
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Eszter E Najbauer
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Supriya Pratihar
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Michele Salvi
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Karin Giller
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Stefan Becker
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany.
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21
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Mukhopadhyay D, Gupta C, Theint T, Jaroniec CP. Peptide bond conformation in peptides and proteins probed by dipolar coupling-chemical shift tensor correlation solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 297:152-160. [PMID: 30396157 PMCID: PMC6289736 DOI: 10.1016/j.jmr.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 05/30/2023]
Abstract
Multidimensional magic-angle spinning solid-state NMR experiments are described that permit cis and trans peptide bonds in uniformly 13C,15N-labeled peptides and proteins to be unambiguously distinguished in residue-specific manner by determining the relative orientations of the amide 13C' CSA and 1H-15N dipolar coupling tensors. The experiments are demonstrated for model peptides glycylglycine and 2,5-diketopiperazine containing trans and cis peptide bonds, respectively. Subsequently, the measurements are extended to two representative proteins that contain exclusively trans peptide bonds, microcrystalline B3 immunoglobulin domain of protein G and Y145Stop human prion protein amyloid fibrils, to illustrate their applicability to a wide range of protein systems.
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Affiliation(s)
- Dwaipayan Mukhopadhyay
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Chitrak Gupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Theint Theint
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States.
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22
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Radoicic J, Park SH, Opella SJ. Macrodiscs Comprising SMALPs for Oriented Sample Solid-State NMR Spectroscopy of Membrane Proteins. Biophys J 2018; 115:22-25. [PMID: 29914645 DOI: 10.1016/j.bpj.2018.05.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 02/07/2023] Open
Abstract
Macrodiscs, which are magnetically alignable lipid bilayer discs with diameters of >30 nm, were obtained by solubilizing protein-containing liposomes with styrene-maleic acid copolymers. Macrodiscs provide a detergent-free phospholipid bilayer environment for biophysical and functional studies of membrane proteins under physiological conditions. The narrow resonance linewidths observed from membrane proteins in styrene-maleic acid macrodiscs advance structure determination by oriented sample solid-state NMR spectroscopy.
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Affiliation(s)
- Jasmina Radoicic
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
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23
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David G, Fogeron ML, Schledorn M, Montserret R, Haselmann U, Penzel S, Badillo A, Lecoq L, André P, Nassal M, Bartenschlager R, Meier BH, Böckmann A. Structural Studies of Self-Assembled Subviral Particles: Combining Cell-Free Expression with 110 kHz MAS NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:4787-4791. [PMID: 29457857 DOI: 10.1002/anie.201712091] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/25/2018] [Indexed: 01/08/2023]
Abstract
Viral membrane proteins are prime targets in combatting infection. Still, the determination of their structure remains a challenge, both with respect to sample preparation and the need for structural methods allowing for analysis in a native-like lipid environment. Cell-free protein synthesis and solid-state NMR spectroscopy are promising approaches in this context, the former with respect to its great potential in the native expression of complex proteins, and the latter for the analysis of membrane proteins in lipids. Herein, we show that milligram amounts of the small envelope protein of the duck hepatitis B virus (DHBV) can be produced by cell-free expression, and that the protein self-assembles into subviral particles. Proton-detected 2D NMR spectra recorded at a magic-angle-spinning frequency of 110 kHz on <500 μg protein show a number of isolated peaks with line widths comparable to those of model membrane proteins, paving the way for structural studies of this protein that is homologous to a potential drug target in HBV infection.
