1
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Delcourte L, Berbon M, Rodriguez M, Subban K, Lends A, Grélard A, Morvan E, Habenstein B, Saupe SJ, Delhaes L, Aimanianda V, Daskalov A, Loquet A. Magic-angle spinning NMR spectral editing of polysaccharides in whole cells using the DREAM scheme. Methods 2024; 230:59-67. [PMID: 39047926 DOI: 10.1016/j.ymeth.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024] Open
Abstract
Most bacterial, plant and fungal cells possess at their surface a protective layer called the cell wall, conferring strength, plasticity and rigidity to withstand the osmotic pressure. This molecular barrier is crucial for pathogenic microorganisms, as it protects the cell from the local environment and often constitutes the first structural component encountered in the host-pathogen interaction. In pathogenic molds and yeasts, the cell wall constitutes the main target for the development of clinically-relevant antifungal drugs. In the past decade, solid-state NMR has emerged as a powerful analytical technique to investigate the molecular organization of microbial cell walls in the context of intact cells. 13C NMR chemical shift is an exquisite source of information to identify the polysaccharides present in the cell wall, and two-dimensional 13C-13C correlation experiments provide an efficient tool to rapidly access the polysaccharide composition in whole cells. Here we investigate the use of the adiabatic DREAM (for dipolar recoupling enhancement through amplitude modulation) recoupling scheme to improve solid-state NMR analysis of polysaccharides in intact cells. We demonstrate the advantages of two-dimensional 13C-13C experiments using the DREAM recoupling scheme. We report the spectral editing of polysaccharide signals by varying the radio-frequency carrier position. We provide practical considerations for the implementation of DREAM experiments to characterize polysaccharides in whole cells. We demonstrate the approach on intact fungal cells of Neurospora crassa and Aspergillus fumigatus, a model and a pathogenic filamentous fungus, respectively. The approach could be envisioned to efficiently reduce the spectral crowding of more complex cell surfaces, such as cell wall and peptidoglycan in bacteria.
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Affiliation(s)
- Loic Delcourte
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Mélanie Berbon
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Marion Rodriguez
- CNR des Aspergilloses Chroniques, Mycology-Parasitology Department, CHU Bordeaux, Bordeaux 33000, France
| | - Kamalraj Subban
- ImmunoConcEpT, CNRS, UMR 5164, University of Bordeaux, Bordeaux, France
| | - Alons Lends
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Axelle Grélard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Estelle Morvan
- Univ. Bordeaux, CNRS, Inserm, IECB, UAR3033, US01, Pessac, France
| | - Birgit Habenstein
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France
| | - Sven J Saupe
- CNRS, Université de Bordeaux, IBGC, UMR 5095, Bordeaux, France
| | - Laurence Delhaes
- CNR des Aspergilloses Chroniques, Mycology-Parasitology Department, CHU Bordeaux, Bordeaux 33000, France; Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Univ Bordeaux, Bordeaux 33000, France
| | - Vishukumar Aimanianda
- Institut Pasteur, Université Paris Cité, Immunobiology of Aspergillus, Mycology Department, Paris, France
| | - Asen Daskalov
- ImmunoConcEpT, CNRS, UMR 5164, University of Bordeaux, Bordeaux, France; State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
| | - Antoine Loquet
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, Pessac, France.
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2
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Nimerovsky E, Kosteletos S, Lange S, Becker S, Lange A, Andreas LB. Homonuclear Simplified Preservation of Equivalent Pathways Spectroscopy. J Phys Chem Lett 2024; 15:6272-6278. [PMID: 38856103 PMCID: PMC11194807 DOI: 10.1021/acs.jpclett.4c00991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
Recently developed homonuclear transverse mixing optimal control pulses (hTROP) revealed an elegant way to enhance the detected signal in multidimensional magic-angle spinning (MAS) nuclear magnetic resonance experiments. Inspired by their work, we present two homonuclear simplified preservation of equivalent pathways spectroscopy (hSPEPS) sequences for recoupling CA-CO and CA-CB dipolar couplings under fast and ultrafast MAS rates, theoretically enabling a √2 improvement in sensitivity for each indirect dimension. The efficiencies of hSPEPS are evaluated for non-deuterated samples of influenza A M2 and bacterial rhomboid protease GlpG under two different external magnetic fields (600 and 1200 MHz) and MAS rates (55 and 100 kHz). Three-dimensional (H)CA(CO)NH, (H)CO(CA)NH, and (H)CB(CA)NH spectra demonstrate the high robustness of hSPEPS elements to excite carbon-carbon correlations, especially in the (H)CB(CA)NH spectrum, where hSPEPS outperforms the J-based sequence by a factor of, on average, 2.85.
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Affiliation(s)
- Evgeny Nimerovsky
- Department
of NMR-Based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Spyridon Kosteletos
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Sascha Lange
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Stefan Becker
- Department
of NMR-Based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Adam Lange
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Loren B. Andreas
- Department
of NMR-Based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
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3
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Duan P, El Mammeri N, Hong M. Milligram-scale assembly and NMR fingerprint of tau fibrils adopting the Alzheimer's disease fold. J Biol Chem 2024; 300:107326. [PMID: 38679331 PMCID: PMC11145547 DOI: 10.1016/j.jbc.2024.107326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
In the Alzheimer's disease (AD) brain, the microtubule-associated protein tau aggregates into paired helical filaments in which each protofilament has a C-shaped conformation. In vitro assembly of tau fibrils adopting this fold is highly valuable for both fundamental and applied studies of AD without requiring patient-brain extracted fibrils. To date, reported methods for forming AD-fold tau fibrils have been irreproducible and sensitive to subtle variations in fibrillization conditions. Here, we describe a route to reproducibly assemble tau fibrils adopting the AD fold on the multi-milligram scale. We investigated the fibrillization conditions of two constructs and found that a tau (297-407) construct that contains four AD phospho-mimetic glutamate mutations robustly formed the C-shaped conformation. 2D and 3D correlation solid-state NMR spectra show a single predominant set of chemical shifts, indicating a single molecular conformation. Negative-stain electron microscopy and cryo-EM data confirm that the protofilament formed by 4E-tau (297-407) adopts the C-shaped conformation, which associates into paired, triple, and quadruple helical filaments. In comparison, NMR spectra indicate that a previously reported construct, tau (297-391), forms a mixture of a four-layered dimer structure and the C-shaped structure, whose populations are sensitive to the environmental conditions. The determination of the NMR chemical shifts of the AD-fold tau opens the possibility for future studies of tau fibril conformations and ligand binding by NMR. The quantitative assembly of tau fibrils adopting the AD fold should facilitate the development of diagnostic and therapeutic compounds that target AD tau.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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4
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Xiao P, Drewniak P, Dingwell DA, Brown LS, Ladizhansky V. Probing the energy barriers and stages of membrane protein unfolding using solid-state NMR spectroscopy. SCIENCE ADVANCES 2024; 10:eadm7907. [PMID: 38758787 DOI: 10.1126/sciadv.adm7907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
Understanding how the amino acid sequence dictates protein structure and defines its stability is a fundamental problem in molecular biology. It is especially challenging for membrane proteins that reside in the complex environment of a lipid bilayer. Here, we obtain an atomic-level picture of the thermally induced unfolding of a membrane-embedded α-helical protein, human aquaporin 1, using solid-state nuclear magnetic resonance spectroscopy. Our data reveal the hierarchical two-step pathway that begins with unfolding of a structured extracellular loop and proceeds to an intermediate state with a native-like helical packing. In the second step, the transmembrane domain unravels as a single unit, resulting in a heterogeneous misfolded state with high helical content but with nonnative helical packing. Our results show the importance of loops for the kinetic stabilization of the whole membrane protein structure and support the three-stage membrane protein folding model.
