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Cerofolini L, Parigi G, Ravera E, Fragai M, Luchinat C. Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101828. [PMID: 36240720 DOI: 10.1016/j.ssnmr.2022.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.
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Affiliation(s)
- Linda Cerofolini
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy; Florence Data Science, Università degli Studi di Firenze, Italy.
| | - Marco Fragai
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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2
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Rodriguez J, Boudjelel M, Mueller LJ, Schrock RR, Conley MP. Ring Contraction of a Tungstacyclopentane Supported on Silica: Direct Conversion of Ethylene to Propylene. J Am Chem Soc 2022; 144:18761-18765. [PMID: 36197795 DOI: 10.1021/jacs.2c07934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction of W(NAr)(13C4H8)(OSiPh3)2 (1) (NAr = 2,6-diisopropylphenylimido) with silica partially dehydroxylated at 700 °C (SiO2-700) is highly dependent on the reaction conditions. The primary product of this reaction is W(NAr)(13C4H8)(OSiPh3)(OSi(O-)3) (2) when the reaction is carried out in the dark. Grafting 1 onto SiO2-700 in ambient lab light results in the formation of 2, W(NAr)(13CH213CH2)(OSiPh3)(OSi(O-)3) (4), and one isomer of square-pyramidal W(NAr)(13CH213CH(13Me)13CH2)(OSiPh3)(OSi(O-)3) (3). Heating 2 to 85 °C for 6 h results in the formation of 3, 4, W(NAr)(13CH(13Me)13CH213CH2)(OSiPh3)(OSi(O-)3) (5), and W(NAr)((13CH2)213CH(13Me)(13CH2)2)(OSiPh3)(OSi(O-)3) (6). Photolysis of 2 with blue LEDs (λmax = 450 nm) produces 4, both isomers of 3, 5, and free ethylene. In the presence of excess ethylene and blue LED irradiation at 85 °C, 1/SiO2-700 catalyzes the direct conversion of ethylene to propylene.
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Affiliation(s)
- Jessica Rodriguez
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Maxime Boudjelel
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Richard R Schrock
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Matthew P Conley
- Department of Chemistry, University of California, Riverside, California 92521, United States
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3
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Adiram-Filiba N, Ohaion E, Verner G, Schremer A, Nadav-Tsubery M, Lublin-Tennenbaum T, Keinan-Adamsky K, Lucci M, Luchinat C, Ravera E, Goobes G. Structure and Dynamics Perturbations in Ubiquitin Adsorbed or Entrapped in Silica Materials Are Related to Disparate Surface Chemistries Resolved by Solid-State NMR Spectroscopy. Biomacromolecules 2021; 22:3718-3730. [PMID: 34333966 DOI: 10.1021/acs.biomac.1c00495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein immobilization on material surfaces is emerging as a powerful tool in the design of devices and active materials for biomedical and pharmaceutical applications as well as for catalysis. Preservation of the protein's biological functionality is crucial to the design process and is dependent on the ability to maintain its structural and dynamical integrity while removed from the natural surroundings. The scientific techniques to validate the structure of immobilized proteins are scarce and usually provide limited information as a result of poor resolution. In this work, we benchmarked the ability of standard solid-state NMR techniques to resolve the effects of binding to dissimilar silica materials on a model protein. In particular, the interactions between ubiquitin and the surfaces of MCM41, SBA15, and silica formed in situ were tested for their influence on the structure and dynamics of the protein. It is shown that the protein's globular fold in the free state is only slightly perturbed in the three silica materials. Local motions on a residue level that are quenched by immobilization or, conversely, that arise from the process are also detailed. NMR measurements show that these perturbations are unique to each silica material and can serve as reporters of the characteristic surface chemistry.
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Affiliation(s)
| | - Eli Ohaion
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Gilit Verner
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Avital Schremer
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | | | | | | | - Massimo Lucci
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Gil Goobes
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
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4
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Fritzsching KJ, Keeler EG, He C, McDermott AE. Scaled recoupling of chemical shift anisotropies at high magnetic fields under MAS with interspersed C-elements. J Chem Phys 2021; 153:104201. [PMID: 32933302 DOI: 10.1063/5.0020682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The power of chemical shift anisotropy (CSA) measurements for probing structure and dynamics of molecules has been long recognized. NMR pulse sequences that allow measurement of CSA values in an indirect dimension of a protein correlation spectrum have been employed for aliphatic groups, but for practical reasons, carbonyl functional groups have been little studied, despite the fact that carbonyls are expected to give particularly varied and informative CSA values. Specifically, the wide spectral widths of carbonyl tensors make their measurements difficult with typically attainable spectrometer settings. We present here an extended family of experiments that enable the recovery of static CSA lineshapes in an indirect dimension of magic angle spinning (MAS) solid-state NMR experiments, except for various real valued scaling factors. The experiment is suitable for uniformly labeled material, at moderate MAS rates (10 kHz-30 kHz) and at higher magnetic fields (ν0H > 600 MHz). Specifically, the experiments are based on pulse sequence elements from a previous commonly used pulse sequence for CSA measurement, recoupling of chemical shift anisotropy (ROCSA), while modification of scaling factors is achieved by interspersing different blocks of C-elements of the same Cnn 1 cycle. Using experimental conditions similar to the parent ROCSA sequence, a CSA scaling factor between 0 and 0.272 can be obtained, thus allowing a useful practical range of possibilities in experimental conditions for measurement of larger CSA values. Using these blocks, it is also possible to make a constant-time CSA recoupling sequence. The effectiveness of this approach, fROCSA, is shown on model compounds 1-13C-Gly, U-13C,15N-l-His, and microcrystalline U-13C,15N-Ubiquitin.
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Affiliation(s)
| | - Eric G Keeler
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Chengming He
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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5
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Shaw WJ, Tarasevich BJ, Buchko GW, Arachchige RMJ, Burton SD. Controls of nature: Secondary, tertiary, and quaternary structure of the enamel protein amelogenin in solution and on hydroxyapatite. J Struct Biol 2020; 212:107630. [PMID: 32979496 PMCID: PMC7744360 DOI: 10.1016/j.jsb.2020.107630] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/12/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
Amelogenin, a protein critical to enamel formation, is presented as a model for understanding how the structure of biomineralization proteins orchestrate biomineral formation. Amelogenin is the predominant biomineralization protein in the early stages of enamel formation and contributes to the controlled formation of hydroxyapatite (HAP) enamel crystals. The resulting enamel mineral is one of the hardest tissues in the human body and one of the hardest biominerals in nature. Structural studies have been hindered by the lack of techniques to evaluate surface adsorbed proteins and by amelogenin's disposition to self-assemble. Recent advancements in solution and solid state nuclear magnetic resonance (NMR) spectroscopy, atomic force microscopy (AFM), and recombinant isotope labeling strategies are now enabling detailed structural studies. These recent studies, coupled with insights from techniques such as CD and IR spectroscopy and computational methodologies, are contributing to important advancements in our structural understanding of amelogenesis. In this review we focus on recent advances in solution and solid state NMR spectroscopy and in situ AFM that reveal new insights into the secondary, tertiary, and quaternary structure of amelogenin by itself and in contact with HAP. These studies have increased our understanding of the interface between amelogenin and HAP and how amelogenin controls enamel formation.