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Affiliation(s)
- Guillaume David
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | | | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Uta Haselmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis Germany, Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Susanne Penzel
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.,RD-Biotech, Recombinant Protein Unit, 3 rue Henri Baigue, 25000, Besançon, France
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
| | - Patrice André
- Centre International de Recherche en Infectiologie, Institut National de la Santé et de la Recherche Médicale Unité 1111, Centre National de la Recherche Scientifique Unités Mixte de Recherche, 5308, Lyon, France.,Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France.,Université de Lyon, Laboratoire de Virologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - Michael Nassal
- University Hospital Freiburg, Internal Medicine II/Molecular Biology, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis Germany, Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France
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24
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David G, Fogeron M, Schledorn M, Montserret R, Haselmann U, Penzel S, Badillo A, Lecoq L, André P, Nassal M, Bartenschlager R, Meier BH, Böckmann A. Strukturelle Untersuchung subviraler Partikel durch die Kombination von zellfreier Proteinherstellung mit 110 kHz MAS‐NMR‐Spektroskopie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Guillaume David
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | - Marie‐Laure Fogeron
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | | | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | - Uta Haselmann
- Department für Infektiologie Molekulare Virologie Universitätsklinikum Heidelberg Im Neuenheimer Feld 345 69120 Heidelberg Deutschland
- Abteilung Virus-assoziierte Karzinogenese Deutsches Krebsforschungszentrum (DKFZ) Im Neuenheimer Feld 242 69120 Heidelberg Deutschland
| | - Susanne Penzel
- Lab. für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | - Aurélie Badillo
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
- RD-Biotech Recombinant Protein Unit 3 rue Henri Baigue 25000 Besançon Frankreich
| | - Lauriane Lecoq
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
| | - Patrice André
- Centre International de Recherche en Infectiologie Institut National de la Santé et de la Recherche Médicale Unité 1111 Centre National de la Recherche Scientifique Unités Mixte de Recherche 5308 Lyon Frankreich
- Ecole Normale Supérieure de Lyon, Lyon, France Université Claude Bernard Lyon 1 Villeurbanne Frankreich
- Université de Lyon, Lyon, France Laboratoire de Virologie Hôpital de la Croix-Rousse Hospices Civils de Lyon Lyon Frankreich
| | - Michael Nassal
- Universitätsklinikum Freiburg Klinik für Innere Medizin II/ Molekulare Biologie Hugstetter Straße 55 79106 Freiburg Deutschland
| | - Ralf Bartenschlager
- Department für Infektiologie Molekulare Virologie Universitätsklinikum Heidelberg Im Neuenheimer Feld 345 69120 Heidelberg Deutschland
- Abteilung Virus-assoziierte Karzinogenese Deutsches Krebsforschungszentrum (DKFZ) Im Neuenheimer Feld 242 69120 Heidelberg Deutschland
| | - Beat H. Meier
- Lab. für Physikalische Chemie ETH Zürich 8093 Zürich Schweiz
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS Université de Lyon 7 passage du Vercors 69367 Lyon Frankreich
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25
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Yang Y, Wang S. RNA Characterization by Solid-State NMR Spectroscopy. Chemistry 2018; 24:8698-8707. [DOI: 10.1002/chem.201705583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Yufei Yang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
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26
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Schubeis T, Le Marchand T, Andreas LB, Pintacuda G. 1H magic-angle spinning NMR evolves as a powerful new tool for membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 287:140-152. [PMID: 29413327 DOI: 10.1016/j.jmr.2017.11.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 06/08/2023]
Abstract
Building on a decade of continuous advances of the community, the recent development of very fast (60 kHz and above) magic-angle spinning (MAS) probes has revolutionised the field of solid-state NMR. This new spinning regime reduces the 1H-1H dipolar couplings, so that direct detection of the larger magnetic moment available from 1H is now possible at high resolution, not only in deuterated molecules but also in fully-protonated substrates. Such capabilities allow rapid "fingerprinting" of samples with a ten-fold reduction of the required sample amounts with respect to conventional approaches, and permit extensive, robust and expeditious assignment of small-to-medium sized proteins (up to ca. 300 residues), and the determination of inter-nuclear proximities, relative orientations of secondary structural elements, protein-cofactor interactions, local and global dynamics. Fast MAS and 1H detection techniques have nowadays been shown to be applicable to membrane-bound systems. This paper reviews the strategies underlying this recent leap forward in sensitivity and resolution, describing its potential for the detailed characterization of membrane proteins.
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Affiliation(s)
- Tobias Schubeis
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Loren B Andreas
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.