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Affiliation(s)
- Peng Xiao
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Philip Drewniak
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Dylan Archer Dingwell
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON N1G2W1, Canada
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5
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Wu D, Koscic A, Schneider S, Dubini RCA, Rodriguez Camargo DC, Schneider S, Rovó P. Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein. Biomacromolecules 2024; 25:1759-1774. [PMID: 38343096 PMCID: PMC10934265 DOI: 10.1021/acs.biomac.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 03/12/2024]
Abstract
Despite the considerable interest in the recombinant production of synthetic spider silk fibers that possess mechanical properties similar to those of native spider silks, such as the cost-effectiveness, tunability, and scalability realization, is still lacking. To address this long-standing challenge, we have constructed an artificial spider silk gene using Golden Gate assembly for the recombinant bacterial production of dragline-mimicking silk, incorporating all the essential components: the N-terminal domain, a 33-residue-long major-ampullate-spidroin-inspired segment repeated 16 times, and the C-terminal domain (N16C). This designed silk-like protein was successfully expressed in Escherichia coli, purified, and cast into films from formic acid. We produced uniformly 13C-15N-labeled N16C films and employed solid-state magic-angle spinning nuclear magnetic resonance (NMR) for characterization. Thus, we could demonstrate that our bioengineered silk-like protein self-assembles into a film where, when hydrated, the solvent-exposed layer of the rigid, β-nanocrystalline polyalanine core undergoes a transition to an α-helical structure, gaining mobility to the extent that it fully dissolves in water and transforms into a highly dynamic random coil. This hydration-induced behavior induces chain dynamics in the glycine-rich amorphous soft segments on the microsecond time scale, contributing to the elasticity of the solid material. Our findings not only reveal the presence of structurally and dynamically distinct segments within the film's superstructure but also highlight the complexity of the self-organization responsible for the exceptional mechanical properties observed in proteins that mimic dragline silk.
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Affiliation(s)
- Dongqing Wu
- Department
of Chemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Anamaria Koscic
- Department
of Chemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Sonja Schneider
- Department
of Chemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Romeo C. A. Dubini
- Department
of Chemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center
for Nanoscience (CeNS), Faculty of Physics, Ludwig-Maximilians-Universität München, 80799 Munich, Germany
| | - Diana C. Rodriguez Camargo
- Department
of Chemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Sabine Schneider
- Department
of Chemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Petra Rovó
- Department
of Chemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Institute
of Science and Technology Austria, 3400 Klosterneuburg, Austria
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6
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Lipiński WP, Zehnder J, Abbas M, Güntert P, Spruijt E, Wiegand T. Fibrils Emerging from Droplets: Molecular Guiding Principles behind Phase Transitions of a Short Peptide-Based Condensate Studied by Solid-State NMR. Chemistry 2023; 29:e202301159. [PMID: 37310801 DOI: 10.1002/chem.202301159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid-liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid-to-solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid-liquid and subsequent liquid-to-solid phase transition as model systems to study both processes. Using solid-state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid-like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR-based structure calculation. The fibrils are stabilised by hydrogen bonds and side-chain π-π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid-to-solid transition of proteins, particularly those related to neurodegenerative diseases.
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Affiliation(s)
- Wojciech P Lipiński
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Johannes Zehnder
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Manzar Abbas
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Peter Güntert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, 192-0397, Tokyo, Japan
| | - Evan Spruijt
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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7
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Xiao H, Zhang Z, Kang H, Yang J. Solid-State NMR Double-Quantum Dipolar Recoupling Enhanced by Additional Phase Modulation. Chemphyschem 2023; 24:e202300141. [PMID: 37309720 DOI: 10.1002/cphc.202300141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Additional phase modulation (APM) is proposed to generally enhance the theoretical efficiency of homonuclear double-quantum (DQ) recoupling in solid-state NMR. APM applies an additional phase list to DQ recoupling in steps of an entire block. The sine-based phase list can enhance the theoretical efficiency by 15-30 %, from 0.52 to 0.68 (non-γ-encoded recoupling) or from 0.73 to 0.84 (γ-encoded recoupling), with doubled recoupling time. The genetic-algorithm (GA) optimized APM can adiabatically enhance the efficiency to ∼1.0 at longer times. The concept of APM has been tested on SPR-51 , BaBa, and SPR-31 , which represent γ-encoded recoupling, non-γ-encoded recoupling, and another kind beyond the former two, respectively. Simulations reveal that enhancements from APM are due to the activation of more crystallites in the powder. Experiments on 2,3-13 C labeled alanine are used to validate the APM recoupling. This new concept shall shed light on developing more efficient homonuclear recoupling methods.
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Affiliation(s)
- Hang Xiao
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Huimin Kang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
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8
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El Mammeri N, Duan P, Dregni AJ, Hong M. Amyloid fibril structures of tau: Conformational plasticity of the second microtubule-binding repeat. SCIENCE ADVANCES 2023; 9:eadh4731. [PMID: 37450599 PMCID: PMC10348678 DOI: 10.1126/sciadv.adh4731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
The intrinsically disordered protein tau associates with microtubules in neurons but aggregates into cross-β amyloid fibrils that propagate in neurodegenerative brains. Different tauopathies have different structures for the rigid fibril core. To understand the molecular basis of tau assembly into different polymorphs, here we use solid-state nuclear magnetic resonance (NMR) spectroscopy to determine the structure of a tau protein that includes all microtubule-binding repeats and a proline-rich domain. This P2R tau assembles into well-ordered filaments when induced by heparin. Two- and three-dimensional NMR spectra indicate that R2 and R3 repeats constitute the rigid β-sheet core of the fibril. Unexpectedly, the amino-terminal half of R2 forms a β-arch at ambient temperature (24°C) but a continuous β-strand at 12°C, which dimerizes with the R2 of another protofilament. This temperature-dependent structure indicates that R2 is conformationally more plastic than the R3 domain. The distinct conformational stabilities of different microtubule-binding repeats give insight into the energy landscape of tau fibril formation.
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Affiliation(s)
- Nadia El Mammeri
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, USA
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9
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Shi X, Kannaian B, Prasanna C, Soman A, Nordenskiöld L. Structural and dynamical investigation of histone H2B in well-hydrated nucleosome core particles by solid-state NMR. Commun Biol 2023; 6:672. [PMID: 37355718 PMCID: PMC10290710 DOI: 10.1038/s42003-023-05050-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/16/2023] [Indexed: 06/26/2023] Open
Abstract
H2A-H2B dimer is a key component of nucleosomes and an important player in chromatin biology. Here, we characterized the structure and dynamics of H2B in precipitated nucleosome core particles (NCPs) with a physiologically relevant concentration using solid-state NMR. Our recent investigation of H3-H4 tetramer determined its unique dynamic properties and the present work provides a deeper understanding of the previously observed dynamic networks in NCP that is potentially functionally significant. Nearly complete 13C, 15N assignments were obtained for H2B R30-A121, which permit extracting unprecedented detailed structural and amino-acid site-specific dynamics. The derived structure of H2B in the well-hydrated NCP sample agrees well with that of X-ray crystals. Dynamics at different timescales were determined semi-quantitatively for H2B in a site-specific manner. Particularly, higher millisecond-microsecond dynamics are observed for H2B core regions including partial α1, L1, partial α2, and partial L3. The analysis of these regions in the context of the tertiary structure reveals the clustering of dynamical residues. Overall, this work fills a gap to a complete resonance assignment of all four histones in nucleosomes and delineates that the dynamic networks in NCP extend to H2B, which suggests a potential mechanism to couple histone core with distant DNA to modulate the DNA activities.
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Affiliation(s)
- Xiangyan Shi
- Department of Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong Province, China.
| | - Bhuvaneswari Kannaian
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chinmayi Prasanna
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Aghil Soman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
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10
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Nimerovsky E, Najbauer EÉ, Becker S, Andreas LB. Great Offset Difference Internuclear Selective Transfer. J Phys Chem Lett 2023; 14:3939-3945. [PMID: 37078685 PMCID: PMC10150390 DOI: 10.1021/acs.jpclett.3c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Carbon-carbon dipolar recoupling sequences are frequently used building blocks in routine magic-angle spinning NMR experiments. While broadband homonuclear first-order dipolar recoupling sequences mainly excite intra-residue correlations, selective methods can detect inter-residue transfers and long-range correlations. Here, we present the great offset difference internuclear selective transfer (GODIST) pulse sequence optimized for selective carbonyl or aliphatic recoupling at fast magic-angle spinning, here, 55 kHz. We observe a 3- to 5-fold increase in intensities compared with broadband RFDR recoupling for perdeuterated microcrystalline SH3 and for the membrane protein influenza A M2 in lipid bilayers. In 3D (H)COCO(N)H and (H)CO(CO)NH spectra, inter-residue carbonyl-carbonyl correlations up to about 5 Å are observed in uniformly 13C-labeled proteins.
