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Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.
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Affiliation(s)
- Yusuke Nishiyama
- JEOL Ltd., Akishima, Tokyo196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa230-0045, Japan
| | - Guangjin Hou
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian116023, China
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad500 046, India
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan41809-1055, United States
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2
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Matlahov I, Boatz JC, C.A. van der Wel P. Selective observation of semi-rigid non-core residues in dynamically complex mutant huntingtin protein fibrils. J Struct Biol X 2022; 6:100077. [PMID: 36419510 PMCID: PMC9677204 DOI: 10.1016/j.yjsbx.2022.100077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/20/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
Abstract
Mutant huntingtin exon 1 fibrils feature a broad range of molecular dynamics. Molecular motion is coupled to water dynamics outside the fiber core. Dynamics-based spectral editing ssNMR reveals mobile non-core residues. Intermediate-motion selection via dipolar dephasing of rigid sites. Semi-mobile glutamines outside the fiber core observed and identified.
Many amyloid-forming proteins, which are normally intrinsically disordered, undergo a disorder-to-order transition to form fibrils with a rigid β-sheet core flanked by disordered domains. Solid-state NMR (ssNMR) and cryogenic electron microscopy (cryoEM) excel at resolving the rigid structures within amyloid cores but studying the dynamically disordered domains remains challenging. This challenge is exemplified by mutant huntingtin exon 1 (HttEx1), which self-assembles into pathogenic neuronal inclusions in Huntington disease (HD). The mutant protein’s expanded polyglutamine (polyQ) segment forms a fibril core that is rigid and sequestered from the solvent. Beyond the core, solvent-exposed surface residues mediate biological interactions and other properties of fibril polymorphs. Here we deploy magic angle spinning ssNMR experiments to probe for semi-rigid residues proximal to the fibril core and examine how solvent dynamics impact the fibrils’ segmental dynamics. Dynamic spectral editing (DYSE) 2D ssNMR based on a combination of cross-polarization (CP) ssNMR with selective dipolar dephasing reveals the weak signals of solvent-mobilized glutamine residues, while suppressing the normally strong background of rigid core signals. This type of ‘intermediate motion selection’ (IMS) experiment based on cross-polarization (CP) ssNMR, is complementary to INEPT- and CP-based measurements that highlight highly flexible or highly rigid protein segments, respectively. Integration of the IMS-DYSE element in standard CP-based ssNMR experiments permits the observation of semi-rigid residues in a variety of contexts, including in membrane proteins and protein complexes. We discuss the relevance of semi-rigid solvent-facing residues outside the fibril core to the latter’s detection with specific dyes and positron emission tomography tracers.
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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Najbauer EE, Tekwani Movellan K, Giller K, Benz R, Becker S, Griesinger C, Andreas LB. Structure and Gating Behavior of the Human Integral Membrane Protein VDAC1 in a Lipid Bilayer. J Am Chem Soc 2022; 144:2953-2967. [PMID: 35164499 PMCID: PMC8874904 DOI: 10.1021/jacs.1c09848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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The voltage-dependent
anion channel (VDAC), the most abundant protein
in the outer mitochondrial membrane, is responsible for the transport
of all ions and metabolites into and out of mitochondria. Larger than
any of the β-barrel structures determined to date by magic-angle
spinning (MAS) NMR, but smaller than the size limit of cryo-electron
microscopy (cryo-EM), VDAC1’s 31 kDa size has long been a bottleneck
in determining its structure in a near-native lipid bilayer environment.
Using a single two-dimensional (2D) crystalline sample of human VDAC1
in lipids, we applied proton-detected fast magic-angle spinning NMR
spectroscopy to determine the arrangement of β strands. Combining
these data with long-range restraints from a spin-labeled sample,
chemical shift-based secondary structure prediction, and previous
MAS NMR and atomic force microscopy (AFM) data, we determined the
channel’s structure at a 2.2 Å root-mean-square deviation
(RMSD). The structure, a 19-stranded β-barrel, with an N-terminal
α-helix in the pore is in agreement with previous data in detergent,
which was questioned due to the potential for the detergent to perturb
the protein’s functional structure. Using a quintuple mutant
implementing the channel’s closed state, we found that dynamics
are a key element in the protein’s gating behavior, as channel
closure leads to the destabilization of not only the C-terminal barrel
residues but also the α2 helix. We showed that cholesterol,
previously shown to reduce the frequency of channel closure, stabilizes
the barrel relative to the N-terminal helix. Furthermore, we observed
channel closure through steric blockage by a drug shown to selectively
bind to the channel, the Bcl2-antisense oligonucleotide G3139.