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27
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Gopinath T, Veglia G. Experimental Aspects of Polarization Optimized Experiments (POE) for Magic Angle Spinning Solid-State NMR of Microcrystalline and Membrane-Bound Proteins. Methods Mol Biol 2018; 1688:37-53. [PMID: 29151203 DOI: 10.1007/978-1-4939-7386-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Conventional NMR pulse sequences record one spectrum per experiment, while spending most of the time waiting for the spin system to return to the equilibrium. As a result, a full set of multidimensional NMR experiments for biological macromolecules may take up to several months to complete. Here, we present a practical guide for setting up a new class of MAS solid-state NMR experiments (POE or polarization optimized experiments) that enable the simultaneous acquisition of multiple spectra of proteins, accelerating data acquisition. POE exploit the long-lived 15N polarization of isotopically labeled proteins and enable one to obtain up to eight spectra, by concatenating classical NMR pulse sequences. This new strategy propels data throughput of solid-state NMR spectroscopy of fibers, microcrystalline preparations, as well as membrane proteins.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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28
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Wang S, Gopinath T, Veglia G. Application of paramagnetic relaxation enhancements to accelerate the acquisition of 2D and 3D solid-state NMR spectra of oriented membrane proteins. Methods 2017; 138-139:54-61. [PMID: 29274874 DOI: 10.1016/j.ymeth.2017.12.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/14/2017] [Accepted: 12/19/2017] [Indexed: 12/21/2022] Open
Abstract
Oriented sample solid-state NMR (OS-ssNMR) spectroscopy is uniquely suited to determine membrane protein topology at the atomic resolution in liquid crystalline bilayers under physiological temperature. However, the inherent low sensitivity of this technique has hindered the throughput of multidimensional experiments necessary for resonance assignments and structure determination. In this work, we show that doping membrane protein bicelle preparations with paramagnetic ion chelated lipids and exploiting paramagnetic relaxation effects it is possible to accelerate the acquisition of both 2D and 3D multidimensional experiments with significant saving in time. We demonstrate the efficacy of this method for a small membrane protein, sarcolipin, reconstituted in DMPC/POPC/DHPC oriented bicelles. In particular, using Cu2+-DMPE-DTPA as a dopant, we observed a decrease of 1H T1 of sarcolipin by 2/3, allowing us to reduce the recycle delay up to 3 times. We anticipate that these new developments will enable the routine acquisition of multidimensional OS-ssNMR experiments.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
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29
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Mukhopadhyay D, Nadaud PS, Shannon MD, Jaroniec CP. Rapid Quantitative Measurements of Paramagnetic Relaxation Enhancements in Cu(II)-Tagged Proteins by Proton-Detected Solid-State NMR Spectroscopy. J Phys Chem Lett 2017; 8:5871-5877. [PMID: 29148785 PMCID: PMC5720925 DOI: 10.1021/acs.jpclett.7b02709] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We demonstrate rapid quantitative measurements of site-resolved paramagnetic relaxation enhancements (PREs), which are a source of valuable structural restraints corresponding to electron-nucleus distances in the ∼10-20 Å regime, in solid-state nuclear magnetic resonance (NMR) spectra of proteins containing covalent Cu2+-binding tags. Specifically, using protein GB1 K28C-EDTA-Cu2+ mutant as a model, we show the determination of backbone amide 15N longitudinal and 1H transverse PREs within a few hours of experiment time based on proton-detected 2D or 3D correlation spectra recorded with magic-angle spinning frequencies ≥ ∼ 60 kHz for samples containing ∼10-50 nanomoles of 2H,13C,15N-labeled protein back-exchanged in H2O. Additionally, we show that the electron relaxation time for the Cu2+ center, needed to convert PREs into distances, can be estimated directly from the experimental data. Altogether, these results are important for establishing solid-state NMR based on paramagnetic-tagging as a routine tool for structure determination of natively diamagnetic proteins.