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Affiliation(s)
- Wendy J Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Barbara J Tarasevich
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA; School of Molecular Bioscience, Washington State University, Pullman, WA 99164, USA
| | - Rajith M J Arachchige
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah D Burton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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6
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Lin B, Hung I, Gan Z, Chien PH, Spencer HL, Smith SP, Wu G. 17 O NMR Studies of Yeast Ubiquitin in Aqueous Solution and in the Solid State. Chembiochem 2020; 22:826-829. [PMID: 33058374 DOI: 10.1002/cbic.202000659] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Indexed: 12/18/2022]
Abstract
We report a general method for amino acid-type specific 17 O-labeling of recombinant proteins in Escherichia coli. In particular, we have prepared several [1-13 C,17 O]-labeled yeast ubiquitin (Ub) samples including Ub-[1-13 C,17 O]Gly, Ub-[1-13 C,17 O]Tyr, and Ub-[1-13 C,17 O]Phe using the auxotrophic E. coli strain DL39 GlyA λDE3 (aspC- tyrB- ilvE- glyA- λDE3). We have also produced Ub-[η-17 O]Tyr, in which the phenolic group of Tyr59 is 17 O-labeled. We show for the first time that 17 O NMR signals from protein terminal residues and side chains can be readily detected in aqueous solution. We also reported solid-state 17 O NMR spectra for Ub-[1-13 C,17 O]Tyr and Ub-[1-13 C,17 O]Phe obtained at an ultrahigh magnetic field, 35.2 T (1.5 GHz for 1 H). This work represents a significant advance in the field of 17 O NMR studies of proteins.
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Affiliation(s)
- Binyang Lin
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ivan Hung
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Zhehong Gan
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Po-Hsiu Chien
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Holly L Spencer
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
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7
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The Droserasin 1 PSI: A Membrane-Interacting Antimicrobial Peptide from the Carnivorous Plant Drosera capensis. Biomolecules 2020; 10:biom10071069. [PMID: 32709016 PMCID: PMC7407137 DOI: 10.3390/biom10071069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
The Droserasins, aspartic proteases from the carnivorous plant Drosera capensis, contain a 100-residue plant-specific insert (PSI) that is post-translationally cleaved and independently acts as an antimicrobial peptide. PSIs are of interest not only for their inhibition of microbial growth, but also because they modify the size of lipid vesicles and strongly interact with biological membranes. PSIs may therefore be useful for modulating lipid systems in NMR studies of membrane proteins. Here we present the expression and biophysical characterization of the Droserasin 1 PSI (D1 PSI.) This peptide is monomeric in solution and maintains its primarily α-helical secondary structure over a wide range of temperatures and pH values, even under conditions where its three disulfide bonds are reduced. Vesicle fusion assays indicate that the D1 PSI strongly interacts with bacterial and fungal lipids at pH 5 and lower, consistent with the physiological pH of D. capensis mucilage. It binds lipids with a variety of head groups, highlighting its versatility as a potential stabilizer for lipid nanodiscs. Solid-state NMR spectra collected at a field strength of 36 T, using a unique series-connected hybrid magnet, indicate that the peptide is folded and strongly bound to the membrane. Molecular dynamics simulations indicate that the peptide is stable as either a monomer or a dimer in a lipid bilayer. Both the monomer and the dimer allow the passage of water through the membrane, albeit at different rates.
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8
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Li J, Sae Her A, Traaseth NJ. Site-specific resolution of anionic residues in proteins using solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2020; 74:355-363. [PMID: 32514875 PMCID: PMC7472563 DOI: 10.1007/s10858-020-00323-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
NMR spectroscopy is commonly used to infer site-specific acid dissociation constants (pKa) since the chemical shift is sensitive to the protonation state. Methods that probe atoms nearest to the functional groups involved in acid/base chemistry are the most sensitive for determining the protonation state. In this work, we describe a magic-angle-spinning (MAS) solid-state NMR approach to measure chemical shifts on the side chain of the anionic residues aspartate and glutamate. This method involves a combination of double quantum spectroscopy in the indirect dimension and REDOR dephasing to provide a sensitive and resolved view of these amino acid residues that are commonly involved in enzyme catalysis and membrane protein transport. To demonstrate the applicability of the approach, we carried out measurements using a microcrystalline soluble protein (ubiquitin) and a membrane protein embedded in lipid bilayers (EmrE). Overall, the resolution available from the double quantum dimension and confidence in identification of aspartate and glutamate residues from the REDOR filter make this method the most convenient for characterizing protonation states and deriving pKa values using MAS solid-state NMR.
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Affiliation(s)
- Jianping Li
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Ampon Sae Her
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Nathaniel J Traaseth
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA.
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Abstract
The epididymal lumen contains a complex cystatin-rich nonpathological amyloid matrix with putative roles in sperm maturation and sperm protection. Given our growing understanding for the biological function of this and other functional amyloids, the problem still remains: how functional amyloids assemble including their initial transition to early oligomeric forms. To examine this, we developed a protocol for the purification of nondenatured mouse CRES, a component of the epididymal amyloid matrix, allowing us to examine its assembly to amyloid under conditions that may mimic those in vivo. Herein we use X-ray crystallography, solution-state NMR, and solid-state NMR to follow at the atomic level the assembly of the CRES amyloidogenic precursor as it progressed from monomeric folded protein to an advanced amyloid. We show the CRES monomer has a typical cystatin fold that assembles into highly branched amyloid matrices, comparable to those in vivo, by forming β-sheet assemblies that our data suggest occur via two distinct mechanisms: a unique conformational switch of a highly flexible disulfide-anchored loop to a rigid β-strand and by traditional cystatin domain swapping. Our results provide key insight into our understanding of functional amyloid assembly by revealing the earliest structural transitions from monomer to oligomer and by showing that some functional amyloid structures may be built by multiple and distinctive assembly mechanisms.
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Nagaraj M, Ahmed M, Lyngsø J, Vad BS, Bøggild A, Fillipsen A, Pedersen JS, Otzen DE, Akbey Ü. Predicted Loop Regions Promote Aggregation: A Study of Amyloidogenic Domains in the Functional Amyloid FapC. J Mol Biol 2020; 432:2232-2252. [DOI: 10.1016/j.jmb.2020.01.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/27/2020] [Accepted: 01/27/2020] [Indexed: 02/08/2023]
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11
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Malär AA, Smith-Penzel S, Camenisch GM, Wiegand T, Samoson A, Böckmann A, Ernst M, Meier BH. Quantifying proton NMR coherent linewidth in proteins under fast MAS conditions: a second moment approach. Phys Chem Chem Phys 2019; 21:18850-18865. [PMID: 31432055 DOI: 10.1039/c9cp03414e] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proton detected solid-state NMR under fast magic-angle-spinning (MAS) conditions is currently redefining the applications of solid-state NMR, in particular in structural biology. Understanding the contributions to the spectral linewidth is thereby of paramount importance. When disregarding the sample-dependent inhomogeneous contributions, the NMR proton linewidth is defined by homogeneous broadening, which has incoherent and coherent contributions. Understanding and disentangling these different contributions in multi-spin systems like proteins is still an open issue. The coherent contribution is mainly caused by the dipolar interaction under MAS and is determined by the molecular structure and the proton chemical shifts. Numerical simulation approaches based on numerically exact direct integration of the Liouville-von Neumann equation can give valuable information about the lineshape, but are limited to small spin systems (<12 spins). We present an alternative simulation method for the coherent contributions based on the rapid and partially analytic calculation of the second moments of large spin systems. We first validate the method on a simple system by predicting the 19F linewidth in CaF2 under MAS. We compare simulation results to experimental data for microcrystalline ubiquitin (deuterated 100% back-exchanged at 110 kHz and fully-protonated at 125 kHz). Our results quantitatively explain the observed linewidth per-residue basis for the vast majority of residues.