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Affiliation(s)
- Evgeny Nimerovsky
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Eszter Éva Najbauer
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Loren B Andreas
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
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11
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Lusky OS, Ernst M, Goldbourt A. Theoretical description of pulse induced resonances in the homonuclear PIRATE experiment. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 124:101859. [PMID: 37015155 DOI: 10.1016/j.ssnmr.2023.101859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 06/19/2023]
Abstract
Rotor-synchronous π pulses applied to protons (S) enhance homonuclear polarisation transfer between two spins (I) such as 13C or 15N as long as at least a single I-S heteronuclear dipolar-coupling interaction exists. The enhancement is maximum when the chemical-shift difference Δν between two spins equals an integer multiple, n, of the pulse-modulation frequency, which is half the rotor frequency νr. This condition, applied in the Pulse Induced Resonance with Angular dependent Total Enhancement (PIRATE) experiment, can be generalised for any spacing of the pulses k/νr such that Δν=nνr2k . We show, using average Hamiltonian theory (AHT) and Floquet theory, that the resonance conditions promote a second-order recoupling consisting of a cross-term between the homonuclear and heteronuclear dipolar interactions in a three-spin system. The minimum requirement is a coupling between the two I spins and a coupling of one of the I spins to the S spin. The effective Hamiltonian at the resonance conditions contains three-spin operators of the form 2I1±I2∓Sz with a non-zero effective dipolar coupling. Theoretical analysis shows that the effective strength of the resonance conditions decreases with increasing values of k and n. The theory is backed by numerical simulations, and experimental results on fully labelled 13C-glycine demonstrating the efficiency of the different resonance condition for k=1,2 at various spinning frequencies.
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Affiliation(s)
- Orr Simon Lusky
- School of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, CH-8093, Zürich, Switzerland
| | - Amir Goldbourt
- School of Chemistry, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel.
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12
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Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.
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Affiliation(s)
- Yusuke Nishiyama
- JEOL Ltd., Akishima, Tokyo196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa230-0045, Japan
| | - Guangjin Hou
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian116023, China
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad500 046, India
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan41809-1055, United States
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13
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Ahlawat S, Mopidevi SMV, Taware PP, Raran-Kurussi S, Mote KR, Agarwal V. Assignment of aromatic side-chain spins and characterization of their distance restraints at fast MAS. J Struct Biol X 2022; 7:100082. [PMID: 36618437 PMCID: PMC9817166 DOI: 10.1016/j.yjsbx.2022.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/18/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022] Open
Abstract
The assignment of aromatic side-chain spins has always been more challenging than assigning backbone and aliphatic spins. Selective labeling combined with mutagenesis has been the approach for assigning aromatic spins. This manuscript reports a method for assigning aromatic spins in a fully protonated protein by connecting them to the backbone atoms using a low-power TOBSY sequence. The pulse sequence employs residual polarization and sequential acquisitions techniques to record HN- and HC-detected spectra in a single experiment. The unambiguous assignment of aromatic spins also enables the characterization of 1H-1H distance restraints involving aromatic spins. Broadband (RFDR) and selective (BASS-SD) recoupling sequences were used to generate HN-ΗC, HC-HN and HC-HC restraints involving the side-chain proton spins of aromatic residues. This approach has been demonstrated on a fully protonated U-[13C,15N] labeled GB1 sample at 95-100 kHz MAS.
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14
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Burakova E, Vasa SK, Linser R. Characterization of conformational heterogeneity via higher-dimensionality, proton-detected solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2022; 76:197-212. [PMID: 36149571 PMCID: PMC9712413 DOI: 10.1007/s10858-022-00405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Site-specific heterogeneity of solid protein samples can be exploited as valuable information to answer biological questions ranging from thermodynamic properties determining fibril formation to protein folding and conformational stability upon stress. In particular, for proteins of increasing molecular weight, however, site-resolved assessment without residue-specific labeling is challenging using established methodology, which tends to rely on carbon-detected 2D correlations. Here we develop purely chemical-shift-based approaches for assessment of relative conformational heterogeneity that allows identification of each residue via four chemical-shift dimensions. High dimensionality diminishes the probability of peak overlap in the presence of multiple, heterogeneously broadened resonances. Utilizing backbone dihedral-angle reconstruction from individual contributions to the peak shape either via suitably adapted prediction routines or direct association with a relational database, the methods may in future studies afford assessment of site-specific heterogeneity of proteins without site-specific labeling.
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Affiliation(s)
- Ekaterina Burakova
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
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15
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Ahlawat S, Mote KR, Raran-Kurussi S, Agarwal V. Mechanism of selective polarization exchange amongst chemically similar and distinct protons during weak rf irradiation at fast magic angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 340:107236. [PMID: 35609347 DOI: 10.1016/j.jmr.2022.107236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/16/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Band Selective Spectral Spin-Diffusion (BASS-SD) is a method to obtain selective 1H-1H contacts between chemically similar protons within a distance range of 5-6 Å in fully protonated proteins. BASS-SD combines low-amplitude proton spinlock radio frequency (rf) pulses with fast MAS frequency to enable selective polarization exchange in fully protonated molecules. The selectivity of transfer is dictated by the bandwidth of the spinlock pulse and has been used to observe selective HN-HN, Hα-Ηα and Hmethyl-Hmethyl correlations. These proton-proton spatial contacts are similar to those observed in perdeuterated samples and serve as useful structural restraints towards de novo protein structure determination. This study employs bimodal Floquet theory to derive the first- and second-order effective Hamiltonians necessary to understand the spin dynamics during BASS-SD. Analytical calculations combined with numerical simulations delineate two different mechanisms for polarization transfer amongst the proton spins. The BASS-SD recoupling condition has been reoptimized to observe selective correlations between chemically different protons (e.g., HN-Hα) while retaining the spatial contacts between chemically similar protons (e.g., HN-HN). The new BASS-SD condition is integrated with simultaneous and sequential acquisition approaches to generate four different types of structural restraints (HN-HN, Hα-Ηα, HN-Hα, Hα-HN) in one experiment. The approach has been demonstrated on microcrystalline U-[13C,15N] labeled GB1 protein at ∼ 95-100 kHz MAS.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Sreejith Raran-Kurussi
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India.
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16
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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17
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Taware PP, Raran-Kurussi S, Mote KR. CURD: a Single-Shot Strategy to Obtain Assignments and Distance Restraints for Proteins Using Solid-State MAS NMR Spectroscopy. J Phys Chem B 2022; 126:3269-3275. [PMID: 35473315 DOI: 10.1021/acs.jpcb.2c00775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a strategy dubbed CURD (correlations using recycle delays) to acquire chemical-shift assignments and distance restraints for proteins in a single experimental block under slow-moderate magic-angle spinning conditions. This is done by concatenating the 3D-CCC and 3D-NNC experiments, both of which individually require long experimental times for sufficient resolution and sensitivity to be realized. Unlike previous approaches, the CURD strategy does not increase the amount of radio-frequency deposition on the sample and does not require lengthy procedures to optimize any of the pulse sequence elements. Instead, time savings is obtained by using the hitherto unused recycle delay of one of the experiments (2D-CC/3D-CCC) to establish inter-residue correlations for the second experiment (2D-NN/3D-NNC). Experiments are demonstrated on a model protein at the MAS frequency of 12.5 kHz and are shown to result in time savings of the order of days for most of the routine cases.
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Affiliation(s)
- Pravin P Taware
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, Telangana 500046, India
| | - Sreejith Raran-Kurussi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, Telangana 500046, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad, Telangana 500046, India
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18
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Paluch P, Augustyniak R, Org ML, Vanatalu K, Kaldma A, Samoson A, Stanek J. NMR Assignment of Methyl Groups in Immobilized Proteins Using Multiple-Bond 13C Homonuclear Transfers, Proton Detection, and Very Fast MAS. Front Mol Biosci 2022; 9:828785. [PMID: 35425812 PMCID: PMC9002630 DOI: 10.3389/fmolb.2022.828785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
In nuclear magnetic resonance spectroscopy of proteins, methyl protons play a particular role as extremely sensitive reporters on dynamics, allosteric effects, and protein–protein interactions, accessible even in high-molecular-weight systems approaching 1 MDa. The notorious issue of their chemical shift assignment is addressed here by a joint use of solid-state 1H-detected methods at very fast (nearly 100 kHz) magic-angle spinning, partial deuteration, and high-magnetic fields. The suitability of a series of RF schemes is evaluated for the efficient coherence transfer across entire 13C side chains of methyl-containing residues, which is key for establishing connection between methyl and backbone 1H resonances. The performance of ten methods for recoupling of either isotropic 13C–13C scalar or anisotropic dipolar interactions (five variants of TOBSY, FLOPSY, DIPSI, WALTZ, RFDR, and DREAM) is evaluated experimentally at two state-of-the-art magic-angle spinning (55 and 94.5 kHz) and static magnetic field conditions (18.8 and 23.5 T). Model isotopically labeled compounds (alanine and Met-Leu-Phe tripeptide) and ILV-methyl and amide-selectively protonated, and otherwise deuterated chicken α-spectrin SH3 protein are used as convenient reference systems. Spin dynamics simulations in SIMPSON are performed to determine optimal parameters of these RF schemes, up to recently experimentally attained spinning frequencies (200 kHz) and B0 field strengths (28.2 T). The concept of linearization of 13C side chain by appropriate isotope labeling is revisited and showed to significantly increase sensitivity of methyl-to-backbone correlations. A resolution enhancement provided by 4D spectroscopy with non-uniform (sparse) sampling is demonstrated to remove ambiguities in simultaneous resonance assignment of methyl proton and carbon chemical shifts.