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30
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Gopinath T, Nelson SED, Veglia G. 1H-detected MAS solid-state NMR experiments enable the simultaneous mapping of rigid and dynamic domains of membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 285:101-107. [PMID: 29173803 PMCID: PMC5764182 DOI: 10.1016/j.jmr.2017.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/30/2017] [Accepted: 09/04/2017] [Indexed: 05/05/2023]
Abstract
Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is emerging as a unique method for the atomic resolution structure determination of native membrane proteins in lipid bilayers. Although 13C-detected ssNMR experiments continue to play a major role, recent technological developments have made it possible to carry out 1H-detected experiments, boosting both sensitivity and resolution. Here, we describe a new set of 1H-detected hybrid pulse sequences that combine through-bond and through-space correlation elements into single experiments, enabling the simultaneous detection of rigid and dynamic domains of membrane proteins. As proof-of-principle, we applied these new pulse sequences to the membrane protein phospholamban (PLN) reconstituted in lipid bilayers under moderate MAS conditions. The cross-polarization (CP) based elements enabled the detection of the relatively immobile residues of PLN in the transmembrane domain using through-space correlations; whereas the most dynamic region, which is in equilibrium between folded and unfolded states, was mapped by through-bond INEPT-based elements. These new 1H-detected experiments will enable one to detect not only the most populated (ground) states of biomacromolecules, but also sparsely populated high-energy (excited) states for a complete characterization of protein free energy landscapes.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Sarah E D Nelson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
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31
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Lacabanne D, Lends A, Danis C, Kunert B, Fogeron ML, Jirasko V, Chuilon C, Lecoq L, Orelle C, Chaptal V, Falson P, Jault JM, Meier BH, Böckmann A. Gradient reconstitution of membrane proteins for solid-state NMR studies. JOURNAL OF BIOMOLECULAR NMR 2017; 69:81-91. [PMID: 28900789 DOI: 10.1007/s10858-017-0135-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
We here adapted the GRecon method used in electron microscopy studies for membrane protein reconstitution to the needs of solid-state NMR sample preparation. We followed in detail the reconstitution of the ABC transporter BmrA by dialysis as a reference, and established optimal reconstitution conditions using the combined sucrose/cyclodextrin/lipid gradient characterizing GRecon. We established conditions under which quantitative reconstitution of active protein at low lipid-to-protein ratios can be obtained, and also how to upscale these conditions in order to produce adequate amounts for NMR. NMR spectra recorded on a sample produced by GRecon showed a highly similar fingerprint as those recorded previously on samples reconstituted by dialysis. GRecon sample preparation presents a gain in time of nearly an order of magnitude for reconstitution, and shall represent a valuable alternative in solid-state NMR membrane protein sample preparation.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Alons Lends
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Clément Danis
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Britta Kunert
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Vlastimil Jirasko
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Claire Chuilon
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Vincent Chaptal
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Pierre Falson
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS-Université de Lyon, IBCP, 7 passage du Vercors, 69367, Lyon, France.
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32
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Loquet A, Tolchard J, Berbon M, Martinez D, Habenstein B. Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy. J Vis Exp 2017:55779. [PMID: 28994783 PMCID: PMC5752270 DOI: 10.3791/55779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13C/15N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.
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Affiliation(s)
- Antoine Loquet
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux;
| | - James Tolchard
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux
| | - Melanie Berbon
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux
| | - Denis Martinez
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux
| | - Birgit Habenstein
- Institute of Chemistry, Biology of Membranes, Nanoobjects, UMR5248 CNRS, Université de Bordeaux;
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33
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Recent advances in biophysical studies of rhodopsins - Oligomerization, folding, and structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1512-1521. [PMID: 28844743 DOI: 10.1016/j.bbapap.2017.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/06/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022]
Abstract
Retinal-binding proteins, mainly known as rhodopsins, function as photosensors and ion transporters in a wide range of organisms. From halobacterial light-driven proton pump, bacteriorhodopsin, to bovine photoreceptor, visual rhodopsin, they have served as prototypical α-helical membrane proteins in a large number of biophysical studies and aided in the development of many cutting-edge techniques of structural biology and biospectroscopy. In the last decade, microbial and animal rhodopsin families have expanded significantly, bringing into play a number of new interesting structures and functions. In this review, we will discuss recent advances in biophysical approaches to retinal-binding proteins, primarily microbial rhodopsins, including those in optical spectroscopy, X-ray crystallography, nuclear magnetic resonance, and electron paramagnetic resonance, as applied to such fundamental biological aspects as protein oligomerization, folding, and structure.
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34
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Zinke M, Fricke P, Samson C, Hwang S, Wall JS, Lange S, Zinn‐Justin S, Lange A. Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. Angew Chem Int Ed Engl 2017; 56:9497-9501. [PMID: 28644511 PMCID: PMC5582604 DOI: 10.1002/anie.201706060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 01/03/2023]
Abstract
Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH, (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.