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Affiliation(s)
- Alexander A Malär
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Susanne Smith-Penzel
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Gian-Marco Camenisch
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Ago Samoson
- School of Information Technologies, Tallinn University of Technology, Tallinn, Estonia. and NMR Institute MTÜ, Tallinn, Estonia
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367 Lyon, France.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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12
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Gopinath T, Wang S, Lee J, Aihara H, Veglia G. Hybridization of TEDOR and NCX MAS solid-state NMR experiments for simultaneous acquisition of heteronuclear correlation spectra and distance measurements. JOURNAL OF BIOMOLECULAR NMR 2019; 73:141-153. [PMID: 30805819 PMCID: PMC6526076 DOI: 10.1007/s10858-019-00237-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/12/2019] [Indexed: 05/05/2023]
Abstract
Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is a major technique for the characterization of the structural dynamics of biopolymers at atomic resolution. However, the intrinsic low sensitivity of this technique poses significant limitations to its routine application in structural biology. Here we achieve substantial savings in experimental time using a new subclass of Polarization Optimized Experiments (POEs) that concatenate TEDOR and SPECIFIC-CP transfers into a single pulse sequence. Specifically, we designed new 2D and 3D experiments (2D TEDOR-NCX, 3D TEDOR-NCOCX, and 3D TEDOR-NCACX) to obtain distance measurements and heteronuclear chemical shift correlations for resonance assignments using only one experiment. We successfully tested these experiments on N-Acetyl-Val-Leu dipeptide, microcrystalline U-13C,15N ubiquitin, and single- and multi-span membrane proteins reconstituted in lipid membranes. These pulse sequences can be implemented on any ssNMR spectrometer equipped with standard solid-state hardware using only one receiver. Since these new POEs speed up data acquisition considerably, we anticipate their broad application to fibrillar, microcrystalline, and membrane-bound proteins.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - John Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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Duan P, Schmidt-Rohr K. Quick, selective NMR spectra of COH moieties in 13C-enriched solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 301:80-84. [PMID: 30852301 DOI: 10.1016/j.jmr.2019.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 02/21/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
A convenient one-dimensional magic-angle spinning NMR method is presented that provides selective NMR spectra of COH moieties in uniformly 13C-enriched organic materials. This method, termed hydroxyl-proton selection (HOPS), eliminates the magnetization of protons directly bonded to carbons by recoupling the 1H-13C dipolar interaction for a short time (∼70 μs), which also serves as a chemical-shift filter to suppress 1H magnetization of CH3 groups. After cross polarization to 13C, the signals of COH and COOH carbons are observed selectively. This makes it possible to distinguish alcohols from ethers, in particular phenols from aromatic ethers such as the furans often formed by dehydration of glucose, and carboxylic acids from carboxylates and ethers. HOPS NMR reveals that orthodiphenols are often a major component of low-temperature carbon materials. For instance, it forces the reassignment of the 143 ppm 13C NMR signal of hydrothermal carbon to such catecholic diphenols, while a previous NMR-based structural model had attributed this peak to a central furan-furan linkage.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Brandeis University, Waltham, MA 02453, United States
| | - Klaus Schmidt-Rohr
- Department of Chemistry, Brandeis University, Waltham, MA 02453, United States.
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14
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Lends A, Ravotti F, Zandomeneghi G, Böckmann A, Ernst M, Meier BH. Direct amide 15N to 13C transfers for solid-state assignment experiments in deuterated proteins. JOURNAL OF BIOMOLECULAR NMR 2018; 72:69-78. [PMID: 30206780 DOI: 10.1007/s10858-018-0207-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
The assignment of protein backbone and side-chain NMR chemical shifts is the first step towards the characterization of protein structure. The recent introduction of proton detection in combination with fast MAS has opened up novel opportunities for assignment experiments. However, typical 3D sequential-assignment experiments using proton detection under fast MAS lead to signal intensities much smaller than the theoretically expected ones due to the low transfer efficiency of some of the steps. Here, we present a selective 3D experiment for deuterated and (amide) proton back-exchanged proteins where polarization is directly transferred from backbone nitrogen to selected backbone or sidechain carbons. The proposed pulse sequence uses only 1H-15N cross-polarization (CP) transfers, which are, for deuterated proteins, about 30% more efficient than 1H-13C CP transfers, and employs a dipolar version of the INEPT experiment for N-C transfer. By avoiding HN-C (HN stands for amide protons) and C-C CP transfers, we could achieve higher selectivity and increased signal intensities compared to other pulse sequences containing long-range CP transfers. The REDOR transfer is designed with an additional selective π pulse, which enables the selective transfer of the polarization to the desired 13C spins.
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Affiliation(s)
- Alons Lends
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Francesco Ravotti
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Giorgia Zandomeneghi
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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15
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Penzel S, Smith AA, Ernst M, Meier BH. Setting the magic angle for fast magic-angle spinning probes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 293:115-122. [PMID: 29929181 DOI: 10.1016/j.jmr.2018.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Fast magic-angle spinning, coupled with 1H detection is a powerful method to improve spectral resolution and signal to noise in solid-state NMR spectra. Commercial probes now provide spinning frequencies in excess of 100 kHz. Then, one has sufficient resolution in the 1H dimension to directly detect protons, which have a gyromagnetic ratio approximately four times larger than 13C spins. However, the gains in sensitivity can quickly be lost if the rotation angle is not set precisely. The most common method of magic-angle calibration is to optimize the number of rotary echoes, or sideband intensity, observed on a sample of KBr. However, this typically uses relatively low spinning frequencies, where the spinning of fast-MAS probes is often unstable, and detection on the 13C channel, for which fast-MAS probes are typically not optimized. Therefore, we compare the KBr-based optimization of the magic angle with two alternative approaches: optimization of the splitting observed in 13C-labeled glycine-ethylester on the carbonyl due to the Cα-C' J-coupling, or optimization of the H-N J-coupling spin echo in the protein sample itself. The latter method has the particular advantage that no separate sample is necessary for the magic-angle optimization.
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Affiliation(s)
- Susanne Penzel
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Albert A Smith
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Matthias Ernst
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Beat H Meier
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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16
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Higman VA. Solid-state MAS NMR resonance assignment methods for proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 106-107:37-65. [PMID: 31047601 DOI: 10.1016/j.pnmrs.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 06/09/2023]
Abstract
The prerequisite to structural or functional studies of proteins by NMR is generally the assignment of resonances. Since the first assignment of proteins by solid-state MAS NMR was conducted almost two decades ago, a wide variety of different pulse sequences and methods have been proposed and continue to be developed. Traditionally, a variety of 2D and 3D 13C-detected experiments have been used for the assignment of backbone and side-chain 13C and 15N resonances. These methods have found widespread use across the field. But as the hardware has changed and higher spinning frequencies and magnetic fields are becoming available, the ability to use direct proton detection is opening up a new set of assignment methods based on triple-resonance experiments. This review describes solid-state MAS NMR assignment methods using carbon detection and proton detection at different deuteration levels. The use of different isotopic labelling schemes as an aid to assignment in difficult cases is discussed as well as the increasing number of software packages that support manual and automated resonance assignment.
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Affiliation(s)
- Victoria A Higman
- Department of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TU, UK.