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Affiliation(s)
- Piotr Paluch
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Łódź, Poland
| | | | - Mai-Liis Org
- Tallin University of Technology, Tallinn, Estonia
| | | | - Ats Kaldma
- Tallin University of Technology, Tallinn, Estonia
| | - Ago Samoson
- Tallin University of Technology, Tallinn, Estonia
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- *Correspondence: Jan Stanek,
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19
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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20
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High-pH structure of EmrE reveals the mechanism of proton-coupled substrate transport. Nat Commun 2022; 13:991. [PMID: 35181664 PMCID: PMC8857205 DOI: 10.1038/s41467-022-28556-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 01/27/2022] [Indexed: 12/20/2022] Open
Abstract
The homo-dimeric bacterial membrane protein EmrE effluxes polyaromatic cationic substrates in a proton-coupled manner to cause multidrug resistance. We recently determined the structure of substrate-bound EmrE in phospholipid bilayers by measuring hundreds of protein-ligand HN–F distances for a fluorinated substrate, 4-fluoro-tetraphenylphosphonium (F4-TPP+), using solid-state NMR. This structure was solved at low pH where one of the two proton-binding Glu14 residues is protonated. Here, to understand how substrate transport depends on pH, we determine the structure of the EmrE-TPP complex at high pH, where both Glu14 residues are deprotonated. The high-pH complex exhibits an elongated and hydrated binding pocket in which the substrate is similarly exposed to the two sides of the membrane. In contrast, the low-pH complex asymmetrically exposes the substrate to one side of the membrane. These pH-dependent EmrE conformations provide detailed insights into the alternating-access model, and suggest that the high-pH conformation may facilitate proton binding in the presence of the substrate, thus accelerating the conformational change of EmrE to export the substrate. EmrE transporter effluxes cationic substrates across lipid membranes in a pH-coupled manner. Here, the authors solve the structure of ligand-bound EmrE at high pH by NMR, with insights into the transport mechanism.
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21
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Nimerovsky E, Najbauer EE, Movellan KT, Xue K, Becker S, Andreas LB. Modest Offset Difference Internuclear Selective Transfer via Homonuclear Dipolar Coupling. J Phys Chem Lett 2022; 13:1540-1546. [PMID: 35133845 PMCID: PMC8859849 DOI: 10.1021/acs.jpclett.1c03871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Homonuclear dipolar recoupling is routinely used for magic-angle spinning NMR-based structure determination. In fully protonated samples, only short proton-proton distances are accessible to broadband recoupling approaches because of high proton density. Selective methods allow detection of longer distances by directing polarization to a subset of spins. Here we introduce the selective pulse sequence MODIST, which recouples spins that have a modest chemical shift offset difference, and demonstrate it to selectively record correlations between amide protons. The sequence was selected for good retention of total signal, leading to up to twice the intensity for proton-proton correlations compared with other selective methods. The sequence is effective across a range of spinning conditions and magnetic fields, here tested at 55.555 and 100 kHz magic-angle spinning and at proton Larmor frequencies from 600 to 1200 MHz. For influenza A M2 in lipid bilayers, cross-peaks characteristic of a helical conformation are observed.
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22
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Římal V, Callon M, Malär A, Cadalbert R, Torosyan A, Wiegand T, Ernst M, Böckmann A, Meier B. Correction of field instabilities in biomolecular solid-state NMR by simultaneous acquisition of a frequency reference. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:15-26. [PMID: 37905180 PMCID: PMC10539777 DOI: 10.5194/mr-3-15-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/26/2022] [Indexed: 11/02/2023]
Abstract
With the advent of faster magic-angle spinning (MAS) and higher magnetic fields, the resolution of biomolecular solid-state nuclear magnetic resonance (NMR) spectra has been continuously increasing. As a direct consequence, the always narrower spectral lines, especially in proton-detected spectroscopy, are also becoming more sensitive to temporal instabilities of the magnetic field in the sample volume. Field drifts in the order of tenths of parts per million occur after probe insertion or temperature change, during cryogen refill, or are intrinsic to the superconducting high-field magnets, particularly in the months after charging. As an alternative to a field-frequency lock based on deuterium solvent resonance rarely available for solid-state NMR, we present a strategy to compensate non-linear field drifts using simultaneous acquisition of a frequency reference (SAFR). It is based on the acquisition of an auxiliary 1D spectrum in each scan of the experiment. Typically, a small-flip-angle pulse is added at the beginning of the pulse sequence. Based on the frequency of the maximum of the solvent signal, the field evolution in time is reconstructed and used to correct the raw data after acquisition, thereby acting in its principle as a digital lock system. The general applicability of our approach is demonstrated on 2D and 3D protein spectra during various situations with a non-linear field drift. SAFR with small-flip-angle pulses causes no significant loss in sensitivity or increase in experimental time in protein spectroscopy. The correction leads to the possibility of recording high-quality spectra in a typical biomolecular experiment even during non-linear field changes in the order of 0.1 ppm h- 1 without the need for hardware solutions, such as stabilizing the temperature of the magnet bore. The improvement of linewidths and peak shapes turns out to be especially important for 1 H-detected spectra under fast MAS, but the method is suitable for the detection of carbon or other nuclei as well.
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Affiliation(s)
- Václav Římal
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | - Morgane Callon
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | | | | | | | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086,
CNRS/Université de Lyon, 69367 Lyon, France
| | - Beat H. Meier
- Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland
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23
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
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24
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Reif B. Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR. Chem Rev 2021; 122:10019-10035. [PMID: 34870415 DOI: 10.1021/acs.chemrev.1c00681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B0 field in a perdeuterated environment are compiled.
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Affiliation(s)
- Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at the Department of Chemistry, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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25
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Xue K, Movellan KT, Zhang XC, Najbauer EE, Forster MC, Becker S, Andreas LB. Towards a native environment: structure and function of membrane proteins in lipid bilayers by NMR. Chem Sci 2021; 12:14332-14342. [PMID: 34880983 PMCID: PMC8580007 DOI: 10.1039/d1sc02813h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/07/2021] [Indexed: 01/17/2023] Open
Abstract
Solid-state NMR (ssNMR) is a versatile technique that can be used for the characterization of various materials, ranging from small molecules to biological samples, including membrane proteins. ssNMR can probe both the structure and dynamics of membrane proteins, revealing protein function in a near-native lipid bilayer environment. The main limitation of the method is spectral resolution and sensitivity, however recent developments in ssNMR hardware, including the commercialization of 28 T magnets (1.2 GHz proton frequency) and ultrafast MAS spinning (<100 kHz) promise to accelerate acquisition, while reducing sample requirement, both of which are critical to membrane protein studies. Here, we review recent advances in ssNMR methodology used for structure determination of membrane proteins in native and mimetic environments, as well as the study of protein functions such as protein dynamics, and interactions with ligands, lipids and cholesterol.
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Affiliation(s)
- Kai Xue
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Kumar Tekwani Movellan
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Xizhou Cecily Zhang
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Eszter E Najbauer
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Marcel C Forster
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Stefan Becker
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
| | - Loren B Andreas
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology Am Fassberg. 11 Goettingen Germany
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26
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Shcherbakov AA, Medeiros-Silva J, Tran N, Gelenter MD, Hong M. From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR. Chem Rev 2021; 122:9848-9879. [PMID: 34694769 DOI: 10.1021/acs.chemrev.1c00662] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Internuclear distances represent one of the main structural constraints in molecular structure determination using solid-state NMR spectroscopy, complementing chemical shifts and orientational restraints. Although a large number of magic-angle-spinning (MAS) NMR techniques have been available for distance measurements, traditional 13C and 15N NMR experiments are inherently limited to distances of a few angstroms due to the low gyromagnetic ratios of these nuclei. Recent development of fast MAS triple-resonance 19F and 1H NMR probes has stimulated the design of MAS NMR experiments that measure distances in the 1-2 nm range with high sensitivity. This review describes the principles and applications of these multiplexed multidimensional correlation distance NMR experiments, with an emphasis on 19F- and 1H-based distance experiments. Representative applications of these long-distance NMR methods to biological macromolecules as well as small molecules are reviewed.