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Affiliation(s)
- Maximilian Zinke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Pascal Fricke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Camille Samson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris-Sud, Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Songhwan Hwang
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | | | - Sascha Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sophie Zinn‐Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris-Sud, Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Adam Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- Institut für BiologieHumboldt-Universität zu BerlinBerlinGermany
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35
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Good D, Pham C, Jagas J, Lewandowski JR, Ladizhansky V. Solid-State NMR Provides Evidence for Small-Amplitude Slow Domain Motions in a Multispanning Transmembrane α-Helical Protein. J Am Chem Soc 2017; 139:9246-9258. [PMID: 28613900 PMCID: PMC5510093 DOI: 10.1021/jacs.7b03974] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 02/06/2023]
Abstract
Proteins are dynamic entities and populate ensembles of conformations. Transitions between states within a conformational ensemble occur over a broad spectrum of amplitude and time scales, and are often related to biological function. Whereas solid-state NMR (SSNMR) spectroscopy has recently been used to characterize conformational ensembles of proteins in the microcrystalline states, its applications to membrane proteins remain limited. Here we use SSNMR to study conformational dynamics of a seven-helical transmembrane (TM) protein, Anabaena Sensory Rhodopsin (ASR) reconstituted in lipids. We report on site-specific measurements of the 15N longitudinal R1 and rotating frame R1ρ relaxation rates at two fields of 600 and 800 MHz and at two temperatures of 7 and 30 °C. Quantitative analysis of the R1 and R1ρ values and of their field and temperature dependencies provides evidence of motions on at least two time scales. We modeled these motions as fast local motions and slower collective motions of TM helices and of structured loops, and used the simple model-free and extended model-free analyses to fit the data and estimate the amplitudes, time scales and activation energies. Faster picosecond (tens to hundreds of picoseconds) local motions occur throughout the protein and are dominant in the middle portions of the TM helices. In contrast, the amplitudes of the slower collective motions occurring on the nanosecond (tens to hundreds of nanoseconds) time scales, are smaller in the central parts of helices, but increase toward their cytoplasmic sides as well as in the interhelical loops. ASR interacts with a soluble transducer protein on its cytoplasmic surface, and its binding affinity is modulated by light. The larger amplitude of motions on the cytoplasmic side of the TM helices correlates with the ability of ASR to undergo large conformational changes in the process of binding/unbinding the transducer.
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Affiliation(s)
- Daryl Good
- Department
of Physics and Biophysics Interdepartmental Group, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Charlie Pham
- Department
of Physics and Biophysics Interdepartmental Group, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jacob Jagas
- Department
of Physics and Biophysics Interdepartmental Group, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Józef R. Lewandowski
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vladimir Ladizhansky
- Department
of Physics and Biophysics Interdepartmental Group, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
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36
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Zinke M, Fricke P, Samson C, Hwang S, Wall JS, Lange S, Zinn-Justin S, Lange A. Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maximilian Zinke
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Pascal Fricke
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Camille Samson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris-Sud, Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Songhwan Hwang
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | | | - Sascha Lange
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris-Sud, Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Adam Lange
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
- Institut für Biologie; Humboldt-Universität zu Berlin; Berlin Germany
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37
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Liu C, Liu J, Xu X, Xiang S, Wang S. Gd 3+-chelated lipid accelerates solid-state NMR spectroscopy of seven-transmembrane proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 68:203-214. [PMID: 28560567 DOI: 10.1007/s10858-017-0120-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/26/2017] [Indexed: 06/07/2023]
Abstract
Solid-state NMR (SSNMR) is an attractive technique for studying large membrane proteins in membrane-mimetic environments. However, SSNMR experiments often suffer from low efficiency, due to the inherent low sensitivity and the long recycle delays needed to recover the magnetization. Here we demonstrate that the incorporation of a small amount of a Gd3+-chelated lipid, Gd3+-DMPE-DTPA, into proteoliposomes greatly shortens the spin-lattice relaxation time (1H-T 1) of lipid-reconstituted membrane proteins and accelerates the data collection. This effect has been evaluated on a 30 kDa, seven-transmembrane protein, Leptosphaeria rhodopsin. With the Gd3+-chelated lipid, we can perform 2D SSNMR experiments 3 times faster than by diamagnetic control. By combining this paramagnetic relaxation-assisted data collection with non-uniform sampling, the 3D experimental times are reduced eightfold with respect to traditional 3D experiments on diamagnetic samples. A comparison between the paramagnetic relaxation enhancement (PRE) effects of Cu2+- and Gd3+-chelated lipids indicates the much higher relaxivity of the latter. Hence, a tenfold lower concentration is needed for Gd3+-chelated lipids to achieve comparable PRE effects to Cu2+-chelated lipids. In addition, Gd3+-chelated lipids neither alter the protein structures nor induce significant line-width broadening of the protein signals. This work is expected to be beneficial for structural and dynamic studies of large membrane proteins by SSNMR.