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17
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Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
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18
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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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19
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Ishii Y, Wickramasinghe A, Matsuda I, Endo Y, Ishii Y, Nishiyama Y, Nemoto T, Kamihara T. Progress in proton-detected solid-state NMR (SSNMR): Super-fast 2D SSNMR collection for nano-mole-scale proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 286:99-109. [PMID: 29223566 PMCID: PMC6387629 DOI: 10.1016/j.jmr.2017.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 05/22/2023]
Abstract
Proton-detected solid-state NMR (SSNMR) spectroscopy has attracted much attention due to its excellent sensitivity and effectiveness in the analysis of trace amounts of amyloid proteins and other important biological systems. In this perspective article, we present the recent sensitivity limit of 1H-detected SSNMR using "ultra-fast" magic-angle spinning (MAS) at a spinning rate (νR) of 80-100 kHz. It was demonstrated that the high sensitivity of 1H-detected SSNMR at νR of 100 kHz and fast recycling using the paramagnetic-assisted condensed data collection (PACC) approach permitted "super-fast" collection of 1H-detected 2D protein SSNMR. A 1H-detected 2D 1H-15N correlation SSNMR spectrum for ∼27 nmol of a uniformly 13C- and 15N-labeled GB1 protein sample in microcrystalline form was acquired in only 9 s with 50% non-uniform sampling and short recycle delays of 100 ms. Additional data suggests that it is now feasible to detect as little as 1 nmol of the protein in 5.9 h by 1H-detected 2D 1H-15N SSNMR at a nominal signal-to-noise ratio of five. The demonstrated sensitivity is comparable to that of modern solution protein NMR. Moreover, this article summarizes the influence of ultra-fast MAS and 1H-detection on the spectral resolution and sensitivity of protein SSNMR. Recent progress in signal assignment and structural elucidation by 1H-detected protein SSNMR is outlined with both theoretical and experimental aspects.
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Affiliation(s)
- Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, Kanagawa 226-8503, Japan; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States; The RIKEN Center for Life Science Technologies (CLST), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Ayesha Wickramasinghe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, Kanagawa 226-8503, Japan; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States; The RIKEN Center for Life Science Technologies (CLST), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Isamu Matsuda
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, Kanagawa 226-8503, Japan; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Yuki Endo
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Yuji Ishii
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan; RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Nemoto
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Takayuki Kamihara
- The RIKEN Center for Life Science Technologies (CLST), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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20
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Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational dynamics studied by 15N and 1H R 1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:86-95. [PMID: 28438365 PMCID: PMC5531261 DOI: 10.1016/j.ssnmr.2017.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/01/2017] [Accepted: 04/12/2017] [Indexed: 05/12/2023]
Abstract
Solid-state NMR spectroscopy can provide site-resolved information about protein dynamics over many time scales. Here we combine protein deuteration, fast magic-angle spinning (~45-60kHz) and proton detection to study dynamics of ubiquitin in microcrystals, and in particular a mutant in a region that undergoes microsecond motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation dispersion, to probe how the G53A mutation alters these dynamics. We report a population-inversion of conformational states: the conformation that in the wild-type protein is populated only sparsely becomes the predominant state. We furthermore explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics. We show that while quantitative interpretation of 1H relaxation remains beyond reach under the experimental conditions, due to coherent contributions to decay, one may extract qualitative information about flexibility.
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Affiliation(s)
- Diego F Gauto
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Audrey Hessel
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Petra Rovó
- Ludwig-Maximilians-Universität, Department Chemie, D-81377 München, Germany
| | - Vilius Kurauskas
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Rasmus Linser
- Ludwig-Maximilians-Universität, Department Chemie, D-81377 München, Germany
| | - Paul Schanda
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
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21
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Applications of solid-state NMR to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1577-1586. [PMID: 28709996 DOI: 10.1016/j.bbapap.2017.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022]
Abstract
Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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22
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Donovan KJ, Silvers R, Linse S, Griffin RG. 3D MAS NMR Experiment Utilizing Through-Space 15N- 15N Correlations. J Am Chem Soc 2017; 139:6518-6521. [PMID: 28447786 DOI: 10.1021/jacs.7b01159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We demonstrate a novel 3D NNC magic angle spinning NMR experiment that generates 15N-15N internuclear contacts in protein systems using an optimized 15N-15N proton assisted recoupling (PAR) mixing period and a 13C dimension for improved resolution. The optimized PAR condition permits the acquisition of high signal-to-noise 3D data that enables backbone chemical shift assignments using a strategy that is complementary to current schemes. The spectra can also provide distance constraints. The utility of the experiment is demonstrated on an M0Aβ1-42 fibril sample that yields high-quality data that is readily assigned and interpreted. The 3D NNC experiment therefore provides a powerful platform for solid-state protein studies and is broadly applicable to a variety of systems and experimental conditions.
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Affiliation(s)
- Kevin J Donovan
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Robert Silvers
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University , Lund 221 00, Sweden
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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23
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Mandal A, Boatz JC, Wheeler TB, van der Wel PCA. On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR. JOURNAL OF BIOMOLECULAR NMR 2017; 67:165-178. [PMID: 28229262 PMCID: PMC5445385 DOI: 10.1007/s10858-017-0089-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/19/2017] [Indexed: 05/07/2023]
Abstract
A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation.
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Affiliation(s)
- Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jennifer C Boatz
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Travis B Wheeler
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
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24
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Seuring C, Verasdonck J, Ringler P, Cadalbert R, Stahlberg H, Böckmann A, Meier BH, Riek R. Amyloid Fibril Polymorphism: Almost Identical on the Atomic Level, Mesoscopically Very Different. J Phys Chem B 2017; 121:1783-1792. [PMID: 28075583 DOI: 10.1021/acs.jpcb.6b10624] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amyloid polymorphism of twisted and straight β-endorphin fibrils was studied by negative-stain transmission electron microscopy, scanning transmission electron microscopy, and solid-state nuclear magnetic resonance spectroscopy. Whereas fibrils assembled in the presence of salt formed flat, striated ribbons, in the absence of salt they formed mainly twisted filaments. To get insights into their structural differences at the atomic level, 3D solid-state NMR spectra of both fibril types were acquired, allowing the detection of the differences in chemical shifts of 13C and 15N atoms in both preparations. The spectral fingerprints and therefore the chemical shifts are very similar for both fibril types. This indicates that the monomer structure and the molecular interfaces are almost the same but that these small differences do propagate to produce flat and twisted morphologies at the mesoscopic scale. This finding is in agreement with both experimental and theoretical considerations on the assembly of polymers (including amyloids) under different salt conditions, which attribute the mesoscopic difference of flat versus twisted fibrils to electrostatic intermolecular repulsions.
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Affiliation(s)
- Carolin Seuring
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Joeri Verasdonck
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Philippe Ringler
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum University of Basel , 4085 Basel, Switzerland
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum University of Basel , 4085 Basel, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon 1 , 7 passage du Vercors, 69367 Lyon, France
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.,Structural Biology Laboratory, The Salk Institute , 10010 N Torrey Pines Road, 92037 La Jolla, California, United States
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25
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Quinn CM, Polenova T. Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q Rev Biophys 2017; 50:e1. [PMID: 28093096 PMCID: PMC5483179 DOI: 10.1017/s0033583516000159] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.
