1
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Wi S, Li C, Pham K, Lee W, Frydman L. Short and long range 2D 15N- 15N NMR correlations among peptide groups by novel solid state dipolar mixing schemes. JOURNAL OF BIOMOLECULAR NMR 2024; 78:19-30. [PMID: 38102490 DOI: 10.1007/s10858-023-00429-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023]
Abstract
A recently developed homonuclear dipolar recoupling scheme, Adiabatic Linearly FREquency Swept reCOupling (AL FRESCO), was applied to record two-dimensional (2D) 15N-15N correlations on uniformly 15N-labeled GB1 powders. A major feature exploited in these 15N-15N correlations was AL FRESCO's remarkably low RF power demands, which enabled seconds-long mixing schemes when establishing direct correlations. These 15N-15N mixing schemes proved efficient regardless of the magic-angle spinning (MAS) rate and, being nearly free from dipolar truncation effects, they enabled the detection of long-range, weak dipolar couplings, even in the presence of strong short-range dipolar couplings. This led to a connectivity information that was significantly better than that obtained with spontaneously proton-driven, 15N spin-diffusion experiments. An indirect approach producing long-range 15N-15N correlations was also tested, relying on short (ms-long) 1HN-1HN mixings schemes while applying AL FRESCO chirped pulses along the 15N channel. These indirect mixing schemes produced numerous long-distance Ni-Ni±n (n = 2 - 5) correlations, that might be useful for characterizing three-dimensional arrangements in proteins. Once again, these AL FRESCO mediated experiments proved more informative than variants based on spin-diffusion-based 1HN-1HN counterparts.
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Affiliation(s)
- Sungsool Wi
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32304, USA.
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Karen Pham
- Department of Chemistry, University of Colorado at Denver, Denver, CO, 80217-3364, USA
| | - Woonghee Lee
- Department of Chemistry, University of Colorado at Denver, Denver, CO, 80217-3364, USA
| | - Lucio Frydman
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32304, USA.
- Department of Chemical and Biological Physics, Weizmann Institute of Sciences, Rehovot, Israel.
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2
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Molecular elucidation of drug-induced abnormal assemblies of the hepatitis B virus capsid protein by solid-state NMR. Nat Commun 2023; 14:471. [PMID: 36709212 PMCID: PMC9884277 DOI: 10.1038/s41467-023-36219-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
Hepatitis B virus (HBV) capsid assembly modulators (CAMs) represent a recent class of anti-HBV antivirals. CAMs disturb proper nucleocapsid assembly, by inducing formation of either aberrant assemblies (CAM-A) or of apparently normal but genome-less empty capsids (CAM-E). Classical structural approaches have revealed the CAM binding sites on the capsid protein (Cp), but conformational information on the CAM-induced off-path aberrant assemblies is lacking. Here we show that solid-state NMR can provide such information, including for wild-type full-length Cp183, and we find that in these assemblies, the asymmetric unit comprises a single Cp molecule rather than the four quasi-equivalent conformers typical for the icosahedral T = 4 symmetry of the normal HBV capsids. Furthermore, while in contrast to truncated Cp149, full-length Cp183 assemblies appear, on the mesoscopic level, unaffected by CAM-A, NMR reveals that on the molecular level, Cp183 assemblies are equally aberrant. Finally, we use a eukaryotic cell-free system to reveal how CAMs modulate capsid-RNA interactions and capsid phosphorylation. Our results establish a structural view on assembly modulation of the HBV capsid, and they provide a rationale for recently observed differences between in-cell versus in vitro capsid assembly modulation.
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3
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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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4
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Bruno F, Gigli L, Ferraro G, Cavallo A, Michaelis VK, Goobes G, Fratini E, Ravera E. Lysozyme is Sterically Trapped Within the Silica Cage in Bioinspired Silica-Lysozyme Composites: A Multi-Technique Understanding of Elusive Protein-Material Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8030-8037. [PMID: 35738569 PMCID: PMC9261187 DOI: 10.1021/acs.langmuir.2c00836] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Lysozyme is widely known to promote the formation of condensed silica networks from solutions containing silicic acid, in a reproducible and cost-effective way. However, little is known about the fate of the protein after the formation of the silica particles. Also, the relative arrangement of the different components in the resulting material is a matter of debate. In this study, we investigate the nature of the protein-silica interactions by means of solid-state nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and electron microscopy. We find that lysozyme and silica are in intimate contact and strongly interacting, but their interaction is neither covalent nor electrostatic: lysozyme is mostly trapped inside the silica by steric effects.