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Affiliation(s)
- Chang Liu
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China
| | - Jing Liu
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China
| | - Xiaojun Xu
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China
| | - ShengQi Xiang
- Department NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering, Peking University, Yiheyuan Rd. 5th, Beijing, China.
- Beijing NMR Center, Peking University, Yiheyuan Rd. 5th, Beijing, China.
- National Laboratories of Beijing National Laboratory for Molecular Science, Beijing, China.
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38
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van der Cruijsen EAW, Prokofyev AV, Pongs O, Baldus M. Probing Conformational Changes during the Gating Cycle of a Potassium Channel in Lipid Bilayers. Biophys J 2017; 112:99-108. [PMID: 28076820 DOI: 10.1016/j.bpj.2016.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/08/2016] [Accepted: 12/01/2016] [Indexed: 01/10/2023] Open
Abstract
Ion conduction across the cellular membrane requires the simultaneous opening of activation and inactivation gates of the K+ channel pore. The bacterial KcsA channel has served as a powerful system for dissecting the structural changes that are related to four major functional states associated with K+ gating. Yet, the direct observation of the full gating cycle of KcsA has remained structurally elusive, and crystal structures mimicking these gating events require mutations in or stabilization of functionally relevant channel segments. Here, we found that changes in lipid composition strongly increased the KcsA open probability. This enabled us to probe all four major gating states in native-like membranes by combining electrophysiological and solid-state NMR experiments. In contrast to previous crystallographic views, we found that the selectivity filter and turret region, coupled to the surrounding bilayer, were actively involved in channel gating. The increase in overall steady-state open probability was accompanied by a reduction in activation-gate opening, underscoring the important role of the surrounding lipid bilayer in the delicate conformational coupling of the inactivation and activation gates.
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Affiliation(s)
- Elwin A W van der Cruijsen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Alexander V Prokofyev
- Department of Physiology, Institute of Cellular Neurophysiology, University of the Saarland, Homburg, Germany
| | - Olaf Pongs
- Department of Physiology, Institute of Cellular Neurophysiology, University of the Saarland, Homburg, Germany.
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.
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39
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Auger M. Membrane solid-state NMR in Canada: A historical perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1483-1489. [PMID: 28652206 DOI: 10.1016/j.bbapap.2017.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/17/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022]
Abstract
This manuscript presents an overview of more than 40years of membrane solid-state nuclear magnetic resonance (NMR) research in Canada. This technique is a method of choice for the study of the structure and dynamics of lipid bilayers; bilayer interactions with a variety of molecules such as membrane peptides, membrane proteins and drugs; and to investigate membrane peptide and protein structure, dynamics, and topology. Canada has a long tradition in this field of research, starting with pioneering work on natural and model membranes in the 1970s in a context of emergence of biophysics in the country. The 1980s and 1990s saw an emphasis on studying lipid structures and dynamics, and peptide-lipid and protein-lipid interactions. The study of bicelles began in the 1990s, and in the 2000s there was a rise in the study of membrane protein structures. Novel perspectives include using dynamic nuclear polarization (DNP) for membrane studies and using NMR in live cells. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Michèle Auger
- Département de chimie, PROTEO, CERMA, CQMF, Université Laval, Québec, Québec G1V 0A6, Canada.