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Affiliation(s)
- Caitlin M. Quinn
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
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26
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Wittmann JJ, Agarwal V, Hellwagner J, Lends A, Cadalbert R, Meier BH, Ernst M. Accelerating proton spin diffusion in perdeuterated proteins at 100 kHz MAS. JOURNAL OF BIOMOLECULAR NMR 2016; 66:233-242. [PMID: 27803998 DOI: 10.1007/s10858-016-0071-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/19/2016] [Indexed: 05/08/2023]
Abstract
Fast magic-angle spinning (>60 kHz) has many advantages but makes spin-diffusion-type proton-proton long-range polarization transfer inefficient and highly dependent on chemical-shift offset. Using 100%-HN-[2H,13C,15N]-ubiquitin as a model substance, we quantify the influence of the chemical-shift difference on the spin diffusion between proton spins and compare two experiments which lead to an improved chemical-shift compensation of the transfer: rotating-frame spin diffusion and a new experiment, reverse amplitude-modulated MIRROR. Both approaches enable broadband spin diffusion, but the application of the first variant is limited due to fast spin relaxation in the rotating frame. The reverse MIRROR experiment, in contrast, is a promising candidate for the determination of structurally relevant distance restraints. The applied tailored rf-irradiation schemes allow full control over the range of recoupled chemical shifts and efficiently drive spin diffusion. Here, the relevant relaxation time is the larger longitudinal relaxation time, which leads to a higher signal-to-noise ratio in the spectra.
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Affiliation(s)
- Johannes J Wittmann
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Vipin Agarwal
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- TIFR Center for Interdisciplinary Science, 21 Brundavan Colony, Narsingi, Hyderabad, 500075, India
| | - Johannes Hellwagner
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Alons Lends
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Riccardo Cadalbert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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27
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Affiliation(s)
- Benjamin J. Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Hoa Q. Do
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Collin G. Borcik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Emily P. Hardy
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
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28
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Seuring C, Gath J, Verasdonck J, Cadalbert R, Rivier J, Böckmann A, Meier BH, Riek R. Solid-state NMR sequential assignment of the β-endorphin peptide in its amyloid form. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:259-268. [PMID: 27165576 DOI: 10.1007/s12104-016-9681-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/12/2016] [Indexed: 06/05/2023]
Abstract
Insights into the three-dimensional structure of hormone fibrils are crucial for a detailed understanding of how an amyloid structure allows the storage of hormones in secretory vesicles prior to hormone secretion into the blood stream. As an example for various hormone amyloids, we have studied the endogenous opioid neuropeptide β-endorphin in one of its fibril forms. We have achieved the sequential assignment of the chemical shifts of the backbone and side-chain heavy atoms of the fibril. The secondary chemical shift analysis revealed that the β-endorphin peptide adopts three β-strands in its fibril state. This finding fosters the amyloid nature of a hormone at the atomic level.
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Affiliation(s)
- Carolin Seuring
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Julia Gath
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Joeri Verasdonck
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Jean Rivier
- Structural Biology Laboratory, The Salk Institute, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69367, Lyon, France
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland.
- Structural Biology Laboratory, The Salk Institute, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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29
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Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P. Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application to Protein Backbone Dynamics Measurements. J Phys Chem B 2016; 120:8905-13. [PMID: 27500976 DOI: 10.1021/acs.jpcb.6b06129] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transverse relaxation rate measurements in magic-angle spinning solid-state nuclear magnetic resonance provide information about molecular motions occurring on nanosecond-to-millisecond (ns-ms) time scales. The measurement of heteronuclear ((13)C, (15)N) relaxation rate constants in the presence of a spin-lock radiofrequency field (R1ρ relaxation) provides access to such motions, and an increasing number of studies involving R1ρ relaxation in proteins have been reported. However, two factors that influence the observed relaxation rate constants have so far been neglected, namely, (1) the role of CSA/dipolar cross-correlated relaxation (CCR) and (2) the impact of fast proton spin flips (i.e., proton spin diffusion and relaxation). We show that CSA/D CCR in R1ρ experiments is measurable and that the CCR rate constant depends on ns-ms motions; it can thus provide insight into dynamics. We find that proton spin diffusion attenuates this CCR due to its decoupling effect on the doublet components. For measurements of dynamics, the use of R1ρ rate constants has practical advantages over the use of CCR rates, and this article reveals factors that have so far been disregarded and which are important for accurate measurements and interpretation.
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Affiliation(s)
- Vilius Kurauskas
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Emmanuelle Weber
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Audrey Hessel
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Isabel Ayala
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Dominique Marion
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
| | - Paul Schanda
- CEA, CNRS, Université Grenoble Alpes, Institut de Biologie Structurale (IBS) , 38027 Grenoble, France
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Gopinath T, Veglia G. Multiple acquisitions via sequential transfer of orphan spin polarization (MAeSTOSO): How far can we push residual spin polarization in solid-state NMR? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 267:1-8. [PMID: 27039168 PMCID: PMC4862926 DOI: 10.1016/j.jmr.2016.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/22/2016] [Accepted: 03/07/2016] [Indexed: 05/05/2023]
Abstract
Conventional multidimensional magic angle spinning (MAS) solid-state NMR (ssNMR) experiments detect the signal arising from the decay of a single coherence transfer pathway (FID), resulting in one spectrum per acquisition time. Recently, we introduced two new strategies, namely DUMAS (DUal acquisition Magic Angle Spinning) and MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), that enable the simultaneous acquisitions of multidimensional ssNMR experiments using multiple coherence transfer pathways. Here, we combined the main elements of DUMAS and MEIOSIS to harness both orphan spin operators and residual polarization and increase the number of simultaneous acquisitions. We show that it is possible to acquire up to eight two-dimensional experiments using four acquisition periods per each scan. This new suite of pulse sequences, called MAeSTOSO for Multiple Acquisitions via Sequential Transfer of Orphan Spin pOlarization, relies on residual polarization of both (13)C and (15)N pathways and combines low- and high-sensitivity experiments into a single pulse sequence using one receiver and commercial ssNMR probes. The acquisition of multiple experiments does not affect the sensitivity of the main experiment; rather it recovers the lost coherences that are discarded, resulting in a significant gain in experimental time. Both merits and limitations of this approach are discussed.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, United States.
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31
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Wang S, Matsuda I, Long F, Ishii Y. Spectral editing at ultra-fast magic-angle-spinning in solid-state NMR: facilitating protein sequential signal assignment by HIGHLIGHT approach. JOURNAL OF BIOMOLECULAR NMR 2016; 64:131-141. [PMID: 26781951 DOI: 10.1007/s10858-016-0014-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 01/12/2016] [Indexed: 06/05/2023]
Abstract
This study demonstrates a novel spectral editing technique for protein solid-state NMR (SSNMR) to simplify the spectrum drastically and to reduce the ambiguity for protein main-chain signal assignments in fast magic-angle-spinning (MAS) conditions at a wide frequency range of 40-80 kHz. The approach termed HIGHLIGHT (Wang et al., in Chem Comm 51:15055-15058, 2015) combines the reverse (13)C, (15)N-isotope labeling strategy and selective signal quenching using the frequency-selective REDOR pulse sequence under fast MAS. The scheme allows one to selectively observe the signals of "highlighted" labeled amino-acid residues that precede or follow unlabeled residues through selectively quenching (13)CO or (15)N signals for a pair of consecutively labeled residues by recoupling (13)CO-(15)N dipolar couplings. Our numerical simulation results showed that the scheme yielded only ~15% loss of signals for the highlighted residues while quenching as much as ~90% of signals for non-highlighted residues. For lysine-reverse-labeled micro-crystalline GB1 protein, the 2D (15)N/(13)Cα correlation and 2D (13)Cα/(13)CO correlation SSNMR spectra by the HIGHLIGHT approach yielded signals only for six residues following and preceding the unlabeled lysine residues, respectively. The experimental dephasing curves agreed reasonably well with the corresponding simulation results for highlighted and quenched residues at spinning speeds of 40 and 60 kHz. The compatibility of the HIGHLIGHT approach with fast MAS allows for sensitivity enhancement by paramagnetic assisted data collection (PACC) and (1)H detection. We also discuss how the HIGHLIGHT approach facilitates signal assignments using (13)C-detected 3D SSNMR by demonstrating full sequential assignments of lysine-reverse-labeled micro-crystalline GB1 protein (~300 nmol), for which data collection required only 11 h. The HIGHLIGHT approach offers valuable means of signal assignments especially for larger proteins through reducing the number of resonance and clarifying multiple starting points in sequential assignment with enhanced sensitivity.