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Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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27
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Ashami K, Falk AS, Hurd C, Garg S, Cervantes SA, Rawat A, Siemer AB. Droplet and fibril formation of the functional amyloid Orb2. J Biol Chem 2021; 297:100804. [PMID: 34044018 PMCID: PMC8294575 DOI: 10.1016/j.jbc.2021.100804] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/10/2021] [Accepted: 05/18/2021] [Indexed: 01/18/2023] Open
Abstract
The functional amyloid Orb2 belongs to the cytoplasmic polyadenylation element binding (CPEB) protein family and plays an important role in long-term memory formation in Drosophila. The Orb2 domain structure combines RNA recognition motifs with low-complexity sequences similar to many RNA-binding proteins shown to form protein droplets via liquid–liquid phase separation (LLPS) in vivo and in vitro. This similarity suggests that Orb2 might also undergo LLPS. However, cellular Orb2 puncta have very little internal protein mobility, and Orb2 forms fibrils in Drosophila brains that are functionally active indicating that LLPS might not play a role for Orb2. In the present work, we reconcile these two views on Orb2 droplet formation. Using fluorescence microscopy, we show that soluble Orb2 can indeed phase separate into protein droplets. However, fluorescence recovery after photobleaching (FRAP) data shows that these droplets have either no or only an extremely short-lived liquid phase and appear maturated right after formation. Orb2 fragments that lack the C-terminal RNA-binding domain (RBD) form fibrils out of these droplets. Solid-state NMR shows that these fibrils have well-ordered static domains in addition to the Gln/His-rich fibril core. Further, we find that full-length Orb2B, which is by far the major component of Orb2 fibrils in vivo, does not transition into fibrils but remains in the droplet phase. Together, our data suggest that phase separation might play a role in initiating the formation of functional Orb2 fibrils.
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Affiliation(s)
- Kidist Ashami
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Alexander S Falk
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Connor Hurd
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Samridhi Garg
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Silvia A Cervantes
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Anoop Rawat
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
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28
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Xiao H, Zhang Z, Zhao Y, Yang J. Spectral editing of alanine, serine, and threonine in uniformly labeled proteins based on frequency-selective homonuclear recoupling in solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2021; 75:193-202. [PMID: 33890210 DOI: 10.1007/s10858-021-00367-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Spectral editing is crucial to simplify the crowded solid-state NMR spectra of proteins. New techniques are introduced to edit 13C-13C correlations of uniformly labeled proteins under moderate magic-angle spinning (MAS), based on our recent frequency-selective homonuclear recoupling sequences [Zhang et al., J. Phys. Chem. Lett. 2020, 11, 8077-8083]. The signals of alanine, serine, or threonine residues are selected out by selective 13Cα-13Cβ double-quantum filtering (DQF). The 13Cα-13Cβ correlations of alanine residues are selectively established with efficiency up to ~ 1.8 times that by dipolar-assisted rotational resonance (DARR). The techniques are shown in 2D/3D NCCX experiments and applied to the uniformly 13C, 15N labeled Aquaporin Z (AqpZ) membrane protein, demonstrating their potential to simplify spectral analyses in biological solid-state NMR.
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Affiliation(s)
- Hang Xiao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhengfeng Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
| | - Yongxiang Zhao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Jun Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China.
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29
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Ji Y, Liang L, Bao X, Hou G. Recent progress in dipolar recoupling techniques under fast MAS in solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 112:101711. [PMID: 33508579 DOI: 10.1016/j.ssnmr.2020.101711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
With the recent advances in NMR hardware and probe design technology, magic-angle spinning (MAS) rates over 100 kHz are accessible now, even on commercial solid NMR probes. Under such fast MAS conditions, excellent spectral resolution has been achieved by efficient suppression of anisotropic interactions, which also opens an avenue to the proton-detected NMR experiments in solids. Numerous methods have been developed to take full advantage of fast MAS during the last decades. Among them, dipolar recoupling techniques under fast MAS play vital roles in the determination of the molecular structure and dynamics, and are also key elements in multi-dimensional correlation NMR experiments. Herein, we review the dipolar recoupling techniques, especially those developed in the past two decades for fast-to-ultrafast MAS conditions. A major focus for our discussion is the ratio of RF field strength (in frequency) to MAS frequency, ν1/νr, in different pulse sequences, which determines whether these dipolar recoupling techniques are suitable for NMR experiments under fast MAS conditions. Systematic comparisons are made among both heteronuclear and homonuclear dipolar recoupling schemes. In addition, the schemes developed specially for proton-detection NMR experiments under ultrafast MAS conditions are highlighted as well.
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Affiliation(s)
- Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinhe Bao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, China.
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30
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Dubini RCA, Jung H, Skidmore CH, Demirel MC, Rovó P. Hydration-Induced Structural Transitions in Biomimetic Tandem Repeat Proteins. J Phys Chem B 2021; 125:2134-2145. [PMID: 33595326 DOI: 10.1021/acs.jpcb.0c11505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A major challenge in developing biomimetic, high-performance, and sustainable products is the accurate replication of the biological materials' striking properties, such as high strength, self-repair, and stimuli-responsiveness. The rationalization of such features on the microscopic scale, together with the rational design of synthetic materials, is currently hindered by our limited understanding of the sequence-structure-property relationship. Here, employing state-of-the-art nuclear magnetic resonance (NMR) spectroscopy, we link the atomistic structural and dynamic properties of an artificial bioinspired tandem repeat protein TR(1,11) to its stunning macroscopic properties including high elasticity, self-healing capabilities, and record-holding proton conductivity among biological materials. We show that the hydration-induced structural rearrangement of the amorphous Gly-rich soft segment and the ordered Ala-rich hard segment is the key to the material's outstanding physical properties. We found that in the hydrated state both the Ala-rich ordered and Gly-rich disordered parts contribute to the formation of the nanoconfined β-sheets, thereby enhancing the strength and toughness of the material. This restructuring is accompanied by fast proline ring puckering and backbone cis-trans isomerization at the water-protein interface, which in turn enhances the elasticity and the thermal conductivity of the hydrated films. Our in-depth characterization provides a solid ground for the development of next-generation materials with improved properties.
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Affiliation(s)
- Romeo C A Dubini
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.,Center for Nanoscience (CeNS), Faculty of Physics, Ludwig-Maximilians-Universität München, Schellingstraße 4, Fifth Floor, 80799 Munich, Germany
| | - Huihun Jung
- Center for Research on Advanced Fiber Technologies (CRAFT), Materials Research Institute, Department of Engineering Science and Mechanics, and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Chloe H Skidmore
- Center for Research on Advanced Fiber Technologies (CRAFT), Materials Research Institute, Department of Engineering Science and Mechanics, and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Melik C Demirel
- Center for Research on Advanced Fiber Technologies (CRAFT), Materials Research Institute, Department of Engineering Science and Mechanics, and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Petra Rovó
- Faculty of Chemistry and Pharmacy, Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.,Center for Nanoscience (CeNS), Faculty of Physics, Ludwig-Maximilians-Universität München, Schellingstraße 4, Fifth Floor, 80799 Munich, Germany
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31
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Zhang X, Forster MC, Nimerovsky E, Movellan KT, Andreas LB. Transferred-Rotational-Echo Double Resonance. J Phys Chem A 2021; 125:754-769. [PMID: 33464081 PMCID: PMC7884007 DOI: 10.1021/acs.jpca.0c09033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/11/2020] [Indexed: 12/21/2022]
Abstract
Internuclear distance determination is the foundation for NMR-based structure calculation. However, high-precision distance measurement is a laborious process requiring lengthy data acquisitions due to the large set of multidimensional spectra needed at different mixing times. This prevents application to large or challenging molecular systems. Here, we present a new approach, transferred-rotational-echo double resonance (TREDOR), a heteronuclear transfer method in which we simultaneously detect both starting and transferred signals in a single spectrum. This co-acquisition is used to compensate for coherence decay, resulting in accurate and precise distance determination by a single parameter fit using a single spectrum recorded at an ideal mixing time. We showcase TREDOR with the microcrystalline SH3 protein using 3D spectra to resolve resonances. By combining the measured N-C and H-C distances, we calculate the structure of SH3, which converges to the correct fold, with a root-mean-square deviation of 2.1 Å compared to a reference X-ray structure. The TREDOR data used in the structure calculation were acquired in only 4 days on a 600 MHz instrument. This is achieved due to the more than 2-fold time saving afforded by co-acquisition of additional information and demonstrates TREDOR as a fast and straightforward method for determining structures via magic-angle spinning NMR.
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Affiliation(s)
| | | | - Evgeny Nimerovsky
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Kumar Tekwani Movellan
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Loren B. Andreas
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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32
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Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers. Nat Commun 2021; 12:172. [PMID: 33420032 PMCID: PMC7794478 DOI: 10.1038/s41467-020-20468-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/01/2020] [Indexed: 01/29/2023] Open
Abstract
The dimeric transporter, EmrE, effluxes polyaromatic cationic drugs in a proton-coupled manner to confer multidrug resistance in bacteria. Although the protein is known to adopt an antiparallel asymmetric topology, its high-resolution drug-bound structure is so far unknown, limiting our understanding of the molecular basis of promiscuous transport. Here we report an experimental structure of drug-bound EmrE in phospholipid bilayers, determined using 19F and 1H solid-state NMR and a fluorinated substrate, tetra(4-fluorophenyl) phosphonium (F4-TPP+). The drug-binding site, constrained by 214 protein-substrate distances, is dominated by aromatic residues such as W63 and Y60, but is sufficiently spacious for the tetrahedral drug to reorient at physiological temperature. F4-TPP+ lies closer to the proton-binding residue E14 in subunit A than in subunit B, explaining the asymmetric protonation of the protein. The structure gives insight into the molecular mechanism of multidrug recognition by EmrE and establishes the basis for future design of substrate inhibitors to combat antibiotic resistance.
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33
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Vallet A, Favier A, Brutscher B, Schanda P. ssNMRlib: a comprehensive library and tool box for acquisition of solid-state nuclear magnetic resonance experiments on Bruker spectrometers. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:331-345. [PMID: 37904819 PMCID: PMC10500710 DOI: 10.5194/mr-1-331-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/16/2020] [Indexed: 11/01/2023]
Abstract
We introduce ssNMRlib, a comprehensive suite of pulse sequences and jython scripts for user-friendly solid-state nuclear magnetic resonance (NMR) data acquisition, parameter optimization and storage on Bruker spectrometers. ssNMRlib allows the straightforward setup of even highly complex multi-dimensional solid-state NMR experiments with a few clicks from an intuitive graphical interface directly from the Bruker Topspin acquisition software. ssNMRlib allows the setup of experiments in a magnetic-field-independent manner and thus facilitates the workflow in a multi-spectrometer setting with a centralized library. Safety checks furthermore assist the user in experiment setup. Currently hosting more than 140 1D to 4D experiments, primarily for biomolecular solid-state NMR, the library can be easily customized and new experiments are readily added as new templates. ssNMRlib is part of the previously introduced NMRlib library, which comprises many solution-NMR pulse sequences and macros.
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Affiliation(s)
- Alicia Vallet
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Adrien Favier
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Bernhard Brutscher
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
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34
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Hoffmann J, Ruta J, Shi C, Hendriks K, Chevelkov V, Franks WT, Oschkinat H, Giller K, Becker S, Lange A. Protein resonance assignment by BSH-CP-based 3D solid-state NMR experiments: A practical guide. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:445-465. [PMID: 31691361 DOI: 10.1002/mrc.4945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/05/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Solid-state NMR (ssNMR) spectroscopy has evolved into a powerful method to obtain structural information and to study the dynamics of proteins at atomic resolution and under physiological conditions. The method is especially well suited to investigate insoluble and noncrystalline proteins that cannot be investigated easily by X-ray crystallography or solution NMR. To allow for detailed analysis of ssNMR data, the assignment of resonances to the protein atoms is essential. For this purpose, a set of three-dimensional (3D) spectra needs to be acquired. Band-selective homo-nuclear cross-polarization (BSH-CP) is an effective method for magnetization transfer between carbonyl carbon (CO) and alpha carbon (CA) atoms, which is an important transfer step in multidimensional ssNMR experiments. This tutorial describes the detailed procedure for the chemical shift assignment of the backbone atoms of 13 C-15 N-labeled proteins by BSH-CP-based 13 C-detected ssNMR experiments. A set of six 3D experiments is used for unambiguous assignment of the protein backbone as well as certain side-chain resonances. The tutorial especially addresses scientists with little experience in the field of ssNMR and provides all the necessary information for protein assignment in an efficient, time-saving approach.
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Affiliation(s)
- Jutta Hoffmann
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Julia Ruta
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Kitty Hendriks
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - W Trent Franks
- Department of NMR-supported Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Hartmut Oschkinat
- Department of NMR-supported Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Karin Giller
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
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35
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Sharma K, Madhu PK, Agarwal V, Mote KR. Simultaneous recording of intra- and inter-residue linking experiments for backbone assignments in proteins at MAS frequencies higher than 60 kHz. JOURNAL OF BIOMOLECULAR NMR 2020; 74:229-237. [PMID: 31894471 DOI: 10.1007/s10858-019-00292-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Obtaining site-specific assignments for the NMR spectra of proteins in the solid state is a significant bottleneck in deciphering their biophysics. This is primarily due to the time-intensive nature of the experiments. Additionally, the low resolution in the [Formula: see text]-dimension requires multiple complementary experiments to be recorded to lift degeneracies in assignments. We present here an approach, gleaned from the techniques used in multiple-acquisition experiments, which allows the recording of forward and backward residue-linking experiments in a single experimental block. Spectra from six additional pathways are also recovered from the same experimental block, without increasing the probe duty cycle. These experiments give intra- and inter residue connectivities for the backbone [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] resonances and should alone be sufficient to assign these nuclei in proteins at MAS frequencies > 60 kHz. The validity of this approach is tested with experiments on a standard tripeptide N-formyl methionyl-leucine-phenylalanine (f-MLF) at a MAS frequency of 62.5 kHz, which is also used as a test-case for determining the sensitivity of each of the experiments. We expect this approach to have an immediate impact on the way assignments are obtained at MAS frequencies [Formula: see text].
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Affiliation(s)
- Kshama Sharma
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally, Serlingampally Mandal, Rangareddy District, Hyderabad, 500107, India
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally, Serlingampally Mandal, Rangareddy District, Hyderabad, 500107, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally, Serlingampally Mandal, Rangareddy District, Hyderabad, 500107, India.
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally, Serlingampally Mandal, Rangareddy District, Hyderabad, 500107, India.
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36
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Wi S, Frydman L. An Efficient, Robust New Scheme for Establishing Broadband Homonuclear Correlations in Biomolecular Solid State NMR. Chemphyschem 2020; 21:284-294. [DOI: 10.1002/cphc.201901071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/17/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Sungsool Wi
- National High Magnetic Field Laboratory Tallahassee Florida 32304 USA
| | - Lucio Frydman
- National High Magnetic Field Laboratory Tallahassee Florida 32304 USA
- Department of Chemical and Biological Physics Weizmann Institute of Sciences Rehovot Israel
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37
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Torosyan A, Wiegand T, Schledorn M, Klose D, Güntert P, Böckmann A, Meier BH. Including Protons in Solid-State NMR Resonance Assignment and Secondary Structure Analysis: The Example of RNA Polymerase II Subunits Rpo4/7. Front Mol Biosci 2019; 6:100. [PMID: 31637245 PMCID: PMC6787281 DOI: 10.3389/fmolb.2019.00100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/17/2019] [Indexed: 11/18/2022] Open
Abstract
1H-detected solid-state NMR experiments feasible at fast magic-angle spinning (MAS) frequencies allow accessing 1H chemical shifts of proteins in solids, which enables their interpretation in terms of secondary structure. Here we present 1H and 13C-detected NMR spectra of the RNA polymerase subunit Rpo7 in complex with unlabeled Rpo4 and use the 13C, 15N, and 1H chemical-shift values deduced from them to study the secondary structure of the protein in comparison to a known crystal structure. We applied the automated resonance assignment approach FLYA including 1H-detected solid-state NMR spectra and show its success in comparison to manual spectral assignment. Our results show that reasonably reliable secondary-structure information can be obtained from 1H secondary chemical shifts (SCS) alone by using the sum of 1Hα and 1HN SCS rather than by TALOS. The confidence, especially at the boundaries of the observed secondary structure elements, is found to increase when evaluating 13C chemical shifts, here either by using TALOS or in terms of 13C SCS.
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Affiliation(s)
- Anahit Torosyan
- Physical Chemistry, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Thomas Wiegand
- Physical Chemistry, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Maarten Schledorn
- Physical Chemistry, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Daniel Klose
- Physical Chemistry, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Peter Güntert
- Physical Chemistry, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland.,Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.,Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, MMSB, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Beat H Meier
- Physical Chemistry, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
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38
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Gallo A, Franks WT, Lewandowski JR. A suite of solid-state NMR experiments to utilize orphaned magnetization for assignment of proteins using parallel high and low gamma detection. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 305:219-231. [PMID: 31319283 DOI: 10.1016/j.jmr.2019.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 05/18/2023]
Abstract
We present a suite of two-receiver solid-state NMR experiments for backbone and side chain resonance assignment. The experiments rely on either dipolar coupling or scalar coupling for polarization transfer and are devised to acquire a 1H-detected 3D experiment AND a nested 13C-detected 2D from a shared excitation pulse. In order to compensate for the lower sensitivity of detection on 13C nucleus, 2D rows are signal averaged during 3D planes. The 3D dual receiver experiments do not suffer from any appreciable signal loss compared to their single receiver versions and require no extra optimization. The resulting data is higher in information content with no additional experiment time. The approach is expected to become widespread as multiple receivers become standard for new NMR spectrometers.
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Affiliation(s)
- A Gallo
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK
| | - W T Franks
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK; Department of Physics, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK
| | - J R Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill Road, CV4 7AL Coventry, UK.
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39
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Hwang S, Öster C, Chevelkov V, Giller K, Lange S, Becker S, Lange A. Characterization of H/D exchange in type 1 pili by proton-detected solid-state NMR and molecular dynamics simulations. JOURNAL OF BIOMOLECULAR NMR 2019; 73:281-291. [PMID: 31028572 PMCID: PMC6692446 DOI: 10.1007/s10858-019-00247-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Uropathogenic Escherichia coli invades and colonizes hosts by attaching to cells using adhesive pili on the bacterial surface. Although many biophysical techniques have been used to study the structure and mechanical properties of pili, many important details are still unknown. Here we use proton-detected solid-state NMR experiments to investigate solvent accessibility and structural dynamics. Deuterium back-exchange at labile sites of the perdeuterated, fully proton back-exchanged pili was conducted to investigate hydrogen/deuterium (H/D) exchange patterns of backbone amide protons in pre-assembled pili. We found distinct H/D exchange patterns in lateral and axial intermolecular interfaces in pili. Amide protons protected from H/D exchange in pili are mainly located in the core region of the monomeric subunit and in the lateral intermolecular interface, whereas the axial intermolecular interface and the exterior region of pili are highly exposed to H/D exchange. Additionally, we performed molecular dynamics simulations of the type 1 pilus rod and estimated the probability of H/D exchange based on hydrogen bond dynamics. The comparison of the experimental observables and simulation data provides insights into stability and mechanical properties of pili.
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Affiliation(s)
- Songhwan Hwang
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
- Institut für Biologie, Humboldt-Universität Zu Berlin, Berlin, Germany.
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40
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Grohe K, Nimerovsky E, Singh H, Vasa SK, Söldner B, Vögeli B, Rienstra CM, Linser R. Exact distance measurements for structure and dynamics in solid proteins by fast-magic-angle-spinning NMR. Chem Commun (Camb) 2019; 55:7899-7902. [PMID: 31199417 DOI: 10.1039/c9cc02317h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fast-magic-angle-spinning solid-state NMR is a developing technique for determination of protein structure and dynamics. Proton-proton correlations usually lead to rough distance restraints, a serious hurdle towards high-resolution structures. Analogous to the "eNOE" concept in solution, an integrative approach for more accurate restraints enables improved structural accuracy with minimal analytical effort.
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Affiliation(s)
- Kristof Grohe
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany. and Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Evgeny Nimerovsky
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Himanshu Singh
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany. and Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Suresh K Vasa
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany. and Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
| | - Benedikt Söldner
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO 80045, USA
| | - Chad M Rienstra
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Rasmus Linser
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany. and Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
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41
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Zhang Z, Liu H, Deng J, Tycko R, Yang J. Optimization of band-selective homonuclear dipolar recoupling in solid-state NMR by a numerical phase search. J Chem Phys 2019; 150:154201. [PMID: 31005077 DOI: 10.1063/1.5092986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Spin polarization transfers among aliphatic 13C nuclei, especially 13Cα-13Cβ transfers, permit correlations of their nuclear magnetic resonance (NMR) frequencies that are essential for signal assignments in multidimensional solid-state NMR of proteins. We derive and demonstrate a new radio-frequency (RF) excitation sequence for homonuclear dipolar recoupling that enhances spin polarization transfers among aliphatic 13C nuclei at moderate magic-angle spinning (MAS) frequencies. The phase-optimized recoupling sequence with five π pulses per MAS rotation period (denoted as PR5) is derived initially from systematic numerical simulations in which only the RF phases are varied. Subsequent theoretical analysis by average Hamiltonian theory explains the favorable properties of numerically optimized phase schemes. The high efficiency of spin polarization transfers in simulations is preserved in experiments, in part because the RF field amplitude in PR5 is only 2.5 times the MAS frequency so that relatively low 1H decoupling powers are required. Experiments on a microcrystalline sample of the β1 immunoglobulin binding domain of protein G demonstrate an average enhancement factor of 1.6 for 13Cα → 13Cβ polarization transfers, compared to the standard 13C-13C spin-diffusion method, implying a two-fold time saving in relevant 2D and 3D experiments.
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Affiliation(s)
- Zhengfeng Zhang
- 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, People's Republic of China
| | - Hui 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, People's Republic of China
| | - Jing Deng
- 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, People's Republic of China
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Jun Yang
- 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, People's Republic of China
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42
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Identifying coupled clusters of allostery participants through chemical shift perturbations. Proc Natl Acad Sci U S A 2019; 116:2078-2085. [PMID: 30679272 DOI: 10.1073/pnas.1811168116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Allosteric couplings underlie many cellular signaling processes and provide an exciting avenue for development of new diagnostics and therapeutics. A general method for identifying important residues in allosteric mechanisms would be very useful, but remains elusive due to the complexity of long-range phenomena. Here, we introduce an NMR method to identify residues involved in allosteric coupling between two ligand-binding sites in a protein, which we call chemical shift detection of allostery participants (CAP). Networks of functional groups responding to each ligand are defined through correlated NMR perturbations. In this process, we also identify allostery participants, groups that respond to both binding events and likely play a role in the coupling between the binding sites. Such residues exhibit multiple functional states with distinct NMR chemical shifts, depending on binding status at both binding sites. Such a strategy was applied to the prototypical ion channel KcsA. We had previously shown that the potassium affinity at the extracellular selectivity filter is strongly dependent on proton binding at the intracellular pH sensor. Here, we analyzed proton and potassium binding networks and identified groups that depend on both proton and potassium binding (allostery participants). These groups are viewed as candidates for transmitting information between functional units. The vital role of one such identified amino acid was validated through site-specific mutagenesis, electrophysiology functional studies, and NMR-detected thermodynamic analysis of allosteric coupling. This strategy for identifying allostery participants is likely to have applications for many other systems.
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43
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Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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44
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Zinke M, Fricke P, Lange S, Zinn‐Justin S, Lange A. Protein-Protein Interfaces Probed by Methyl Labeling and Proton-Detected Solid-State NMR Spectroscopy. Chemphyschem 2018; 19:2457-2460. [PMID: 29917302 PMCID: PMC6220863 DOI: 10.1002/cphc.201800542] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 12/18/2022]
Abstract
Proton detection and fast magic-angle spinning have advanced biological solid-state NMR, allowing for the backbone assignment of complex protein assemblies with high sensitivity and resolution. However, so far no method has been proposed to detect intermolecular interfaces in these assemblies by proton detection. Herein, we introduce a concept based on methyl labeling that allows for the assignment of these moieties and for the study of protein-protein interfaces at atomic resolution.
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Affiliation(s)
- Maximilian Zinke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Pascal Fricke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sascha Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sophie Zinn‐Justin
- Institute for Integrative Biology of the Cell (I2BC) CEA, CNRSUniversité Paris-Sud Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Adam Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- Institut für BiologieHumboldt-Universität zu BerlinBerlinGermany
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45
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Gelenter MD, Hong M. Efficient 15N- 13C Polarization Transfer by Third-Spin-Assisted Pulsed Cross-Polarization Magic-Angle-Spinning NMR for Protein Structure Determination. J Phys Chem B 2018; 122:8367-8379. [PMID: 30106585 DOI: 10.1021/acs.jpcb.8b06400] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We introduce a pulsed third-spin-assisted recoupling experiment that produces high-intensity long-range 15N-13C cross peaks using low radiofrequency (rf) energy. This Proton-Enhanced Rotor-echo Short-Pulse IRradiATION Cross-Polarization (PERSPIRATIONCP) pulse sequence operates with the same principle as the Proton-Assisted Insensitive-Nuclei Cross-Polarization (PAINCP) experiment but uses only a fraction of the rf energy by replacing continuous-wave 13C and 15N irradiation with rotor-echo 90° pulses. Using formyl-Met-Leu-Phe (f-MLF) and β1 immunoglobulin binding domain of protein G (GB1) as model proteins, we demonstrate experimentally how PERSPIRATIONCP polarization transfer depends on the CP contact time, rf power, pulse flip angle, and 13C carrier frequency and compare the PERSPIRATIONCP performance with the performances of PAINCP, RESPIRATIONCP, and SPECIFICCP for measuring 15N-13C cross peaks. PERSPIRATIONCP achieves long-range 15N-13C transfer and yields higher cross peak-intensities than that of the other techniques. Numerical simulations reproduce the experimental trends and moreover indicate that PERSPIRATIONCP relies on 15N-1H and 13C-1H dipolar couplings rather than 15N-13C dipolar coupling for polarization transfer. Therefore, PERSPIRATIONCP is an rf-efficient and higher-sensitivity alternative to PAINCP for measuring long-range 15N-13C correlations, which are essential for protein resonance assignment and structure determination. Using cross peaks from two PERSPIRATIONCP 15N-13C correlation spectra as the sole distance restraints, supplemented with (φ, ψ) torsion angles obtained from chemical shifts, we calculated the GB1 structure and obtained a backbone root-mean-square deviation of 2.0 Å from the high-resolution structure of the protein. Therefore, this rf-efficient PERSPIRATIONCP method is useful for obtaining many long-range distance restraints for protein structure determination.
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Affiliation(s)
- Martin D Gelenter
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Mei Hong
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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46
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Higman VA. Solid-state MAS NMR resonance assignment methods for proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 106-107:37-65. [PMID: 31047601 DOI: 10.1016/j.pnmrs.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 06/09/2023]
Abstract
The prerequisite to structural or functional studies of proteins by NMR is generally the assignment of resonances. Since the first assignment of proteins by solid-state MAS NMR was conducted almost two decades ago, a wide variety of different pulse sequences and methods have been proposed and continue to be developed. Traditionally, a variety of 2D and 3D 13C-detected experiments have been used for the assignment of backbone and side-chain 13C and 15N resonances. These methods have found widespread use across the field. But as the hardware has changed and higher spinning frequencies and magnetic fields are becoming available, the ability to use direct proton detection is opening up a new set of assignment methods based on triple-resonance experiments. This review describes solid-state MAS NMR assignment methods using carbon detection and proton detection at different deuteration levels. The use of different isotopic labelling schemes as an aid to assignment in difficult cases is discussed as well as the increasing number of software packages that support manual and automated resonance assignment.
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Affiliation(s)
- Victoria A Higman
- Department of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TU, UK.
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47
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Stöppler D, Macpherson A, Smith-Penzel S, Basse N, Lecomte F, Deboves H, Taylor RD, Norman T, Porter J, Waters LC, Westwood M, Cossins B, Cain K, White J, Griffin R, Prosser C, Kelm S, Sullivan AH, Fox D, Carr MD, Henry A, Taylor R, Meier BH, Oschkinat H, Lawson AD. Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR. PLoS Biol 2018; 16:e2006192. [PMID: 29782488 PMCID: PMC5983862 DOI: 10.1371/journal.pbio.2006192] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/01/2018] [Accepted: 05/02/2018] [Indexed: 01/09/2023] Open
Abstract
Aiming at the design of an allosteric modulator of the neonatal Fc receptor (FcRn)-Immunoglobulin G (IgG) interaction, we developed a new methodology including NMR fragment screening, X-ray crystallography, and magic-angle-spinning (MAS) NMR at 100 kHz after sedimentation, exploiting very fast spinning of the nondeuterated soluble 42 kDa receptor construct to obtain resolved proton-detected 2D and 3D NMR spectra. FcRn plays a crucial role in regulation of IgG and serum albumin catabolism. It is a clinically validated drug target for the treatment of autoimmune diseases caused by pathogenic antibodies via the inhibition of its interaction with IgG. We herein present the discovery of a small molecule that binds into a conserved cavity of the heterodimeric, extracellular domain composed of an α-chain and β2-microglobulin (β2m) (FcRnECD, 373 residues). X-ray crystallography was used alongside NMR at 100 kHz MAS with sedimented soluble protein to explore possibilities for refining the compound as an allosteric modulator. Proton-detected MAS NMR experiments on fully protonated [13C,15N]-labeled FcRnECD yielded ligand-induced chemical-shift perturbations (CSPs) for residues in the binding pocket and allosteric changes close to the interface of the two receptor heterodimers present in the asymmetric unit as well as potentially in the albumin interaction site. X-ray structures with and without ligand suggest the need for an optimized ligand to displace the α-chain with respect to β2m, both of which participate in the FcRnECD-IgG interaction site. Our investigation establishes a method to characterize structurally small molecule binding to nondeuterated large proteins by NMR, even in their glycosylated form, which may prove highly valuable for structure-based drug discovery campaigns.
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Affiliation(s)
- Daniel Stöppler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | | | | | | | | | | | | | | | | | - Lorna C. Waters
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
| | | | | | | | | | | | | | | | - Amy H. Sullivan
- Beryllium Discovery, Bedford, Massachusetts, United States of America
| | - David Fox
- Beryllium Discovery, Bedford, Massachusetts, United States of America
| | - Mark D. Carr
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom
| | | | | | - Beat H. Meier
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
- * E-mail: (HO); (ADL)
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48
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Tan KO, Agarwal V, Lakomek NA, Penzel S, Meier BH, Ernst M. Efficient low-power TOBSY sequences for fast MAS. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 89:27-34. [PMID: 29233617 DOI: 10.1016/j.ssnmr.2017.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
Through-bond J-coupling based experiments in solid-state NMR spectroscopy are challenging because the J couplings are typically much smaller than the dipolar couplings. This often leads to a lower transfer efficiency compared to dipolar-coupling based sequences. One of the reasons for the low transfer efficiency are the second-order cross terms involving the strong heteronuclear dipolar couplings leading to fast magnetization decay. Here, we show that by employing a symmetry-based C9 sequence, which was carefully selected to suppress second-order terms, efficient polarization transfers of up to 80% can be achieved without decoupling on fully protonated two-spin model systems at a MAS frequency of 55.5 kHz with rf-field amplitudes of about 25 kHz. In addition, we analyse the effects of rf inhomogeneity and crystallites selection due to the polarization preparation method on the TOBSY transfer efficiency. We demonstrate on small model substances as well as on deuterated and 100% back-exchanged ubiquitin that C9391 and C9481 are efficient and practical TOBSY sequences at experimental conditions ranging from proton Larmor frequencies of 400-850 MHz, and MAS frequencies ranging from 55.5 to 111.1 kHz.
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Affiliation(s)
- Kong Ooi Tan
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Vipin Agarwal
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | | | - Susanne Penzel
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.
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49
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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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50
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Gopinath T, Veglia G. Experimental Aspects of Polarization Optimized Experiments (POE) for Magic Angle Spinning Solid-State NMR of Microcrystalline and Membrane-Bound Proteins. Methods Mol Biol 2018; 1688:37-53. [PMID: 29151203 DOI: 10.1007/978-1-4939-7386-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Conventional NMR pulse sequences record one spectrum per experiment, while spending most of the time waiting for the spin system to return to the equilibrium. As a result, a full set of multidimensional NMR experiments for biological macromolecules may take up to several months to complete. Here, we present a practical guide for setting up a new class of MAS solid-state NMR experiments (POE or polarization optimized experiments) that enable the simultaneous acquisition of multiple spectra of proteins, accelerating data acquisition. POE exploit the long-lived 15N polarization of isotopically labeled proteins and enable one to obtain up to eight spectra, by concatenating classical NMR pulse sequences. This new strategy propels data throughput of solid-state NMR spectroscopy of fibers, microcrystalline preparations, as well as membrane proteins.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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