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Affiliation(s)
- Eszter E Najbauer
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Kumar Tekwani Movellan
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Roland Benz
- Life Sciences and Chemistry, Jacobs University of Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
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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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6
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Nimerovsky E, Movellan KT, Zhang XC, Forster MC, Najbauer E, Xue K, Dervişoǧlu R, Giller K, Griesinger C, Becker S, Andreas LB. Proton Detected Solid-State NMR of Membrane Proteins at 28 Tesla (1.2 GHz) and 100 kHz Magic-Angle Spinning. Biomolecules 2021; 11:752. [PMID: 34069858 PMCID: PMC8157399 DOI: 10.3390/biom11050752] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 12/25/2022] Open
Abstract
The available magnetic field strength for high resolution NMR in persistent superconducting magnets has recently improved from 23.5 to 28 Tesla, increasing the proton resonance frequency from 1 to 1.2 GHz. For magic-angle spinning (MAS) NMR, this is expected to improve resolution, provided the sample preparation results in homogeneous broadening. We compare two-dimensional (2D) proton detected MAS NMR spectra of four membrane proteins at 950 and 1200 MHz. We find a consistent improvement in resolution that scales superlinearly with the increase in magnetic field for three of the four examples. In 3D and 4D spectra, which are now routinely acquired, this improvement indicates the ability to resolve at least 2 and 2.5 times as many signals, respectively.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Loren B. Andreas
- Department for NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany; (E.N.); (K.T.M.); (X.C.Z.); (M.C.F.); (E.N.); (K.X.); (R.D.); (K.G.); (C.G.); (S.B.)
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7
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Najbauer EE, Becker S, Giller K, Zweckstetter M, Lange A, Steinem C, de Groot BL, Griesinger C, Andreas LB. Structure, gating and interactions of the voltage-dependent anion channel. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:159-172. [PMID: 33782728 PMCID: PMC8071794 DOI: 10.1007/s00249-021-01515-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 02/19/2021] [Accepted: 03/08/2021] [Indexed: 12/14/2022]
Abstract
The voltage-dependent anion channel (VDAC) is one of the most highly abundant proteins found in the outer mitochondrial membrane, and was one of the earliest discovered. Here we review progress in understanding VDAC function with a focus on its structure, discussing various models proposed for voltage gating as well as potential drug targets to modulate the channel's function. In addition, we explore the sensitivity of VDAC structure to variations in the membrane environment, comparing DMPC-only, DMPC with cholesterol, and near-native lipid compositions, and use magic-angle spinning NMR spectroscopy to locate cholesterol on the outside of the β-barrel. We find that the VDAC protein structure remains unchanged in different membrane compositions, including conditions with cholesterol.
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Affiliation(s)
- Eszter E Najbauer
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Markus Zweckstetter
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- Senior Research Group of Translational Structural Biology in Dementia, Deutsches Zentrum Für Neurodegenerative Erkrankungen (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
- Department of Neurology, University Medical Center Göttingen, University of Göttingen, Waldweg 33, 37073, 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
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Göttingen, Germany
- Max-Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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Silvers R, Eddy MT. NMR Spectroscopic Studies of Ion Channels in Lipid Bilayers: Sample Preparation Strategies Exemplified by the Voltage Dependent Anion Channel. Methods Mol Biol 2021; 2302:201-217. [PMID: 33877629 PMCID: PMC9206852 DOI: 10.1007/978-1-0716-1394-8_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We describe approaches for the preparation of membrane proteins in detergent micelles and lipid bilayers for solution and magic angle spinning NMR studies, respectively, as exemplified by the human voltage dependent anion channel 1 (hVDAC1). Here, we report protocols for the preparation of homogenous samples of recombinant hVDAC1 in detergent micelles and lipid two-dimensional crystals yielding high resolution NMR spectra. Procedures are described for the recombinant production of stable-isotope labeled hVDAC1 in E. coli, the isolation of hVDAC1 from inclusion bodies and the refolding into detergent micelles, as well as the reconstitution of hVDAC1 into lipids to form 2D crystals.
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Affiliation(s)
- Robert Silvers
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA.
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
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9
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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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10
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Eddy MT, Yu TY, Wagner G, Griffin RG. Structural characterization of the human membrane protein VDAC2 in lipid bilayers by MAS NMR. JOURNAL OF BIOMOLECULAR NMR 2019; 73:451-460. [PMID: 31407201 PMCID: PMC6819253 DOI: 10.1007/s10858-019-00242-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 03/19/2019] [Indexed: 05/25/2023]
Abstract
The second isoform of the human voltage dependent anion channel (VDAC2) is a mitochondrial porin that translocates calcium and other metabolites across the outer mitochondrial membrane. VDAC2 has been implicated in cardioprotection and plays a critical role in a unique apoptotic pathway in tumor cells. Despite its medical importance, there have been few biophysical studies of VDAC2 in large part due to the difficulty of obtaining homogeneous preparations of the protein for spectroscopic characterization. Here we present high resolution magic angle spinning nuclear magnetic resonance (NMR) data obtained from homogeneous preparation of human VDAC2 in 2D crystalline lipid bilayers. The excellent resolution in the spectra permit several sequence-specific assignments of the signals for a large portion of the VDAC2 N-terminus and several other residues in two- and three-dimensional heteronuclear correlation experiments. The first 12 residues appear to be dynamic, are not visible in cross polarization experiments, and they are not sufficiently mobile on very fast timescales to be visible in 13C INEPT experiments. A comparison of the NMR spectra of VDAC2 and VDAC1 obtained from highly similar preparations demonstrates that the spectral quality, line shapes and peak dispersion exhibited by the two proteins are nearly identical. This suggests an overall similar dynamic behavior and conformational homogeneity, which is in contrast to two earlier reports that suggested an inherent conformational heterogeneity of VDAC2 in membranes. The current data suggest that the sample preparation and spectroscopic methods are likely applicable to studying other human membrane porins, including human VDAC3, which has not yet been structurally characterized.
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Affiliation(s)
- Matthew T Eddy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Departments of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Tsyr-Yan Yu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, 10617, Taiwan, Republic of China
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Robert G 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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11
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Salnikov ES, Aisenbrey C, Anantharamaiah G, Bechinger B. Solid-state NMR structural investigations of peptide-based nanodiscs and of transmembrane helices in bicellar arrangements. Chem Phys Lipids 2019; 219:58-71. [DOI: 10.1016/j.chemphyslip.2019.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 02/08/2023]
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12
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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: 10] [Impact Index Per Article: 2.0] [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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13
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Aisenbrey C, Marquette A, Bechinger B. The Mechanisms of Action of Cationic Antimicrobial Peptides Refined by Novel Concepts from Biophysical Investigations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1117:33-64. [PMID: 30980352 DOI: 10.1007/978-981-13-3588-4_4] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Even 30 years after the discovery of magainins, biophysical and structural investigations on how these peptides interact with membranes can still bear surprises and add new interesting detail to how these peptides exert their antimicrobial action. Early on, using oriented solid-state NMR spectroscopy, it was found that the amphipathic helices formed by magainins are active when being oriented parallel to the membrane surface. More recent investigations indicate that this in-planar alignment is also found when PGLa and magainin in combination exert synergistic pore-forming activities, where studies on the mechanism of synergistic interaction are ongoing. In a related manner, the investigation of dimeric antimicrobial peptide sequences has become an interesting topic of research which bears promise to refine our views how antimicrobial action occurs. The molecular shape concept has been introduced to explain the effects of lipids and peptides on membrane morphology, locally and globally, and in particular of cationic amphipathic helices that partition into the membrane interface. This concept has been extended in this review to include more recent ideas on soft membranes that can adapt to external stimuli including membrane-disruptive molecules. In this manner, the lipids can change their shape in the presence of low peptide concentrations, thereby maintaining the bilayer properties. At higher peptide concentrations, phase transitions occur which lead to the formation of pores and membrane lytic processes. In the context of the molecular shape concept, the properties of lipopeptides, including surfactins, are shortly presented, and comparisons with the hydrophobic alamethicin sequence are made.
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Affiliation(s)
| | - Arnaud Marquette
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France
| | - Burkhard Bechinger
- Université de Strasbourg/CNRS, UMR7177, Institut de Chimie, Strasbourg, France. .,Faculté de chimie, Institut le Bel, Strasbourg, France.
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14
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Najbauer EE, Movellan KT, Schubeis T, Schwarzer T, Castiglione K, Giller K, Pintacuda G, Becker S, Andreas LB. Probing Membrane Protein Insertion into Lipid Bilayers by Solid-State NMR. Chemphyschem 2018; 20:302-310. [PMID: 30452110 DOI: 10.1002/cphc.201800793] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/08/2018] [Indexed: 11/09/2022]
Abstract
Determination of the environment surrounding a protein is often key to understanding its function and can also be used to infer the structural properties of the protein. By using proton-detected solid-state NMR, we show that reduced spin diffusion within the protein under conditions of fast magic-angle spinning, high magnetic field, and sample deuteration allows the efficient measurement of site-specific exposure to mobile water and lipids. We demonstrate this site specificity on two membrane proteins, the human voltage dependent anion channel, and the alkane transporter AlkL from Pseudomonas putida. Transfer from lipids is observed selectively in the membrane spanning region, and an average lipid-protein transfer rate of 6 s-1 was determined for residues protected from exchange. Transfer within the protein, as tracked in the 15 N-1 H 2D plane, was estimated from initial rates and found to be in a similar range of about 8 to 15 s-1 for several resolved residues, explaining the site specificity.
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Affiliation(s)
- Eszter E Najbauer
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Kumar Tekwani Movellan
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Tobias Schubeis
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280/CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, Villeurbanne, France
| | - Tom Schwarzer
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, D-85748, Garching, Germany
| | - Kathrin Castiglione
- Institute of Bioprocess Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Straße 3, 91052, Erlangen, Germany
| | - Karin Giller
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 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, Villeurbanne, France
| | - Stefan Becker
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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15
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Supramolecular Organization of Apolipoprotein-A-I-Derived Peptides within Disc-like Arrangements. Biophys J 2018; 115:467-477. [PMID: 30054032 DOI: 10.1016/j.bpj.2018.06.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 01/05/2023] Open
Abstract
Apolipoprotein A-I is the major protein component of high-density lipoproteins and fulfils important functions in lipid metabolism. Its structure consists of a chain of tandem domains of amphipathic helices. Using this protein as a template membrane scaffolding protein, class A amphipathic helical peptides were designed to support the amphipathic helix theory and later as therapeutic tools in biomedicine. Here, we investigated the lipid interactions of two apolipoprotein-A-I-derived class A amphipathic peptides, 14A (Ac-DYLKA FYDKL KEAF-NH2) and 18A (Ac-DWLKA FYDKV AEKLK EAF- NH2), including the disc-like supramolecular structures they form with phospholipids. Thus, the topologies of 14A and 18A in phospholipid bilayers have been determined by oriented solid-state NMR spectroscopy. Whereas at a peptide-to-lipid ratio of 2 mol% the peptides align parallel to the bilayer surface, at 7.5 mol% disc-like structures are formed that spontaneously orient in the magnetic field of the NMR spectrometer. From a comprehensive data set of four 15N- or 2H-labeled positions of 14A, a tilt angle, which deviates from perfectly in-planar by 14°, and a model for the peptidic rim structure have been obtained. The tilt and helical pitch angles are well suited to cover the hydrophobic chain region of the bilayer when two peptide helices form a head-to-tail dimer. Thus, the detailed topology found in this work agrees with the peptides forming the rim of nanodiscs in a double belt arrangement.
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16
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Higman VA. Solid-state MAS NMR resonance assignment methods for proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 106-107:37-65. [PMID: 31047601 DOI: 10.1016/j.pnmrs.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 06/09/2023]
Abstract
The prerequisite to structural or functional studies of proteins by NMR is generally the assignment of resonances. Since the first assignment of proteins by solid-state MAS NMR was conducted almost two decades ago, a wide variety of different pulse sequences and methods have been proposed and continue to be developed. Traditionally, a variety of 2D and 3D 13C-detected experiments have been used for the assignment of backbone and side-chain 13C and 15N resonances. These methods have found widespread use across the field. But as the hardware has changed and higher spinning frequencies and magnetic fields are becoming available, the ability to use direct proton detection is opening up a new set of assignment methods based on triple-resonance experiments. This review describes solid-state MAS NMR assignment methods using carbon detection and proton detection at different deuteration levels. The use of different isotopic labelling schemes as an aid to assignment in difficult cases is discussed as well as the increasing number of software packages that support manual and automated resonance assignment.
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Affiliation(s)
- Victoria A Higman
- Department of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TU, UK.
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17
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Abstract
Solid-state nuclear magnetic resonance (SSNMR) spectroscopy elucidates membrane protein structures and dynamics in atomic detail to yield mechanistic insights. By interrogating membrane proteins in phospholipid bilayers that closely resemble biological membranes, SSNMR spectroscopists have revealed ion conduction mechanisms, substrate transport dynamics, and oligomeric interfaces of seven-transmembrane helix proteins. Research has also identified conformational plasticity underlying virus-cell membrane fusions by complex protein machineries, and β-sheet folding and assembly by amyloidogenic proteins bound to lipid membranes. These studies collectively show that membrane proteins exhibit extensive structural plasticity to carry out their functions. Because of the inherent dependence of NMR frequencies on molecular orientations and the sensitivity of NMR frequencies to dynamical processes on timescales from nanoseconds to seconds, SSNMR spectroscopy is ideally suited to elucidate such structural plasticity, local and global conformational dynamics, protein-lipid and protein-ligand interactions, and protonation states of polar residues. New sensitivity-enhancement techniques, resolution enhancement by ultrahigh magnetic fields, and the advent of 3D and 4D correlation NMR techniques are increasingly aiding these mechanistically important structural studies.
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Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Jonathan K Williams
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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18
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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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19
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Asymmetric Cryo-EM Structure of Anthrax Toxin Protective Antigen Pore with Lethal Factor N-Terminal Domain. Toxins (Basel) 2017; 9:toxins9100298. [PMID: 28937604 PMCID: PMC5666345 DOI: 10.3390/toxins9100298] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 11/17/2022] Open
Abstract
The anthrax lethal toxin consists of protective antigen (PA) and lethal factor (LF). Understanding both the PA pore formation and LF translocation through the PA pore is crucial to mitigating and perhaps preventing anthrax disease. To better understand the interactions of the LF-PA engagement complex, the structure of the LFN-bound PA pore solubilized by a lipid nanodisc was examined using cryo-EM. CryoSPARC was used to rapidly sort particle populations of a heterogeneous sample preparation without imposing symmetry, resulting in a refined 17 Å PA pore structure with 3 LFN bound. At pH 7.5, the contributions from the three unstructured LFN lysine-rich tail regions do not occlude the Phe clamp opening. The open Phe clamp suggests that, in this translocation-compromised pH environment, the lysine-rich tails remain flexible and do not interact with the pore lumen region.
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20
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Lalli D, Idso MN, Andreas LB, Hussain S, Baxter N, Han S, Chmelka BF, Pintacuda G. Proton-Based Structural Analysis of a Heptahelical Transmembrane Protein in Lipid Bilayers. J Am Chem Soc 2017; 139:13006-13012. [PMID: 28724288 PMCID: PMC5741281 DOI: 10.1021/jacs.7b05269] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
structures and properties of membrane proteins in lipid bilayers are
expected to closely resemble those in native cell-membrane environments,
although they have been difficult to elucidate. By performing solid-state
NMR measurements at very fast (100 kHz) magic-angle spinning rates
and at high (23.5 T) magnetic field, severe sensitivity and resolution
challenges are overcome, enabling the atomic-level characterization
of membrane proteins in lipid environments. This is demonstrated by
extensive 1H-based resonance assignments of the fully protonated
heptahelical membrane protein proteorhodopsin, and the efficient identification
of numerous 1H–1H dipolar interactions,
which provide distance constraints, inter-residue proximities, relative
orientations of secondary structural elements, and protein–cofactor
interactions in the hydrophobic transmembrane regions. These results
establish a general approach for high-resolution structural studies
of membrane proteins in lipid environments via solid-state NMR.
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Affiliation(s)
- Daniela Lalli
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 69100 Villeurbanne, France
| | - Matthew N Idso
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 69100 Villeurbanne, France
| | - Sunyia Hussain
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Naomi Baxter
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States.,Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Bradley F Chmelka
- Department of Chemical Engineering, University of California , Santa Barbara, California 93106, United States
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 69100 Villeurbanne, France
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21
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Lakomek NA, Frey L, Bibow S, Böckmann A, Riek R, Meier BH. Proton-Detected NMR Spectroscopy of Nanodisc-Embedded Membrane Proteins: MAS Solid-State vs Solution-State Methods. J Phys Chem B 2017; 121:7671-7680. [PMID: 28737919 DOI: 10.1021/acs.jpcb.7b06944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structural and dynamical characterization of membrane proteins in a lipid bilayer at physiological pH and temperature and free of crystal constraints is crucial for the elucidation of a structure/dynamics-activity relationship. Toward this aim, we explore here the properties of the outer-membrane protein OmpX embedded in lipid bilayer nanodiscs using proton-detected magic angle spinning (MAS) solid-state NMR at 60 and 110 kHz. [1H,15N]-correlation spectra overlay well with the corresponding solution-state NMR spectra. Line widths as well as line intensities in solid and solution both depend critically on the sample temperature and, in particular, on the crossing of the lipid phase transition temperature. MAS (110 kHz) experiments yield well-resolved NMR spectra also for fully protonated OmpX and both below and above the lipid phase transition temperature.
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Affiliation(s)
| | - Lukas Frey
- ETH Zürich , Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Stefan Bibow
- ETH Zürich , Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon , 7 passage du Vercors, 69367 Lyon, France
| | - Roland Riek
- ETH Zürich , Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Beat H Meier
- ETH Zürich , Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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22
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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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23
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Yao Y, Dutta SK, Park SH, Rai R, Fujimoto LM, Bobkov AA, Opella SJ, Marassi FM. High resolution solid-state NMR spectroscopy of the Yersinia pestis outer membrane protein Ail in lipid membranes. JOURNAL OF BIOMOLECULAR NMR 2017; 67:179-190. [PMID: 28239773 PMCID: PMC5490241 DOI: 10.1007/s10858-017-0094-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/08/2017] [Indexed: 06/06/2023]
Abstract
The outer membrane protein Ail (Adhesion invasion locus) is one of the most abundant proteins on the cell surface of Yersinia pestis during human infection. Its functions are expressed through interactions with a variety of human host proteins, and are essential for microbial virulence. Structures of Ail have been determined by X-ray diffraction and solution NMR spectroscopy, but those samples contained detergents that interfere with functionality, thus, precluding analysis of the structural basis for Ail's biological activity. Here, we demonstrate that high-resolution solid-state NMR spectra can be obtained from samples of Ail in detergent-free phospholipid liposomes, prepared with a lipid to protein molar ratio of 100. The spectra, obtained with 13C or 1H detection, have very narrow line widths (0.40-0.60 ppm for 13C, 0.11-0.15 ppm for 1H, and 0.46-0.64 ppm for 15N) that are consistent with a high level of sample homogeneity. The spectra enable resonance assignments to be obtained for N, CO, CA and CB atomic sites from 75 out of 156 residues in the sequence of Ail, including 80% of the transmembrane region. The 1H-detected solid-state NMR 1H/15N correlation spectra obtained for Ail in liposomes compare very favorably with the solution NMR 1H/15N TROSY spectra obtained for Ail in nanodiscs prepared with a similar lipid to protein molar ratio. These results set the stage for studies of the molecular basis of the functional interactions of Ail with its protein partners from human host cells, as well as the development of drugs targeting Ail.
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Affiliation(s)
- Yong Yao
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Samit Kumar Dutta
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0307, USA
| | - Ratan Rai
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0307, USA
| | - L Miya Fujimoto
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0307, USA
| | - Francesca M Marassi
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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24
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Saurel O, Iordanov I, Nars G, Demange P, Le Marchand T, Andreas LB, Pintacuda G, Milon A. Local and Global Dynamics in Klebsiella pneumoniae Outer Membrane Protein a in Lipid Bilayers Probed at Atomic Resolution. J Am Chem Soc 2017; 139:1590-1597. [DOI: 10.1021/jacs.6b11565] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olivier Saurel
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Iordan Iordanov
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Guillaume Nars
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Pascal Demange
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
| | - Tanguy Le Marchand
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Loren B. Andreas
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Guido Pintacuda
- Institut de Sciences
Analytiques (UMR 5280 CNRS/ENS-Lyon/UCB Lyon 1), Université
de Lyon, 69007 Lyon, France
| | - Alain Milon
- Institut de Pharmacologie
et de Biologie Structurale (CNRS/Université Paul Sabatier),
Université de Toulouse, 31077 Toulouse, France
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25
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Senicourt L, Duma L, Papadopoulos V, Lacapere JJ. Solid-State NMR of Membrane Protein Reconstituted in Proteoliposomes, the Case of TSPO. Methods Mol Biol 2017; 1635:329-344. [PMID: 28755378 DOI: 10.1007/978-1-4939-7151-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural studies of membrane proteins (MP) in a native or native-like environment remain a challenge. X-ray crystallography of three-dimensional crystals of MP in lipids and cryo-electron microscopy of two-dimensional crystals also in lipids have given atomic structures of several MP. Recent developments of solid-state NMR (ssNMR) provided structural data of MP in lipids and should give access to the dynamic behavior of MP's in a native-like environment. Preparation of samples for ssNMR is not trivial with overexpressed proteins since purified recombinant MP have to be reincorporated in proteoliposomes and concentrated in the small volume of the rotor used for ssNMR studies. We present here the protocol that we have used to study the recombinant mouse TSPO1, an integral membrane protein of 20 kDa mostly found in the outer membrane of mitochondria and overexpressed in E. coli bacteria.
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Affiliation(s)
- Lucile Senicourt
- Sorbonne Universités-UPMC University of Paris 06, Département de Chimie, École Normale Supérieure-PSL Research University, CNRS UMR 7203 LBM, 4 Place Jussieu, 75005, Paris Cedex 05, France
| | - Luminita Duma
- CNRS Enzyme and Cell Engineering Laboratory, Sorbonne Universités, Université de Technologie de Compiègne, Rue Roger Couttolenc, CS 60319, 60203, Compiègne Cedex, France
| | - Vassilios Papadopoulos
- The Research Institute of the McGill, University Health Center, Montreal, QC, Canada, H4A 3J1.,Department of Medicine, McGill University, Montreal, QC, Canada, H4A 3J1
| | - Jean-Jacques Lacapere
- Sorbonne Universités-UPMC University of Paris 06, Département de Chimie, École Normale Supérieure-PSL Research University, CNRS UMR 7203 LBM, 4 Place Jussieu, 75005, Paris Cedex 05, France.
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26
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Stanek J, Andreas LB, Jaudzems K, Cala D, Lalli D, Bertarello A, Schubeis T, Akopjana I, Kotelovica S, Tars K, Pica A, Leone S, Picone D, Xu ZQ, Dixon NE, Martinez D, Berbon M, Mammeri NE, Noubhani A, Saupe S, Habenstein B, Loquet A, Pintacuda G. Zuordnung der Rückgrat- und Seitenketten-Protonen in vollständig protonierten Proteinen durch Festkörper-NMR-Spektroskopie: Mikrokristalle, Sedimente und Amyloidfibrillen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jan Stanek
- 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 Frankreich
| | - Loren B. Andreas
- 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 Frankreich
| | - Kristaps Jaudzems
- 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 Frankreich
| | - Diane Cala
- 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 Frankreich
| | - Daniela Lalli
- 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 Frankreich
| | - Andrea Bertarello
- 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 Frankreich
| | - 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 Frankreich
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Lettland
| | | | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Lettland
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia 80126 Naples Italien
| | - Serena Leone
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia 80126 Naples Italien
| | - Delia Picone
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia 80126 Naples Italien
| | - Zhi-Qiang Xu
- School of Chemistry; University of Wollongong; NSW 2522 Australien
| | | | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac Frankreich
| | - Mélanie Berbon
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac Frankreich
| | - Nadia El Mammeri
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac Frankreich
| | - Abdelmajid Noubhani
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac Frankreich
| | - Sven Saupe
- Institut de Biochimie et de Génétique Cellulaire (UMR 5095, CNRS -; Université de Bordeaux); 33077 Bordeaux Frankreich
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac Frankreich
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac Frankreich
| | - 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 Frankreich
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27
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Stanek J, Andreas LB, Jaudzems K, Cala D, Lalli D, Bertarello A, Schubeis T, Akopjana I, Kotelovica S, Tars K, Pica A, Leone S, Picone D, Xu ZQ, Dixon NE, Martinez D, Berbon M, El Mammeri N, Noubhani A, Saupe S, Habenstein B, Loquet A, Pintacuda G. NMR Spectroscopic Assignment of Backbone and Side-Chain Protons in Fully Protonated Proteins: Microcrystals, Sedimented Assemblies, and Amyloid Fibrils. Angew Chem Int Ed Engl 2016; 55:15504-15509. [DOI: 10.1002/anie.201607084] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/05/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Jan Stanek
- 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
- 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
| | - Kristaps Jaudzems
- 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
| | - Diane Cala
- 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
| | - Daniela Lalli
- 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
| | - Andrea Bertarello
- 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
| | - 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
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | | | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia 80126 Naples Italy
| | - Serena Leone
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia 80126 Naples Italy
| | - Delia Picone
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia 80126 Naples Italy
| | - Zhi-Qiang Xu
- School of Chemistry; University of Wollongong; NSW 2522 Australia
| | | | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac France
| | - Mélanie Berbon
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac France
| | - Nadia El Mammeri
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac France
| | - Abdelmajid Noubhani
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac France
| | - Sven Saupe
- Institut de Biochimie et de Génétique Cellulaire (UMR 5095, CNRS -; Université de Bordeaux); 33077 Bordeaux France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR 5248 CBMN - CNRS; University of Bordeaux, Bordeaux INP), All. Geoffroy Saint-Hillaire; 33600 Pessac France
| | - 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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28
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Structure of fully protonated proteins by proton-detected magic-angle spinning NMR. Proc Natl Acad Sci U S A 2016; 113:9187-92. [PMID: 27489348 DOI: 10.1073/pnas.1602248113] [Citation(s) in RCA: 187] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins.
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29
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Harris MJ, Struppe JO, Wylie BJ, McDermott AE, Thompson LK. Multidimensional Solid-State Nuclear Magnetic Resonance of a Functional Multiprotein Chemoreceptor Array. Biochemistry 2016; 55:3616-24. [PMID: 27295350 PMCID: PMC5022360 DOI: 10.1021/acs.biochem.6b00234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The bacterial chemoreceptor complex governs signal detection and the upstream elements of chemotactic behavior, but the detailed molecular mechanism is still unclear. We have assembled nativelike functional arrays of an aspartate receptor cytoplasmic fragment (CF) with its two cytoplasmic protein partners (CheA and CheW) for solid-state nuclear magnetic resonance (NMR) studies of structural changes involved in signaling. In this initial study of the uniformly (13)C- and (15)N-enriched CF in these >13.8 MDa size arrays, residue-type assignments are made for amino acids that together make up 90% of the protein. We demonstrate that homo- and heteronuclear two-dimensional spectra are consistent with structure-based chemical shift predictions: a number of major assignable correlations are consistent with the predominantly α-helical secondary structure, and minor correlations are consistent with the disordered C-terminal tail. Sub-parts per million line widths and spectral changes upon freezing of samples suggest these arrays are structurally homogeneous and sufficiently immobilized for efficient solid-state NMR.
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Affiliation(s)
- Michael J. Harris
- Department of Chemistry, University of Massachusetts, 710 N Pleasant St, Amherst, Massachusetts 01003, USA
| | - Jochem O. Struppe
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - Benjamin J. Wylie
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Ann E. McDermott
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Lynmarie K. Thompson
- Department of Chemistry, University of Massachusetts, 710 N Pleasant St, Amherst, Massachusetts 01003, USA
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30
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Dannatt HRW, Felletti M, Jehle S, Wang Y, Emsley L, Dixon NE, Lesage A, Pintacuda G. Weak and Transient Protein Interactions Determined by Solid‐State NMR. Angew Chem Int Ed Engl 2016; 55:6638-41. [DOI: 10.1002/anie.201511609] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Hugh R. W. Dannatt
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Michele Felletti
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Stefan Jehle
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Yao Wang
- Centre for Medical and Molecular Bioscience School of Chemistry University of Wollongong Wollongong New South Wales 2522 Australia
| | - Lyndon Emsley
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Nicholas E. Dixon
- Centre for Medical and Molecular Bioscience School of Chemistry University of Wollongong Wollongong New South Wales 2522 Australia
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
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31
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Dannatt HRW, Felletti M, Jehle S, Wang Y, Emsley L, Dixon NE, Lesage A, Pintacuda G. Weak and Transient Protein Interactions Determined by Solid‐State NMR. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511609] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hugh R. W. Dannatt
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Michele Felletti
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Stefan Jehle
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Yao Wang
- Centre for Medical and Molecular Bioscience School of Chemistry University of Wollongong Wollongong New South Wales 2522 Australia
| | - Lyndon Emsley
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne 1015 Lausanne Switzerland
| | - Nicholas E. Dixon
- Centre for Medical and Molecular Bioscience School of Chemistry University of Wollongong Wollongong New South Wales 2522 Australia
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs— Université de Lyon Institut de Sciences Analytiques (CNRS/ ENS-Lyon/ UCB Lyon 1) 69100 Villeurbanne France
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32
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Maurya SR, Mahalakshmi R. N-helix and Cysteines Inter-regulate Human Mitochondrial VDAC-2 Function and Biochemistry. J Biol Chem 2015; 290:30240-52. [PMID: 26487717 PMCID: PMC4683249 DOI: 10.1074/jbc.m115.693978] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 12/25/2022] Open
Abstract
Human voltage-dependent anion channel-2 (hVDAC-2) functions primarily as the crucial anti-apoptotic protein in the outer mitochondrial membrane, and additionally as a gated bidirectional metabolite transporter. The N-terminal helix (NTH), involved in voltage sensing, bears an additional 11-residue extension (NTE) only in hVDAC-2. In this study, we assign a unique role for the NTE as influencing the chaperone-independent refolding kinetics and overall thermodynamic stability of hVDAC-2. Our electrophysiology data shows that the N-helix is crucial for channel activity, whereas NTE sensitizes this isoform to voltage gating. Additionally, hVDAC-2 possesses the highest cysteine content, possibly for regulating reactive oxygen species content. We identify interdependent contributions of the N-helix and cysteines to channel function, and the measured stability in micellar environments with differing physicochemical properties. The evolutionary demand for the NTE in the presence of cysteines clearly emerges from our biochemical and functional studies, providing insight into factors that functionally demarcate hVDAC-2 from the other VDACs.
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Affiliation(s)
- Svetlana Rajkumar Maurya
- From the Department of Biological Sciences, Molecular Biophysics Laboratory, Indian Institute of Science Education and Research, Bhopal 462023, India
| | - Radhakrishnan Mahalakshmi
- From the Department of Biological Sciences, Molecular Biophysics Laboratory, Indian Institute of Science Education and Research, Bhopal 462023, India
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33
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Shahid SA, Nagaraj M, Chauhan N, Franks TW, Bardiaux B, Habeck M, Orwick-Rydmark M, Linke D, van Rossum BJ. Festkörper-NMR-Studien an der Membrananker-Domäne von YadA in der bakteriellen Außenmembran. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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34
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Shahid SA, Nagaraj M, Chauhan N, Franks TW, Bardiaux B, Habeck M, Orwick-Rydmark M, Linke D, van Rossum BJ. Solid-state NMR Study of the YadA Membrane-Anchor Domain in the Bacterial Outer Membrane. Angew Chem Int Ed Engl 2015; 54:12602-6. [PMID: 26332158 DOI: 10.1002/anie.201505506] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/17/2015] [Indexed: 12/12/2022]
Abstract
MAS-NMR was used to study the structure and dynamics at ambient temperatures of the membrane-anchor domain of YadA (YadA-M) in a pellet of the outer membrane of E. coli in which it was expressed. YadA is an adhesin from the pathogen Yersinia enterocolitica that is involved in interactions with the host cell, and it is a model protein for studying the autotransport process. Existing assignments were sucessfully transferred to a large part of the YadA-M protein in the E. coli lipid environment by using (13) C-(13) C DARR and PDSD spectra at different mixing times. The chemical shifts in most regions of YadA-M are unchanged relative to those in microcrystalline YadA-M preparations from which a structure has previously been solved, including the ASSA region that is proposed to be involved in transition-state hairpin formation for transport of the soluble domain. Comparisons of the dynamics between the microcrystalline and membrane-embedded samples indicate greater flexibility of the ASSA region in the outer-membrane preparation at physiological temperatures. This study will pave the way towards MAS-NMR structure determination of membrane proteins, and a better understanding of functionally important dynamic residues in native membrane environments.
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Affiliation(s)
- Shakeel A Shahid
- Max-Planck-Institute for Developmental Biology, Department 1, Tübingen (Germany).,Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str. 10, 13125 Berlin (Germany)
| | - Madhu Nagaraj
- Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str. 10, 13125 Berlin (Germany)
| | - Nandini Chauhan
- University of Oslo, Department of Biosciences, POBox 1066 Blindern, 0316 Oslo (Norway)
| | - Trent W Franks
- Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str. 10, 13125 Berlin (Germany)
| | - Benjamin Bardiaux
- Unité de Bioinformatique Structurale, CNRS UMR3528, Institut Pasteur, Paris (France)
| | - Michael Habeck
- Felix-Bernstein Institute for Mathematical Statistics, Georg-August-Universität Göttingen (Germany).,Max Planck Institute for Biophysical Chemistry, Göttingen (Germany)
| | | | - Dirk Linke
- Max-Planck-Institute for Developmental Biology, Department 1, Tübingen (Germany). .,University of Oslo, Department of Biosciences, POBox 1066 Blindern, 0316 Oslo (Norway).
| | - Barth-J van Rossum
- Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Str. 10, 13125 Berlin (Germany).
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35
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Affiliation(s)
- Rob Kaptein
- Bijvoet Centre, Utrecht University, 3584 CH, Utrecht, The Netherlands
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