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40
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Zhang R, Duong NT, Nishiyama Y, Ramamoorthy A. 3D Double-Quantum/Double-Quantum Exchange Spectroscopy of Protons under 100 kHz Magic Angle Spinning. J Phys Chem B 2017; 121:5944-5952. [DOI: 10.1021/acs.jpcb.7b03480] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rongchun Zhang
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Nghia Tuan Duong
- RIKEN
CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Yusuke Nishiyama
- RIKEN
CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- JEOL Resonance Inc., Musashino, Akishima, Tokyo 196-8558, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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41
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NMR as a tool to investigate the structure, dynamics and function of membrane proteins. Nat Struct Mol Biol 2017; 23:468-74. [PMID: 27273629 DOI: 10.1038/nsmb.3226] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/12/2016] [Indexed: 12/29/2022]
Abstract
Membrane-protein NMR occupies a unique niche for determining structures, assessing dynamics, examining folding, and studying the binding of lipids, ligands and drugs to membrane proteins. However, NMR analyses of membrane proteins also face special challenges that are not encountered with soluble proteins, including sample preparation, size limitation, spectral crowding and sparse data accumulation. This Perspective provides a snapshot of current achievements, future opportunities and possible limitations in this rapidly developing field.
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Oligomeric Structure of Anabaena Sensory Rhodopsin in a Lipid Bilayer Environment by Combining Solid-State NMR and Long-range DEER Constraints. J Mol Biol 2017; 429:1903-1920. [DOI: 10.1016/j.jmb.2017.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/27/2017] [Accepted: 05/06/2017] [Indexed: 11/22/2022]
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43
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Applications of NMR to membrane proteins. Arch Biochem Biophys 2017; 628:92-101. [PMID: 28529197 DOI: 10.1016/j.abb.2017.05.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 01/14/2023]
Abstract
Membrane proteins present a challenge for structural biology. In this article, we review some of the recent developments that advance the application of NMR to membrane proteins, with emphasis on structural studies in detergent-free, lipid bilayer samples that resemble the native environment. NMR spectroscopy is not only ideally suited for structure determination of membrane proteins in hydrated lipid bilayer membranes, but also highly complementary to the other principal techniques based on X-ray and electron diffraction. Recent advances in NMR instrumentation, spectroscopic methods, computational methods, and sample preparations are driving exciting new efforts in membrane protein structural biology.
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Gopinath T, Nelson SED, Soller KJ, Veglia G. Probing the Conformationally Excited States of Membrane Proteins via 1H-Detected MAS Solid-State NMR Spectroscopy. J Phys Chem B 2017; 121:4456-4465. [DOI: 10.1021/acs.jpcb.7b03268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- T. Gopinath
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sarah E. D. Nelson
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kailey J. Soller
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Gianluigi Veglia
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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45
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Backbone assignment of perdeuterated proteins by solid-state NMR using proton detection and ultrafast magic-angle spinning. Nat Protoc 2017; 12:764-782. [PMID: 28277547 DOI: 10.1038/nprot.2016.190] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Solid-state NMR (ssNMR) is a technique that allows the study of protein structure and dynamics at atomic detail. In contrast to X-ray crystallography and cryo-electron microscopy, proteins can be studied under physiological conditions-for example, in a lipid bilayer and at room temperature (0-35 °C). However, ssNMR requires considerable amounts (milligram quantities) of isotopically labeled samples. In recent years, 1H-detection of perdeuterated protein samples has been proposed as a method of alleviating the sensitivity issue. Such methods are, however, substantially more demanding to the spectroscopist, as compared with traditional 13C-detected approaches. As a guide, this protocol describes a procedure for the chemical shift assignment of the backbone atoms of proteins in the solid state by 1H-detected ssNMR. It requires a perdeuterated, uniformly 13C- and 15N-labeled protein sample with subsequent proton back-exchange to the labile sites. The sample needs to be spun at a minimum of 40 kHz in the NMR spectrometer. With a minimal set of five 3D NMR spectra, the protein backbone and some of the side-chain atoms can be completely assigned. These spectra correlate resonances within one amino acid residue and between neighboring residues; taken together, these correlations allow for complete chemical shift assignment via a 'backbone walk'. This results in a backbone chemical shift table, which is the basis for further analysis of the protein structure and/or dynamics by ssNMR. Depending on the spectral quality and complexity of the protein, data acquisition and analysis are possible within 2 months.
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46
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Mandal A, Boatz JC, Wheeler TB, van der Wel PCA. On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR. JOURNAL OF BIOMOLECULAR NMR 2017; 67:165-178. [PMID: 28229262 PMCID: PMC5445385 DOI: 10.1007/s10858-017-0089-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/19/2017] [Indexed: 05/07/2023]
Abstract
A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation.
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Affiliation(s)
- Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jennifer C Boatz
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Travis B Wheeler
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
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47
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Quinn CM, Polenova T. Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q Rev Biophys 2017; 50:e1. [PMID: 28093096 PMCID: PMC5483179 DOI: 10.1017/s0033583516000159] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.
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Affiliation(s)
- Caitlin M. Quinn
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
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Wang S, Ing C, Emami S, Jiang Y, Liang H, Pomès R, Brown LS, Ladizhansky V. Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics. J Phys Chem B 2016; 120:9887-902. [DOI: 10.1021/acs.jpcb.6b06731] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shenlin Wang
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Christopher Ing
- Molecular
Structure and Function, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
- Department
of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Sanaz Emami
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
- Biophysics
Interdepartmental Group, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Yunjiang Jiang
- Department
of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hongjun Liang
- Department
of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Régis Pomès
- Molecular
Structure and Function, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8
- Department
of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Leonid S. Brown
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
- Biophysics
Interdepartmental Group, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Vladimir Ladizhansky
- Department
of Physics, University of Guelph, Guelph, ON, Canada N1G 2W1
- Biophysics
Interdepartmental Group, University of Guelph, Guelph, ON, Canada N1G 2W1
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49
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Characterizing Aciniform Silk Repetitive Domain Backbone Dynamics and Hydrodynamic Modularity. Int J Mol Sci 2016; 17:ijms17081305. [PMID: 27517921 PMCID: PMC5000702 DOI: 10.3390/ijms17081305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/13/2023] Open
Abstract
Spider aciniform (wrapping) silk is a remarkable fibrillar biomaterial with outstanding mechanical properties. It is a modular protein consisting, in Argiope trifasciata, of a core repetitive domain of 200 amino acid units (W units). In solution, the W units comprise a globular folded core, with five α-helices, and disordered tails that are linked to form a ~63-residue intrinsically disordered linker in concatemers. Herein, we present nuclear magnetic resonance (NMR) spectroscopy-based 15N spin relaxation analysis, allowing characterization of backbone dynamics as a function of residue on the ps–ns timescale in the context of the single W unit (W1) and the two unit concatemer (W2). Unambiguous mapping of backbone dynamics throughout W2 was made possible by segmental NMR active isotope-enrichment through split intein-mediated trans-splicing. Spectral density mapping for W1 and W2 reveals a striking disparity in dynamics between the folded core and the disordered linker and tail regions. These data are also consistent with rotational diffusion behaviour where each globular domain tumbles almost independently of its neighbour. At a localized level, helix 5 exhibits elevated high frequency dynamics relative to the proximal helix 4, supporting a model of fibrillogenesis where this helix unfolds as part of the transition to a mixed α-helix/β-sheet fibre.
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50
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Abstract
AbstractIncreasing evidence suggests that most proteins occur and function in complexes rather than as isolated entities when embedded in cellular membranes. Nuclear magnetic resonance (NMR) provides increasing possibilities to study structure, dynamics and assembly of such systems. In our review, we discuss recent methodological progress to study membrane–protein complexes (MPCs) by NMR, starting with expression, isotope-labeling and reconstitution protocols. We review approaches to deal with spectral complexity and limited spectral spectroscopic sensitivity that are usually encountered in NMR-based studies of MPCs. We highlight NMR applications in various classes of MPCs, including G-protein-coupled receptors, ion channels and retinal proteins and extend our discussion to protein–protein complexes that span entire cellular compartments or orchestrate processes such as protein transport across or within membranes. These examples demonstrate the growing potential of NMR-based studies of MPCs to provide critical insight into the energetics of protein–ligand and protein–protein interactions that underlie essential biological functions in cellular membranes.
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