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Affiliation(s)
- Songlin Wang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Isamu Matsuda
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Fei Long
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Yoshitaka Ishii
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Center for Structural Biology, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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32
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Wickramasinghe A, Wang S, Matsuda I, Nishiyama Y, Nemoto T, Endo Y, Ishii Y. Evolution of CPMAS under fast magic-angle-spinning at 100 kHz and beyond. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 72:9-16. [PMID: 26476810 PMCID: PMC4674312 DOI: 10.1016/j.ssnmr.2015.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 05/19/2023]
Abstract
This article describes recent trends of high-field solid-state NMR (SSNMR) experiments for small organic molecules and biomolecules using (13)C and (15)N CPMAS under ultra-fast MAS at a spinning speed (νR) of 80-100kHz. First, we illustrate major differences between a modern low-power RF scheme using UFMAS in an ultra-high field and a traditional CPMAS scheme using a moderate sample spinning in a lower field. Features and sensitivity advantage of a low-power RF scheme using UFMAS and a small sample coil are summarized for CPMAS-based experiments. Our 1D (13)C CPMAS experiments for uniformly (13)C- and (15)N-labeled alanine demonstrated that the sensitivity per given sample amount obtained at νR of 100kHz and a (1)H NMR frequency (νH) of 750.1MHz is ~10 fold higher than that of a traditional CPMAS experiment obtained at νR of 20kHz and νH of 400.2MHz. A comparison of different (1)H-decoupling schemes in CPMAS at νR of 100kHz for the same sample demonstrated that low-power WALTZ-16 decoupling unexpectedly displayed superior performance over traditional low-power schemes designed for SSNMR such as TPPM and XiX in a range of decoupling field strengths of 5-20kHz. Excellent (1)H decoupling performance of WALTZ-16 was confirmed on a protein microcrystal sample of GB1 at νR of 80kHz. We also discuss the feasibility of a SSNMR microanalysis of a GB1 protein sample in a scale of 1nmol to 80nmol by (1)H-detected 2D (15)N/(1)H SSNMR by a synergetic use of a high field, a low-power RF scheme, a paramagnetic-assisted condensed data collection (PACC), and UFMAS.
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Affiliation(s)
- Ayesha Wickramasinghe
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Songlin Wang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Isamu Matsuda
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan; RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Nemoto
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Yuki Endo
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Yoshitaka Ishii
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States; Center for Structural Biology, University of Illinois at Chicago, Chicago, IL 60607, United States.
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33
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Structure and assembly of the mouse ASC inflammasome by combined NMR spectroscopy and cryo-electron microscopy. Proc Natl Acad Sci U S A 2015; 112:13237-42. [PMID: 26464513 DOI: 10.1073/pnas.1507579112] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Inflammasomes are multiprotein complexes that control the innate immune response by activating caspase-1, thus promoting the secretion of cytokines in response to invading pathogens and endogenous triggers. Assembly of inflammasomes is induced by activation of a receptor protein. Many inflammasome receptors require the adapter protein ASC [apoptosis-associated speck-like protein containing a caspase-recruitment domain (CARD)], which consists of two domains, the N-terminal pyrin domain (PYD) and the C-terminal CARD. Upon activation, ASC forms large oligomeric filaments, which facilitate procaspase-1 recruitment. Here, we characterize the structure and filament formation of mouse ASC in vitro at atomic resolution. Information from cryo-electron microscopy and solid-state NMR spectroscopy is combined in a single structure calculation to obtain the atomic-resolution structure of the ASC filament. Perturbations of NMR resonances upon filament formation monitor the specific binding interfaces of ASC-PYD association. Importantly, NMR experiments show the rigidity of the PYD forming the core of the filament as well as the high mobility of the CARD relative to this core. The findings are validated by structure-based mutagenesis experiments in cultured macrophages. The 3D structure of the mouse ASC-PYD filament is highly similar to the recently determined human ASC-PYD filament, suggesting evolutionary conservation of ASC-dependent inflammasome mechanisms.
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34
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Courtney JM, Ye Q, Nesbitt AE, Tang M, Tuttle MD, Watt ED, Nuzzio KM, Sperling LJ, Comellas G, Peterson JR, Morrissey JH, Rienstra CM. Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum. Structure 2015; 23:1958-1966. [PMID: 26365800 PMCID: PMC4786943 DOI: 10.1016/j.str.2015.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 01/05/2023]
Abstract
Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins--GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor--and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure.
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Affiliation(s)
- Joseph M Courtney
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qing Ye
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anna E Nesbitt
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ming Tang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marcus D Tuttle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Eric D Watt
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kristin M Nuzzio
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lindsay J Sperling
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Gemma Comellas
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph R Peterson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - James H Morrissey
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chad M Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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35
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Observing the overall rocking motion of a protein in a crystal. Nat Commun 2015; 6:8361. [PMID: 26436197 PMCID: PMC4600728 DOI: 10.1038/ncomms9361] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/13/2015] [Indexed: 12/25/2022] Open
Abstract
The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall ‘rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1–100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments. Small-amplitude overall motion of molecules in crystals limits the achievable resolution in X-ray diffraction, yet little is known about its exact nature. Here, the authors obtain NMR, XRD and MD data from three different crystal forms of a protein (ubiquitin) to gain insight into amplitude and timescale of such motions.
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36
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Penzel S, Smith AA, Agarwal V, Hunkeler A, Org ML, Samoson A, Böckmann A, Ernst M, Meier BH. Protein resonance assignment at MAS frequencies approaching 100 kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods. JOURNAL OF BIOMOLECULAR NMR 2015; 63:165-186. [PMID: 26267840 DOI: 10.1007/s10858-015-9975-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/25/2015] [Indexed: 06/04/2023]
Abstract
We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T 2' times and a site-specific comparison of T 2' at 93 kHz versus 60 kHz MAS frequency. A quantitative analysis of transfer efficiencies of building blocks, as they are used for typical 3D experiments, was performed. To do this, we compared dipolar-coupling and J-coupling based transfer steps. The building blocks were then combined into 3D experiments for sequential resonance assignment, where we evaluated signal-to-noise ratio and information content of the different 3D spectra in order to identify the best assignment strategy. Based on this comparison, six experiments were selected to optimally assign the model protein ubiquitin, solely using spectra acquired at 93 kHz MAS. Within 3 days of instrument time, the required spectra were recorded from which the backbone resonances have been assigned to over 96%.
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Affiliation(s)
- Susanne Penzel
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Albert A Smith
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Vipin Agarwal
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Andreas Hunkeler
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Mai-Liis Org
- NMR Instituut, Tartu Teadus, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia
| | - Ago Samoson
- NMR Instituut, Tartu Teadus, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, 7, passage du Vercors, 69367, Lyon, France.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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37
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Brown LS, Ladizhansky V. Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy. Protein Sci 2015; 24:1333-46. [PMID: 25973959 DOI: 10.1002/pro.2700] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022]
Abstract
Membrane proteins play many critical roles in cells, mediating flow of material and information across cell membranes. They have evolved to perform these functions in the environment of a cell membrane, whose physicochemical properties are often different from those of common cell membrane mimetics used for structure determination. As a result, membrane proteins are difficult to study by traditional methods of structural biology, and they are significantly underrepresented in the protein structure databank. Solid-state Nuclear Magnetic Resonance (SSNMR) has long been considered as an attractive alternative because it allows for studies of membrane proteins in both native-like membranes composed of synthetic lipids and in cell membranes. Over the past decade, SSNMR has been rapidly developing into a major structural method, and a growing number of membrane protein structures obtained by this technique highlights its potential. Here we discuss membrane protein sample requirements, review recent progress in SSNMR methodologies, and describe recent advances in characterizing membrane proteins in the environment of a cellular membrane.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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38
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Wang S, Parthasarathy S, Nishiyama Y, Endo Y, Nemoto T, Yamauchi K, Asakura T, Takeda M, Terauchi T, Kainosho M, Ishii Y. Nano-mole scale side-chain signal assignment by 1H-detected protein solid-state NMR by ultra-fast magic-angle spinning and stereo-array isotope labeling. PLoS One 2015; 10:e0122714. [PMID: 25856081 PMCID: PMC4391754 DOI: 10.1371/journal.pone.0122714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 02/14/2015] [Indexed: 11/19/2022] Open
Abstract
We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52-57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.
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Affiliation(s)
- Songlin Wang
- Department of Chemistry and University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Sudhakar Parthasarathy
- Department of Chemistry and University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., Akishima, Tokyo, Japan
- RIKEN CLST-JEOL collaboration center, RIKEN, Yokohama, Kanagawa, Japan
| | - Yuki Endo
- JEOL RESONANCE Inc., Akishima, Tokyo, Japan
| | | | - Kazuo Yamauchi
- School of Science and Technology, Nazarbayev University, Astana, Kazakhstan
- Nuclear Magnetic Resonance Core Lab., King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Mitsuhiro Takeda
- Structural Biology Research Center, Graduate School of Science, Furocho, Chikusa-ku, Nagoya University, Nagoya, Japan 464–8601
| | - Tsutomu Terauchi
- SAIL Technologies Co., Inc., Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Masatsune Kainosho
- Structural Biology Research Center, Graduate School of Science, Furocho, Chikusa-ku, Nagoya University, Nagoya, Japan 464–8601
- Center for Priority Areas, Tokyo Metropolitan University, Tokyo, Japan
| | - Yoshitaka Ishii
- Department of Chemistry and University of Illinois at Chicago, Chicago, Illinois, United States of America
- Center for Structural Biology, University of Illinois at Chicago, Chicago, Illinois, United States of America
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39
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Abramov G, Morag O, Goldbourt A. Magic-angle spinning NMR of intact bacteriophages: insights into the capsid, DNA and their interface. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:80-90. [PMID: 25797007 DOI: 10.1016/j.jmr.2015.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/05/2015] [Accepted: 01/18/2015] [Indexed: 06/04/2023]
Abstract
Bacteriophages are viruses that infect bacteria. They are complex macromolecular assemblies, which are composed of multiple protein subunits that protect genomic material and deliver it to specific hosts. Various biophysical techniques have been used to characterize their structure in order to unravel phage morphogenesis. Yet, most bacteriophages are non-crystalline and have very high molecular weights, in the order of tens of MegaDaltons. Therefore, complete atomic-resolution characterization on such systems that encompass both capsid and DNA is scarce. In this perspective article we demonstrate how magic-angle spinning solid-state NMR has and is used to characterize in detail bacteriophage viruses, including filamentous and icosahedral phage. We discuss the process of sample preparation, spectral assignment of both capsid and DNA and the use of chemical shifts and dipolar couplings to probe the capsid-DNA interface, describe capsid structure and dynamics and extract structural differences between viruses.
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Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Omry Morag
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel.
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Ravera E, Schubeis T, Martelli T, Fragai M, Parigi G, Luchinat C. NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:60-70. [PMID: 25797005 DOI: 10.1016/j.jmr.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/06/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tobias Schubeis
- Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tommaso Martelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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Xue Y, Skrynnikov NR. Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics. Protein Sci 2015; 23:488-507. [PMID: 24452989 DOI: 10.1002/pro.2433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 01/06/2014] [Accepted: 01/18/2014] [Indexed: 11/07/2022]
Abstract
Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for (15) N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields.
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Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana, 47907-2084, USA
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Structure of CrgA, a cell division structural and regulatory protein from Mycobacterium tuberculosis, in lipid bilayers. Proc Natl Acad Sci U S A 2014; 112:E119-26. [PMID: 25548160 DOI: 10.1073/pnas.1415908112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The 93-residue transmembrane protein CrgA in Mycobacterium tuberculosis is a central component of the divisome, a large macromolecular machine responsible for cell division. Through interactions with multiple other components including FtsZ, FtsQ, FtsI (PBPB), PBPA, and CwsA, CrgA facilitates the recruitment of the proteins essential for peptidoglycan synthesis to the divisome and stabilizes the divisome. CrgA is predicted to have two transmembrane helices. Here, the structure of CrgA was determined in a liquid-crystalline lipid bilayer environment by solid-state NMR spectroscopy. Oriented-sample data yielded orientational restraints, whereas magic-angle spinning data yielded interhelical distance restraints. These data define a complete structure for the transmembrane domain and provide rich information on the conformational ensembles of the partially disordered N-terminal region and interhelical loop. The structure of the transmembrane domain was refined using restrained molecular dynamics simulations in an all-atom representation of the same lipid bilayer environment as in the NMR samples. The two transmembrane helices form a left-handed packing arrangement with a crossing angle of 24° at the conserved Gly39 residue. This helix pair exposes other conserved glycine and alanine residues to the fatty acyl environment, which are potential sites for binding CrgA's partners such as CwsA and FtsQ. This approach combining oriented-sample and magic-angle spinning NMR spectroscopy in native-like lipid bilayers with restrained molecular dynamics simulations represents a powerful tool for structural characterization of not only isolated membrane proteins, but their complexes, such as those that form macromolecular machines.
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Agarwal V, Penzel S, Szekely K, Cadalbert R, Testori E, Oss A, Past J, Samoson A, Ernst M, Böckmann A, Meier BH. De-novo-3D-Strukturaufklärung mit Proteinmengen unter einem Milligramm mittels 100-kHz-MAS-Festkörper-NMR-Spektroskopie. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405730] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Agarwal V, Penzel S, Szekely K, Cadalbert R, Testori E, Oss A, Past J, Samoson A, Ernst M, Böckmann A, Meier BH. De Novo 3D Structure Determination from Sub-milligram Protein Samples by Solid-State 100 kHz MAS NMR Spectroscopy. Angew Chem Int Ed Engl 2014; 53:12253-6. [DOI: 10.1002/anie.201405730] [Citation(s) in RCA: 263] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Indexed: 01/10/2023]
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Nielsen JT, Nielsen NC. VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra. JOURNAL OF BIOMOLECULAR NMR 2014; 60:51-66. [PMID: 25119482 DOI: 10.1007/s10858-014-9851-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 08/01/2014] [Indexed: 06/03/2023]
Abstract
NMR spectroscopy is a widely used technique for characterizing the structure and dynamics of macromolecules. Often large amounts of NMR data are required to characterize the structure of proteins. To save valuable time and resources on data acquisition, simulated data is useful in the developmental phase, for data analysis, and for comparison with experimental data. However, existing tools for this purpose can be difficult to use, are sometimes specialized for certain types of molecules or spectra, or produce too idealized data. Here we present a fast, flexible and robust tool, VirtualSpectrum, for generating peak lists for most multi-dimensional NMR experiments for both liquid and solid state NMR. It is possible to tune the quality of the generated peak lists to include sources of artifacts from peak overlap, noise and missing signals. VirtualSpectrum uses an analytic expression to represent the spectrum and derive the peak positions, seamlessly handling overlap between signals. We demonstrate our tool by comparing simulated and experimental spectra for different multi-dimensional NMR spectra and analyzing systematically three cases where overlap between peaks is particularly relevant; solid state NMR data, liquid state NMR homonuclear (1)H and (15)N-edited spectra, and 2D/3D heteronuclear correlation spectra of unstructured proteins. We analyze the impact of protein size and secondary structure on peak overlap and on the accuracy of structure determination based on data of different qualities simulated by VirtualSpectrum.
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Affiliation(s)
- Jakob Toudahl Nielsen
- Department of Chemistry, Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark,
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Nielsen JT, Kulminskaya N, Bjerring M, Nielsen NC. Automated robust and accurate assignment of protein resonances for solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2014; 59:119-34. [PMID: 24817190 DOI: 10.1007/s10858-014-9835-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/29/2014] [Indexed: 05/26/2023]
Abstract
The process of resonance assignment represents a time-consuming and potentially error-prone bottleneck in structural studies of proteins by solid-state NMR (ssNMR). Software for the automation of this process is therefore of high interest. Procedures developed through the last decades for solution-state NMR are not directly applicable for ssNMR due to the inherently lower data quality caused by lower sensitivity and broader lines, leading to overlap between peaks. Recently, the first efforts towards procedures specifically aimed for ssNMR have been realized (Schmidt et al. in J Biomol NMR 56(3):243-254, 2013). Here we present a robust automatic method, which can accurately assign protein resonances using peak lists from a small set of simple 2D and 3D ssNMR experiments, applicable in cases with low sensitivity. The method is demonstrated on three uniformly (13)C, (15)N labeled biomolecules with different challenges on the assignments. In particular, for the immunoglobulin binding domain B1 of streptococcal protein G automatic assignment shows 100% accuracy for the backbone resonances and 91.8% when including all side chain carbons. It is demonstrated, by using a procedure for generating artificial spectra with increasing line widths, that our method, GAMES_ASSIGN can handle a significant amount of overlapping peaks in the assignment. The impact of including different ssNMR experiments is evaluated as well.
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Affiliation(s)
- Jakob Toudahl Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark,
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Shi C, Fasshuber HK, Chevelkov V, Xiang S, Habenstein B, Vasa SK, Becker S, Lange A. BSH-CP based 3D solid-state NMR experiments for protein resonance assignment. JOURNAL OF BIOMOLECULAR NMR 2014; 59:15-22. [PMID: 24584701 DOI: 10.1007/s10858-014-9820-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/20/2014] [Indexed: 05/10/2023]
Abstract
We have recently presented band-selective homonuclear cross-polarization (BSH-CP) as an efficient method for CO-CA transfer in deuterated as well as protonated solid proteins. Here we show how the BSH-CP CO-CA transfer block can be incorporated in a set of three-dimensional (3D) solid-state NMR (ssNMR) pulse schemes tailored for resonance assignment of proteins at high static magnetic fields and moderate magic-angle spinning rates. Due to the achieved excellent transfer efficiency of 33 % for BSH-CP, a complete set of 3D spectra needed for unambiguous resonance assignment could be rapidly recorded within 1 week for the model protein ubiquitin. Thus we expect that BSH-CP could replace the typically used CO-CA transfer schemes in well-established 3D ssNMR approaches for resonance assignment of solid biomolecules.
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Affiliation(s)
- Chaowei Shi
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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Watt ED, Rienstra CM. Recent advances in solid-state nuclear magnetic resonance techniques to quantify biomolecular dynamics. Anal Chem 2014; 86:58-64. [PMID: 24313950 PMCID: PMC3988533 DOI: 10.1021/ac403956k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Eric D Watt
- Department of Chemistry, ‡Department of Biochemistry, and §Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, Unites States
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Yang Y, Fritzsching KJ, Hong M. Resonance assignment of the NMR spectra of disordered proteins using a multi-objective non-dominated sorting genetic algorithm. JOURNAL OF BIOMOLECULAR NMR 2013; 57:281-96. [PMID: 24132778 PMCID: PMC4004382 DOI: 10.1007/s10858-013-9788-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 10/03/2013] [Indexed: 05/05/2023]
Abstract
A multi-objective genetic algorithm is introduced to predict the assignment of protein solid-state NMR (SSNMR) spectra with partial resonance overlap and missing peaks due to broad linewidths, molecular motion, and low sensitivity. This non-dominated sorting genetic algorithm II (NSGA-II) aims to identify all possible assignments that are consistent with the spectra and to compare the relative merit of these assignments. Our approach is modeled after the recently introduced Monte-Carlo simulated-annealing (MC/SA) protocol, with the key difference that NSGA-II simultaneously optimizes multiple assignment objectives instead of searching for possible assignments based on a single composite score. The multiple objectives include maximizing the number of consistently assigned peaks between multiple spectra ("good connections"), maximizing the number of used peaks, minimizing the number of inconsistently assigned peaks between spectra ("bad connections"), and minimizing the number of assigned peaks that have no matching peaks in the other spectra ("edges"). Using six SSNMR protein chemical shift datasets with varying levels of imperfection that was introduced by peak deletion, random chemical shift changes, and manual peak picking of spectra with moderately broad linewidths, we show that the NSGA-II algorithm produces a large number of valid and good assignments rapidly. For high-quality chemical shift peak lists, NSGA-II and MC/SA perform similarly well. However, when the peak lists contain many missing peaks that are uncorrelated between different spectra and have chemical shift deviations between spectra, the modified NSGA-II produces a larger number of valid solutions than MC/SA, and is more effective at distinguishing good from mediocre assignments by avoiding the hazard of suboptimal weighting factors for the various objectives. These two advantages, namely diversity and better evaluation, lead to a higher probability of predicting the correct assignment for a larger number of residues. On the other hand, when there are multiple equally good assignments that are significantly different from each other, the modified NSGA-II is less efficient than MC/SA in finding all the solutions. This problem is solved by a combined NSGA-II/MC algorithm, which appears to have the advantages of both NSGA-II and MC/SA. This combination algorithm is robust for the three most difficult chemical shift datasets examined here and is expected to give the highest-quality de novo assignment of challenging protein NMR spectra.
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Affiliation(s)
- Yu Yang
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
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50
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Fragai M, Luchinat C, Parigi G, Ravera E. Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 57:155-66. [PMID: 23990200 DOI: 10.1007/s10858-013-9776-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/23/2013] [Indexed: 05/09/2023]
Abstract
Great theoretical and methodological advances are pushing the limits of resolution and sensitivity in solid state NMR (SSNMR). However, sample preparation remains a critical issue for the success of an experiment. The factors affecting spectral quality in SSNMR samples are discussed, examining cases encountered in the literature and presenting new experimental data. A discussion on resolution and sensitivity in sedimented solutes is framed in this context.
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Affiliation(s)
- Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
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