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Affiliation(s)
- Francesco Bruno
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Lucia Gigli
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Giovanni Ferraro
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia, 3, Sesto Fiorentino 50019, Italy
| | - Andrea Cavallo
- CERTEMA
S.c.a.r.l., S.P. Del
Cipressino Km 10, Cinigiano 58044, Italy
| | | | - Gil Goobes
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Emiliano Fratini
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia, 3, Sesto Fiorentino 50019, Italy
| | - Enrico Ravera
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, Sesto Fiorentino 50019, Italy
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5
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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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6
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Parigi G, Ravera E, Fragai M, Luchinat C. Unveiling protein dynamics in solution with field-cycling NMR relaxometry. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 124-125:85-98. [PMID: 34479712 DOI: 10.1016/j.pnmrs.2021.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Field-cycling NMR relaxometry is a well-established technique that can give information on molecular structure and dynamics of biological systems. It provides the nuclear relaxation rates as a function of the applied magnetic field, starting from fields as low as ~ 10-4 T up to about 1-3 T. The profiles so collected, called nuclear magnetic relaxation dispersion (NMRD) profiles, can be extended to include the relaxation rates at the largest fields achievable with high resolution NMR spectrometers. By exploiting this wide range of frequencies, the NMRD profiles can provide information on motions occurring on time scales from 10-6 to 10-9 s. 1H NMRD measurements have proved very useful also for the characterization of paramagnetic proteins, because they can help characterise a number of parameters including the number, distance and residence time of water molecules coordinated to the paramagnetic center, the reorientation correlation times and the electron spin relaxation time, and the electronic structure at the metal site.
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Affiliation(s)
- Giacomo Parigi
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy.
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy
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7
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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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8
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Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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9
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Petrović D, Wang X, Strodel B. How accurately do force fields represent protein side chain ensembles? Proteins 2018; 86:935-944. [DOI: 10.1002/prot.25525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/02/2018] [Accepted: 05/14/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Dušan Petrović
- Institute of Complex Systems, Structural Biochemistry, Forschungszentrum Jülich; Jülich, 52425 Germany
- Department of Cell and Molecular Biology; Uppsala University, BMC Box 596; Uppsala, 751 24 Sweden
| | - Xue Wang
- Institute of Complex Systems, Structural Biochemistry, Forschungszentrum Jülich; Jülich, 52425 Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf, Universitätsstraße 1; Düsseldorf, 40225 Germany
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry, Forschungszentrum Jülich; Jülich, 52425 Germany
- Institute of Theoretical and Computational Chemistry; Heinrich Heine University Düsseldorf, Universitätsstraße 1; Düsseldorf, 40225 Germany
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10
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Giuntini S, Balducci E, Cerofolini L, Ravera E, Fragai M, Berti F, Luchinat C. Characterization of the Conjugation Pattern in Large Polysaccharide-Protein Conjugates by NMR Spectroscopy. Angew Chem Int Ed Engl 2017; 56:14997-15001. [PMID: 29024352 PMCID: PMC5813213 DOI: 10.1002/anie.201709274] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Indexed: 11/08/2022]
Abstract
Carbohydrate-based vaccines are among the safest and most effective vaccines and represent potent tools for prevention of life-threatening bacterial infectious diseases, like meningitis and pneumonia. The chemical conjugation of a weak antigen to protein as a source of T-cell epitopes generates a glycoconjugate vaccine that results more immunogenic. Several methods have been used so far to characterize the resulting polysaccharide-protein conjugates. However, a reduced number of methodologies has been proposed for measuring the degree of saccharide conjugation at the possible protein sites. Here we show that detailed information on large proteins conjugated with large polysaccharides can be achieved by a combination of solution and solid-state NMR spectroscopy. As a test case, a large protein assembly, l-asparaginase II, has been conjugated with Neisseria meningitidis serogroup C capsular polysaccharide and the pattern and degree of conjugation were determined.
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Affiliation(s)
- Stefano Giuntini
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | - Evita Balducci
- GSK VaccinesPreclinical R&DVia Fiorentina 153100SienaItaly
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | - Enrico Ravera
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | - Marco Fragai
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
| | | | - Claudio Luchinat
- Department of ChemistryUniversity of FlorenceVia della Lastruccia 350019Sesto FiorentinoItaly
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP)Via L. Sacconi 650019Sesto FiorentinoItaly
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11
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Giuntini S, Balducci E, Cerofolini L, Ravera E, Fragai M, Berti F, Luchinat C. Characterization of the Conjugation Pattern in Large Polysaccharide-Protein Conjugates by NMR Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Stefano Giuntini
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Evita Balducci
- GSK Vaccines; Preclinical R&D; Via Fiorentina 1 53100 Siena Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Enrico Ravera
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Francesco Berti
- GSK Vaccines; Preclinical R&D; Via Fiorentina 1 53100 Siena Italy
| | - Claudio Luchinat
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
- Magnetic Resonance Center (CERM); University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
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12
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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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13
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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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14
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Zhang Z, Chen Y, Yang J. Band-selective heteronuclear dipolar recoupling with dual back-to-back pulses in rotating solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 272:46-52. [PMID: 27623242 DOI: 10.1016/j.jmr.2016.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/31/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
We propose a robust band-selective heteronuclear 15N-13C recoupling method using dual back-to-back (BABA) pulses (DBP). It contains four 90° pulses in each rotor period and corresponding phase cycling on each channel (13C and 15N). DBP aims at rapid band-selective heteronuclear magnetization transfer between 15N and 13Cα/13C', whose efficiency is close to that of the well-known SPECIFIC CP in membrane proteins with relatively short relaxation time in rotating frame (T1ρ). