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Abstract
Various recent developments in solid-state nuclear magnetic resonance (ssNMR) spectroscopy have enabled an array of new insights regarding the structure, dynamics, and interactions of biomolecules. In the ever more integrated world of structural biology, ssNMR studies provide structural and dynamic information that is complementary to the data accessible by other means. ssNMR enables the study of samples lacking a crystalline lattice, featuring static as well as dynamic disorder, and does so independent of higher-order symmetry. The present study surveys recent applications of biomolecular ssNMR and examines how this technique is increasingly integrated with other structural biology techniques, such as (cryo) electron microscopy, solution-state NMR, and X-ray crystallography. Traditional ssNMR targets include lipid bilayer membranes and membrane proteins in a lipid bilayer environment. Another classic application has been in the area of protein misfolding and aggregation disorders, where ssNMR has provided essential structural data on oligomers and amyloid fibril aggregates. More recently, the application of ssNMR has expanded to a growing array of biological assemblies, ranging from non-amyloid protein aggregates, protein–protein complexes, viral capsids, and many others. Across these areas, multidimensional magic angle spinning (MAS) ssNMR has, in the last decade, revealed three-dimensional structures, including many that had been inaccessible by other structural biology techniques. Equally important insights in structural and molecular biology derive from the ability of MAS ssNMR to probe information beyond comprehensive protein structures, such as dynamics, solvent exposure, protein–protein interfaces, and substrate–enzyme interactions.
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152
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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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153
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Quinn CM, Wang M, Polenova T. NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology. Methods Mol Biol 2018; 1688:1-35. [PMID: 29151202 PMCID: PMC6217836 DOI: 10.1007/978-1-4939-7386-6_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
As a result of profound gains in sensitivity and resolution afforded by ultrahigh magnetic fields, transformative applications in the fields of structural biology and materials science are being realized. The development of dual low temperature superconducting (LTS)/high-temperature superconducting (HTS) magnets has enabled the achievement of magnetic fields above 1 GHz (23.5 T), which will open doors to an unprecedented new range of applications. In this contribution, we discuss the promise of ultrahigh field magnetic resonance. We highlight several methodological developments pertinent at high-magnetic fields including measurement of 1H-1H distances and 1H chemical shift anisotropy in the solid state as well as studies of quadrupolar nuclei such as 17O. Higher magnetic fields have advanced heteronuclear detection in solution NMR, valuable for applications including metabolomics and disordered proteins, as well as expanded use of proton detection in the solid state in conjunction with ultrafast magic angle spinning. We also present several recent applications to structural studies of the AP205 bacteriophage, the M2 channel from Influenza A, and biomaterials such as human bone. Gains in sensitivity and resolution from increased field strengths will enable advanced applications of NMR spectroscopy including in vivo studies of whole cells and intact virions.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA.
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154
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Ishii Y, Wickramasinghe A, Matsuda I, Endo Y, Ishii Y, Nishiyama Y, Nemoto T, Kamihara T. Progress in proton-detected solid-state NMR (SSNMR): Super-fast 2D SSNMR collection for nano-mole-scale proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 286:99-109. [PMID: 29223566 PMCID: PMC6387629 DOI: 10.1016/j.jmr.2017.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 05/22/2023]
Abstract
Proton-detected solid-state NMR (SSNMR) spectroscopy has attracted much attention due to its excellent sensitivity and effectiveness in the analysis of trace amounts of amyloid proteins and other important biological systems. In this perspective article, we present the recent sensitivity limit of 1H-detected SSNMR using "ultra-fast" magic-angle spinning (MAS) at a spinning rate (νR) of 80-100 kHz. It was demonstrated that the high sensitivity of 1H-detected SSNMR at νR of 100 kHz and fast recycling using the paramagnetic-assisted condensed data collection (PACC) approach permitted "super-fast" collection of 1H-detected 2D protein SSNMR. A 1H-detected 2D 1H-15N correlation SSNMR spectrum for ∼27 nmol of a uniformly 13C- and 15N-labeled GB1 protein sample in microcrystalline form was acquired in only 9 s with 50% non-uniform sampling and short recycle delays of 100 ms. Additional data suggests that it is now feasible to detect as little as 1 nmol of the protein in 5.9 h by 1H-detected 2D 1H-15N SSNMR at a nominal signal-to-noise ratio of five. The demonstrated sensitivity is comparable to that of modern solution protein NMR. Moreover, this article summarizes the influence of ultra-fast MAS and 1H-detection on the spectral resolution and sensitivity of protein SSNMR. Recent progress in signal assignment and structural elucidation by 1H-detected protein SSNMR is outlined with both theoretical and experimental aspects.
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Affiliation(s)
- Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, Kanagawa 226-8503, Japan; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States; The RIKEN Center for Life Science Technologies (CLST), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Ayesha Wickramasinghe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, Kanagawa 226-8503, Japan; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States; The RIKEN Center for Life Science Technologies (CLST), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Isamu Matsuda
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, Kanagawa 226-8503, Japan; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Yuki Endo
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Yuji Ishii
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan; RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Nemoto
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Takayuki Kamihara
- The RIKEN Center for Life Science Technologies (CLST), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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155
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Barbet-Massin E, van der Sluis E, Musial J, Beckmann R, Reif B. Reconstitution of Isotopically Labeled Ribosomal Protein L29 in the 50S Large Ribosomal Subunit for Solution-State and Solid-State NMR. Methods Mol Biol 2018; 1764:87-100. [PMID: 29605910 DOI: 10.1007/978-1-4939-7759-8_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Solid-state nuclear magnetic resonance (NMR) has recently emerged as a method of choice to study structural and dynamic properties of large biomolecular complexes at atomic resolution. Indeed, recent technological and methodological developments have enabled the study of ever more complex systems in the solid-state. However, to explore multicomponent protein complexes by NMR, specific labeling schemes need to be developed that are dependent on the biological question to be answered. We show here how to reconstitute an isotopically labeled protein within the unlabeled 50S or 70S ribosomal subunit. In particular, we focus on the 63-residue ribosomal protein L29 (~7 kDa), which is located at the exit of the tunnel of the large 50S ribosomal subunit (~1.5 MDa). The aim of this work is the preparation of a suitable sample to investigate allosteric conformational changes in a ribosomal protein that are induced by the nascent polypeptide chain and that trigger the interaction with different chaperones (e.g., trigger factor or SRP).
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Affiliation(s)
- Emeline Barbet-Massin
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Garching, Germany.,Dynamic Biosensors, Planegg, Germany
| | - Eli van der Sluis
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Bionanoscience, Faculty of Applied Sciences, TU Delft, Delft, The Netherlands
| | - Joanna Musial
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bernd Reif
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Garching, Germany. .,Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz-Zentrum München (HMGU), Neuherberg, Germany.
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156
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Advanced solid-state NMR methods for characterising structure and self-assembly in supramolecular chemistry, polymers and hydrogels. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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157
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Jolly MM, Jarvis JA, Carravetta M, Levitt MH, Williamson PTF. Bidirectional band-selective magnetization transfer along the protein backbone doubles the information content of solid-state NMR correlation experiments. JOURNAL OF BIOMOLECULAR NMR 2017; 69:197-205. [PMID: 29116557 PMCID: PMC5736786 DOI: 10.1007/s10858-017-0147-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 10/21/2017] [Indexed: 05/05/2023]
Abstract
Resonance assignment is the first stage towards solving the structure of a protein. This is normally achieved by the employment of separate inter and intra residue experiments. By utilising the mixed rotation and rotary recoupling (MIRROR) condition it is possible to double the information content through the efficient bidirectional transfer of magnetization from the CO to its adjacent Cα and the Cα of the subsequent amino acid. We have incorporated this into a 3D experiment, a 3D-MIRROR-NCOCA, where correlations present in the 3D spectrum permit the sequential assignment of the protein backbone from a single experiment as we have demonstrated on a microcrystalline preparation of GB3. Furthermore, the low-power requirements of the MIRROR recoupling sequence facilitate the development of a low-power 3D-NCOCA experiment. This has enabled us to realise significant reductions in acquisition times, allowing the acquisition of a single 3D-NCOCA spectrum suitable for a full backbone resonance assignment of GB3 in less than 24 h.
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Affiliation(s)
- M M Jolly
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - J A Jarvis
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - M Carravetta
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - M H Levitt
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - P T F Williamson
- Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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158
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Lilly Thankamony AS, Wittmann JJ, Kaushik M, Corzilius B. Dynamic nuclear polarization for sensitivity enhancement in modern solid-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:120-195. [PMID: 29157490 DOI: 10.1016/j.pnmrs.2017.06.002] [Citation(s) in RCA: 273] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/03/2017] [Accepted: 06/08/2017] [Indexed: 05/03/2023]
Abstract
The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.
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Affiliation(s)
- Aany Sofia Lilly Thankamony
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Johannes J Wittmann
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Monu Kaushik
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany.
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159
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Ge Y, Hung I, Liu X, Liu M, Gan Z, Li C. Measurement of amide proton chemical shift anisotropy in perdeuterated proteins using CSA amplification. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 284:33-38. [PMID: 28957683 DOI: 10.1016/j.jmr.2017.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/07/2017] [Accepted: 09/16/2017] [Indexed: 06/07/2023]
Abstract
Measuring 1H chemical shift anisotropy (CSA) is useful for probing proton environments and dynamics but remains a challenge due to strong homonuclear interaction and relatively small shift anisotropy, especially in proteins with multiple proton sites. Here the extended chemical shift anisotropy amplification (xCSA) method is applied for amide proton CSA measurement in uniformly 2H enriched proteins under fast magic angle spinning. The xCSA method is capable of distinguishing the sign of the CSA asymmetry parameter, complimenting other multiple-pulse recoupling methods. A three-dimensional xCSA experiment is demonstrated for measuring the proton CSA of amide sites in aGB1 protein sample and the possible correlation of amide proton CSA with protein secondary structure is discussed.
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Affiliation(s)
- Yuwei Ge
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
| | - Xiaoli Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA.
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
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160
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van der Wel PCA. Insights into protein misfolding and aggregation enabled by solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 88:1-14. [PMID: 29035839 PMCID: PMC5705391 DOI: 10.1016/j.ssnmr.2017.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 05/17/2023]
Abstract
The aggregation of proteins and peptides into a variety of insoluble, and often non-native, aggregated states plays a central role in many devastating diseases. Analogous processes undermine the efficacy of polypeptide-based biological pharmaceuticals, but are also being leveraged in the design of biologically inspired self-assembling materials. This Trends article surveys the essential contributions made by recent solid-state NMR (ssNMR) studies to our understanding of the structural features of polypeptide aggregates, and how such findings are informing our thinking about the molecular mechanisms of misfolding and aggregation. A central focus is on disease-related amyloid fibrils and oligomers involved in neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntington's disease. SSNMR-enabled structural and dynamics-based findings are surveyed, along with a number of resulting emerging themes that appear common to different amyloidogenic proteins, such as their compact alternating short-β-strand/β-arc amyloid core architecture. Concepts, methods, future prospects and challenges are discussed.
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Affiliation(s)
- Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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161
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Fraga H, Arnaud CA, Gauto DF, Audin M, Kurauskas V, Macek P, Krichel C, Guan JY, Boisbouvier J, Sprangers R, Breyton C, Schanda P. Solid-State NMR H-N-(C)-H and H-N-C-C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins. Chemphyschem 2017; 18:2697-2703. [PMID: 28792111 PMCID: PMC5632560 DOI: 10.1002/cphc.201700572] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/08/2017] [Indexed: 12/16/2022]
Abstract
Solid-state NMR spectroscopy can provide insight into protein structure and dynamics at the atomic level without inherent protein size limitations. However, a major hurdle to studying large proteins by solid-state NMR spectroscopy is related to spectral complexity and resonance overlap, which increase with molecular weight and severely hamper the assignment process. Here the use of two sets of experiments is shown to expand the tool kit of 1 H-detected assignment approaches, which correlate a given amide pair either to the two adjacent CO-CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide 1 H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to 5D). The experiments are based on efficient coherence transfers between backbone atoms using INEPT transfers between carbons and cross-polarization for heteronuclear transfers. The utility of these experiments is exemplified with application to assemblies of deuterated, fully amide-protonated proteins from approximately 20 to 60 kDa monomer, at magic-angle spinning (MAS) frequencies from approximately 40 to 55 kHz. These experiments will also be applicable to protonated proteins at higher MAS frequencies. The resonance assignment of a domain within the 50.4 kDa bacteriophage T5 tube protein pb6 is reported, and this is compared to NMR assignments of the isolated domain in solution. This comparison reveals contacts of this domain to the core of the polymeric tail tube assembly.
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Affiliation(s)
- Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
- Departamento de Bioquimica, Faculdade de Medicina da Universidade do Porto, Portugal
| | - Charles-Adrien Arnaud
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Diego F. Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Maxime Audin
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen (Germany)
| | - Vilius Kurauskas
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Carsten Krichel
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Jia-Ying Guan
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen (Germany)
- Department of Biophysics I, University of Regensburg, 93053, Regensburg (Germany)
| | - Cécile Breyton
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institute for Structural Biology (IBS), 71 avenue des martyrs, F-38044 Grenoble (France)
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162
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Cala-De Paepe D, Stanek J, Jaudzems K, Tars K, Andreas LB, Pintacuda G. Is protein deuteration beneficial for proton detected solid-state NMR at and above 100 kHz magic-angle spinning? SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:126-136. [PMID: 28802890 DOI: 10.1016/j.ssnmr.2017.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/14/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
1H-detection in solid-state NMR of proteins has been traditionally combined with deuteration for both resolution and sensitivity reasons, with the optimal level of proton dilution being dependent on MAS rate. Here we present 1H-detected 15N and 13C CP-HSQC spectra on two microcrystalline samples acquired at 60 and 111 kHz MAS and at ultra-high field. We critically compare the benefits of three labeling schemes yielding different levels of proton content in terms of resolution, coherence lifetimes and feasibility of scalar-based 2D correlations under these experimental conditions. We observe unexpectedly high resolution and sensitivity of aromatic resonances in 2D 13C-1H correlation spectra of protonated samples. Ultrafast MAS reduces or even removes the necessity of 1H dilution for high-resolution 1H-detection in biomolecular solid-state NMR. It yields 15N,1H and 13C,1H fingerprint spectra of exceptional resolution for fully protonated samples, with notably superior 1H and 13C lineshapes for side-chain resonances.
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Affiliation(s)
- Diane Cala-De Paepe
- 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
| | - 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
| | - 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
| | - Kaspars Tars
- Biomedical Research and Study Centre, Rātsupītes 1, LV1067, Riga, Latvia
| | - 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; 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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163
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Struppe J, Quinn CM, Lu M, Wang M, Hou G, Lu X, Kraus J, Andreas LB, Stanek J, Lalli D, Lesage A, Pintacuda G, Maas W, Gronenborn AM, Polenova T. Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:117-125. [PMID: 28732673 PMCID: PMC5824719 DOI: 10.1016/j.ssnmr.2017.07.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/28/2017] [Accepted: 07/02/2017] [Indexed: 05/20/2023]
Abstract
The recent breakthroughs in NMR probe technologies resulted in the development of MAS NMR probes with rotation frequencies exceeding 100 kHz. Herein, we explore dramatic increases in sensitivity and resolution observed at MAS frequencies of 110-111 kHz in a novel 0.7 mm HCND probe that enable structural analysis of fully protonated biological systems. Proton- detected 2D and 3D correlation spectroscopy under such conditions requires only 0.1-0.5 mg of sample and a fraction of time compared to conventional 13C-detected experiments. We discuss the performance of several proton- and heteronuclear- (13C-,15N-) based correlation experiments in terms of sensitivity and resolution, using a model microcrystalline fMLF tripeptide. We demonstrate the applications of ultrafast MAS to a large, fully protonated protein assembly of the 231-residue HIV-1 CA capsid protein. Resonance assignments of protons and heteronuclei, as well as 1H-15N dipolar and 1HN CSA tensors are readily obtained from the high sensitivity and resolution proton-detected 3D experiments. The approach demonstrated here is expected to enable the determination of atomic-resolution structures of large protein assemblies, inaccessible by current methodologies.
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Affiliation(s)
- Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States.
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Jodi Kraus
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Jan Stanek
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Daniela Lalli
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Werner Maas
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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164
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Linser R. Solid-state NMR spectroscopic trends for supramolecular assemblies and protein aggregates. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:45-53. [PMID: 28869877 DOI: 10.1016/j.ssnmr.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Solid-state NMR is able to generate structural data on sample preparations that are explicitly non-crystalline. In particular, for amyloid fibril samples, which can comprise significant degrees of sample disorder, solid-state NMR has been used very successfully. But also solid-state NMR studies of other supramolecular assemblies that have resisted assessment by more standard methods are being performed with increasing ease and biological impact, many of which are briefly reviewed here. New technical trends with respect to structure calculation, protein dynamics and smaller sample amounts have reshaped the field of solid-state NMR recently. In particular, proton-detected approaches based on fast Magic-Angle Spinning (MAS) were demonstrated for crystalline systems initially. Currently, such approaches are being expanded to the above-mentioned non-crystalline targets, the characterization of which can now be pursued with sample amounts on the order of a milligram. In this Trends article, I am giving a brief overview about achievements of the last years as well as the directions that the field has been heading into and delineate some satisfactory perspectives for solid-state NMR's future striving.
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Affiliation(s)
- Rasmus Linser
- Department Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
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165
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Medeiros-Silva J, Jekhmane S, Baldus M, Weingarth M. Hydrogen bond strength in membrane proteins probed by time-resolved 1H-detected solid-state NMR and MD simulations. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:80-85. [PMID: 28342732 DOI: 10.1016/j.ssnmr.2017.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 06/06/2023]
Abstract
1H-detected solid-state NMR in combination with 1H/2D exchange steps allows for the direct identification of very strong hydrogen bonds in membrane proteins. On the example of the membrane-embedded potassium channel KcsA, we quantify the longevity of such very strong hydrogen bonds by combining time-resolved 1H-detected solid-state NMR experiments and molecular dynamics simulations. In particular, we show that the carboxyl-side chain of the highly conserved residue Glu51 is involved in ultra-strong hydrogen bonds, which are fully-water-exposed and yet stable for weeks. The astonishing stability of these hydrogen bonds is important for the structural integrity of potassium channels, which we further corroborate by computational studies.
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Affiliation(s)
- João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Pandualaan 8, 3584 CH Utrecht, The Netherlands
| | - Shehrazade Jekhmane
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Pandualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Pandualaan 8, 3584 CH Utrecht, The Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Pandualaan 8, 3584 CH Utrecht, The Netherlands.
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166
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Albert BJ, Pahng SH, Alaniva N, Sesti EL, Rand PW, Saliba EP, Scott FJ, Choi EJ, Barnes AB. Instrumentation for cryogenic magic angle spinning dynamic nuclear polarization using 90L of liquid nitrogen per day. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 283:71-78. [PMID: 28888182 PMCID: PMC6411293 DOI: 10.1016/j.jmr.2017.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 05/05/2023]
Abstract
Cryogenic sample temperatures can enhance NMR sensitivity by extending spin relaxation times to improve dynamic nuclear polarization (DNP) and by increasing Boltzmann spin polarization. We have developed an efficient heat exchanger with a liquid nitrogen consumption rate of only 90L per day to perform magic-angle spinning (MAS) DNP experiments below 85K. In this heat exchanger implementation, cold exhaust gas from the NMR probe is returned to the outer portion of a counterflow coil within an intermediate cooling stage to improve cooling efficiency of the spinning and variable temperature gases. The heat exchange within the counterflow coil is calculated with computational fluid dynamics to optimize the heat transfer. Experimental results using the novel counterflow heat exchanger demonstrate MAS DNP signal enhancements of 328±3 at 81±2K, and 276±4 at 105±2K.
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Affiliation(s)
- Brice J Albert
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Seong Ho Pahng
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas Alaniva
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Erika L Sesti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Peter W Rand
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Edward P Saliba
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Faith J Scott
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Eric J Choi
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexander B Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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167
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Shen M, Wegner S, Trébosc J, Hu B, Lafon O, Amoureux JP. Minimizing the t 1-noise when using an indirect 1H high-resolution detection of unlabeled samples. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:111-116. [PMID: 28688541 DOI: 10.1016/j.ssnmr.2017.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/25/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
The most utilized through-space correlation 1H-{X} methods with proton indirect detection use two consecutive transfers, 1H → X and then X → 1H, with the evolution time t1 in the middle. When the X isotope is not 100% naturally abundant (NA), only the signal of the protons close to these isotopes is modulated by the 1H-X dipolar interactions. This signal is theoretically disentangled with phase-cycling from the un-modulated one. However, this separation is never perfect and it may lead to t1-noise in case of isotopes with very small NA, such as 13C or even worse 15N. One way to reduce this t1-noise is to minimize, 'purge', during t1 the un-modulated 1H magnetization before trying to suppress it with phase-cycling. We analyze experimentally several sequences following the HORROR condition, which allow purging the 1H transverse magnetization. The comparison is made at three spinning speeds, including very fast ones for 1H resolution: 27.75, 55.5 and 111 kHz. We show (i) that the efficiency of this purging process increases with the spinning speed, and (ii) that the best recoupling sequences are the two simplest ones: XY and S1 = SR212. We then compare the S/N that can be achieved with the two most used 1H-{X} 2D methods, called D-HMQC and CP-CP. The only difference in between these two methods is that the transfers are done with either two π/2-pulses on X channel (D-HMQC), or two Cross-Polarization (CP) transfers (CP-CP). The first method, D-HMQC, is very robust and should be preferred when indirectly detecting nuclei with high NA. The second method, CP-CP, (i) requires experimental precautions to limit the t1-noise, and (ii) is difficult to use with quadrupolar nuclei because the two CP transfers are then not efficient nor robust. However, CP-CP is presently the best method to indirectly detect isotopes with small NA, such as 13C and 15N.
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Affiliation(s)
- M Shen
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - S Wegner
- Bruker BioSpin GmbH, 4 Silberstreifen, 76287 Rheinstetten, Germany
| | - J Trébosc
- Univ. Lille, UMR 8181, UCCS: Unit of Catalysis and Chemistry of Solids, 59000 Lille, France
| | - B Hu
- Shanghai Key Laboratory of Magnetic Resonance, School of Physics and Materials Science, East China Normal University, Shanghai 200062, PR China
| | - O Lafon
- Univ. Lille, UMR 8181, UCCS: Unit of Catalysis and Chemistry of Solids, 59000 Lille, France; Institut Universitaire de France, 1 Rue Descartes, 75231 Paris, France
| | - J P Amoureux
- Univ. Lille, UMR 8181, UCCS: Unit of Catalysis and Chemistry of Solids, 59000 Lille, France; Bruker France, 34 Rue de l'Industrie, 67166 Wissembourg, France.
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168
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Asami S, Reif B. Comparative Study of REDOR and CPPI Derived Order Parameters by 1H-Detected MAS NMR and MD Simulations. J Phys Chem B 2017; 121:8719-8730. [DOI: 10.1021/acs.jpcb.7b06812] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sam Asami
- Munich
Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany
| | - Bernd Reif
- Munich
Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
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169
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Öster C, Kosol S, Hartlmüller C, Lamley JM, Iuga D, Oss A, Org ML, Vanatalu K, Samoson A, Madl T, Lewandowski JR. Characterization of Protein-Protein Interfaces in Large Complexes by Solid-State NMR Solvent Paramagnetic Relaxation Enhancements. J Am Chem Soc 2017; 139:12165-12174. [PMID: 28780861 PMCID: PMC5590091 DOI: 10.1021/jacs.7b03875] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Solid-state NMR is becoming a viable
alternative for obtaining
information about structures and dynamics of large biomolecular complexes,
including ones that are not accessible to other high-resolution biophysical
techniques. In this context, methods for probing protein–protein
interfaces at atomic resolution are highly desirable. Solvent paramagnetic
relaxation enhancements (sPREs) proved to be a powerful method for
probing protein–protein interfaces in large complexes in solution
but have not been employed toward this goal in the solid state. We
demonstrate that 1H and 15N relaxation-based
sPREs provide a powerful tool for characterizing intermolecular interactions
in large assemblies in the solid state. We present approaches for
measuring sPREs in practically the entire range of magic angle spinning
frequencies used for biomolecular studies and discuss their benefits
and limitations. We validate the approach on crystalline GB1, with
our experimental results in good agreement with theoretical predictions.
Finally, we use sPREs to characterize protein–protein interfaces
in the GB1 complex with immunoglobulin G (IgG). Our results suggest
the potential existence of an additional binding site and provide
new insights into GB1:IgG complex structure that amend and revise
the current model available from studies with IgG fragments. We demonstrate
sPREs as a practical, widely applicable, robust, and very sensitive
technique for determining intermolecular interaction interfaces in
large biomolecular complexes in the solid state.
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Affiliation(s)
- Carl Öster
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Simone Kosol
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Christoph Hartlmüller
- Center for Integrated Protein Science, Department of Chemistry, Munich Technische Universität München , Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Jonathan M Lamley
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Dinu Iuga
- Department of Physics, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Andres Oss
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Mai-Liis Org
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Kalju Vanatalu
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Ago Samoson
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Tobias Madl
- Center for Integrated Protein Science, Department of Chemistry, Munich Technische Universität München , Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz , Harrachgasse 21, 8010 Graz, Austria
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
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170
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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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171
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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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172
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Xue K, Sarkar R, Motz C, Asami S, Camargo DCR, Decker V, Wegner S, Tosner Z, Reif B. Limits of Resolution and Sensitivity of Proton Detected MAS Solid-State NMR Experiments at 111 kHz in Deuterated and Protonated Proteins. Sci Rep 2017; 7:7444. [PMID: 28785098 PMCID: PMC5547042 DOI: 10.1038/s41598-017-07253-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/21/2017] [Indexed: 01/23/2023] Open
Abstract
MAS solid-state NMR is capable of determining structures of protonated solid proteins using proton-detected experiments. These experiments are performed at MAS rotation frequency of around 110 kHz, employing 0.5 mg of material. Here, we compare 1H, 13C correlation spectra obtained from protonated and deuterated microcrystalline proteins at MAS rotation frequency of 111 kHz, and show that the spectral quality obtained from deuterated samples is superior to those acquired using protonated samples in terms of resolution and sensitivity. In comparison to protonated samples, spectra obtained from deuterated samples yield a gain in resolution on the order of 3 and 2 in the proton and carbon dimensions, respectively. Additionally, the spectrum from the deuterated sample yields approximately 2–3 times more sensitivity compared to the spectrum of a protonated sample. This gain could be further increased by a factor of 2 by making use of stereospecific precursors for biosynthesis. Although the overall resolution and sensitivity of 1H, 13C correlation spectra obtained using protonated solid samples with rotation frequencies on the order of 110 kHz is high, the spectral quality is still poor when compared to the deuterated samples. We believe that experiments involving large protein complexes in which sensitivity is limiting will benefit from the application of deuteration schemes.
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Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
| | - Carina Motz
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Sam Asami
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Diana C Rodriguez Camargo
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Venita Decker
- Bruker BioSpin, Silberstreifen 4, 76287, Rheinstetten, Germany
| | | | - Zdenek Tosner
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.,Deptartment of chemistry, Faculty of Science, Charles University, Hlavova 8, 12842, Praha 2, Czech Republic
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
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173
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Applications of solid-state NMR to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1577-1586. [PMID: 28709996 DOI: 10.1016/j.bbapap.2017.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022]
Abstract
Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). 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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174
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Venkatesh A, Hanrahan MP, Rossini AJ. Proton detection of MAS solid-state NMR spectra of half-integer quadrupolar nuclei. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 84:171-181. [PMID: 28392024 DOI: 10.1016/j.ssnmr.2017.03.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/25/2017] [Accepted: 03/28/2017] [Indexed: 05/09/2023]
Abstract
Fast magic angle spinning (MAS) and proton detection has found widespread application to enhance the sensitivity of solid-state NMR experiments with spin-1/2 nuclei such as 13C, 15N and 29Si, however, this approach is not yet routinely applied to half-integer quadrupolar nuclei. Here we have investigated the feasibility of using fast MAS and proton detection to enhance the sensitivity of solid-state NMR experiments with half-integer quadrupolar nuclei. The previously described dipolar hetero-nuclear multiple quantum correlation (D-HMQC) and dipolar refocused insensitive nuclei enhanced by polarization transfer (D-RINEPT) pulse sequences were used for proton detection of half-integer quadrupolar nuclei. Quantitative comparisons of signal-to-noise ratios and the sensitivity of proton detected D-HMQC and D-RINEPT and direct detection spin echo and quadrupolar Carr-Purcell Meiboom-Gill (QCPMG) solid-state NMR spectra, demonstrate that one dimensional proton detected experiments can provide sensitivity similar to or exceeding that obtainable with direct detection QCPMG experiments. 2D D-HMQC and D-RINEPT experiments provide less sensitivity than QCPMG experiments but proton detected 2D hetero-nuclear correlation solid-state NMR spectra of half-integer nuclei can still be acquired in about the same time as a 1D spin echo spectrum. Notably, the rarely used D-RINEPT pulse sequence is found to provide similar, or better sensitivity than D-HMQC in some cases. Proton detected D-RINEPT benefits from the short longitudinal relaxation times (T1) normally associated with half-integer quadrupolar nuclei, it can be combined with existing signal enhancement methods for quadrupolar nuclei, and t1-noise in the indirect dimension can easily be removed by pre-saturation of the 1H nuclei. The rapid acquisition of proton detected 2D HETCOR solid-state NMR spectra of a range of half-integer quadrupolar nuclei such as 17O, 27Al, 35Cl and 71Ga is demonstrated.
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Affiliation(s)
- Amrit Venkatesh
- Iowa State University, Department of Chemistry, Ames, IA 50011, USA; US DOE Ames Laboratory, Ames, IA 50011, USA
| | - Michael P Hanrahan
- Iowa State University, Department of Chemistry, Ames, IA 50011, USA; US DOE Ames Laboratory, Ames, IA 50011, USA
| | - Aaron J Rossini
- Iowa State University, Department of Chemistry, Ames, IA 50011, USA; US DOE Ames Laboratory, Ames, IA 50011, USA.
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175
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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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176
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Jain MG, Lalli D, Stanek J, Gowda C, Prakash S, Schwarzer TS, Schubeis T, Castiglione K, Andreas LB, Madhu PK, Pintacuda G, Agarwal V. Selective 1H- 1H Distance Restraints in Fully Protonated Proteins by Very Fast Magic-Angle Spinning Solid-State NMR. J Phys Chem Lett 2017; 8:2399-2405. [PMID: 28492324 DOI: 10.1021/acs.jpclett.7b00983] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Very fast magic-angle spinning (MAS > 80 kHz) NMR combined with high-field magnets has enabled the acquisition of proton-detected spectra in fully protonated solid samples with sufficient resolution and sensitivity. One of the primary challenges in structure determination of protein is observing long-range 1H-1H contacts. Here we use band-selective spin-lock pulses to obtain selective 1H-1H contacts (e.g., HN-HN) on the order of 5-6 Å in fully protonated proteins at 111 kHz MAS. This approach is a major advancement in structural characterization of proteins given that magnetization can be selectively transferred between protons that are 5-6 Å apart despite the presence of other protons at shorter distance. The observed contacts are similar to those previously observed only in perdeuterated proteins with selective protonation. Simulations and experiments show the proposed method has performance that is superior to that of the currently used methods. The method is demonstrated on GB1 and a β-barrel membrane protein, AlkL.
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Affiliation(s)
- Mukul G Jain
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - 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
| | - 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
| | - Chandrakala Gowda
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Satya Prakash
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Tom S Schwarzer
- Institute of Biochemical Engineering, Technical University of Munich , Boltzmannstraße 15, D-85748 Garching, 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 , 5 rue de la Doua, 69100 Villeurbanne, France
| | - Kathrin Castiglione
- Institute of Biochemical Engineering, Technical University of Munich , Boltzmannstraße 15, D-85748 Garching, Germany
| | - Loren B Andreas
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, D-37077 Göttingen, Germany
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - 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
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
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177
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Bertarello A, Schubeis T, Fuccio C, Ravera E, Fragai M, Parigi G, Emsley L, Pintacuda G, Luchinat C. Paramagnetic Properties of a Crystalline Iron–Sulfur Protein by Magic-Angle Spinning NMR Spectroscopy. Inorg Chem 2017; 56:6624-6629. [DOI: 10.1021/acs.inorgchem.7b00674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Andrea Bertarello
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Carmelo Fuccio
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Lyndon Emsley
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Guido Pintacuda
- Centre de RMN à
Très Hauts Champs, Institut des Sciences Analytiques (CNRS,
ENS Lyon, UCB Lyon 1), Université de Lyon, 69100 Villeurbanne, France
| | - Claudio Luchinat
- Giotto Biotech S.R.L., Via Madonna
del Piano 6, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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178
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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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179
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Oikawa T, Okumura M, Kimura T, Nishiyama Y. Solid-state NMR meets electron diffraction: determination of crystalline polymorphs of small organic microcrystalline samples. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2017; 73:219-228. [PMID: 28257016 DOI: 10.1107/s2053229617003084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/24/2017] [Indexed: 01/24/2023]
Abstract
A combination of solid-state NMR (ssNMR) and electron diffraction (ED) has been used to determine the crystalline polymorphs in small-organic microcrystalline molecules. Although 13C cross-polarization magic angle spinning (CPMAS) is a widely used method for determining crystalline polymorphs, even in a mixture, it sometimes fails if the molecular conformations are similar. On the other hand, ED can, in principle, differentiate crystalline forms with different lattice parameters, even when they have very similar molecular conformations. However, its application is usually limited to inorganic molecules only. This is because the ED measurements of organic molecules are very challenging due to degradation of the sample by electron irradiation. We overcame these difficulties by the use of 1H double-quantum/single-quantum correlation experiments at very fast magic angle spinning, together with ED observations under mild electron irradiation. The experiments were demonstrated on L-histidine samples in L-histidine·HCl·H2O, orthorhombic L-histidine and monoclinic L-histidine.
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Affiliation(s)
| | - Manabu Okumura
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Tsunehisa Kimura
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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180
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Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IJL, Gronenborn AM, Polenova T, Zhang P. CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. J Phys Chem B 2017; 121:3853-3863. [PMID: 28181439 DOI: 10.1021/acs.jpcb.6b13105] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many systems, the resolution of cryoEM density map has been limited to 4-6 Å, which only allows for resolving bulky amino acids side chains, thus hindering accurate model building from the density map. On the other hand, experimental chemical shifts (CS) from solution and solid state MAS NMR spectra provide atomic level data for each amino acid within a molecule or a complex; however, structure determination of large complexes and assemblies based on NMR data alone remains challenging. Here, we present a novel integrated strategy to combine the highly complementary experimental data from cryoEM and NMR computationally by molecular dynamics simulations to derive an atomistic model, which is not attainable by either approach alone. We use the HIV-1 capsid protein (CA) C-terminal domain as well as the large capsid assembly to demonstrate the feasibility of this approach, termed NMR CS-biased cryoEM structure refinement.
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Affiliation(s)
- Juan R Perilla
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Gongpu Zhao
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Manman Lu
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Jiying Ning
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Guangjin Hou
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - In-Ja L Byeon
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Tatyana Polenova
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States.,Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine , Headington, Oxford OX3 7BN, U.K.,Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus , Didcot OX11 0DE, U.K
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181
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Guo C, Hou G, Lu X, Polenova T. Mapping protein-protein interactions by double-REDOR-filtered magic angle spinning NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2017; 67:95-108. [PMID: 28120201 PMCID: PMC6258002 DOI: 10.1007/s10858-016-0086-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/25/2016] [Indexed: 05/03/2023]
Abstract
REDOR-based experiments with simultaneous 1H-13C and 1H-15N dipolar dephasing are explored for investigating intermolecular protein-protein interfaces in complexes formed by a U-13C,15N-labeled protein and its natural abundance binding partner. The application of a double-REDOR filter (dREDOR) results in a complete dephasing of proton magnetization in the U-13C,15N-enriched molecule while the proton magnetization of the unlabeled binding partner is not dephased. This retained proton magnetization is then transferred across the intermolecular interface by 1H-13C or 1H-15N cross polarization, permitting to establish the residues of the U-13C,15N-labeled protein, which constitute the binding interface. To assign the interface residues, this dREDOR-CPMAS element is incorporated as a building block into 13C-13C correlation experiments. We established the validity of this approach on U-13C,15N-histidine and on a structurally characterized complex of dynactin's U-13C,15N-CAP-Gly domain with end-binding protein 1 (EB1). The approach introduced here is broadly applicable to the analysis of intermolecular interfaces when one of the binding partners in a complex cannot be isotopically labeled.
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Affiliation(s)
- Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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182
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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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183
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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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184
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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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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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Faster spinning for better structure resolution. Nat Methods 2016. [DOI: 10.1038/nmeth.4007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Shishovs M, Rumnieks J, Diebolder C, Jaudzems K, Andreas LB, Stanek J, Kazaks A, Kotelovica S, Akopjana I, Pintacuda G, Koning RI, Tars K. Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages. J Mol Biol 2016; 428:4267-4279. [PMID: 27591890 DOI: 10.1016/j.jmb.2016.08.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/18/2016] [Accepted: 08/27/2016] [Indexed: 12/18/2022]
Abstract
AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruction of the assembled particle, together with secondary structure information from site-specific solid-state NMR data. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions.
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Affiliation(s)
- Mihails Shishovs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Christoph Diebolder
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kristaps Jaudzems
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Loren B Andreas
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Jan Stanek
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Andris Kazaks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Svetlana Kotelovica
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Inara Akopjana
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Roman I Koning
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands; Department of Cell Biology, Leiden University Medical Center, Postal Zone S1-P, P.O.Box 9600, 2300 RC Leiden, The Netherlands
| | - Kaspars Tars
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia; Faculty of Biology, Department of Molecular Biology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia.
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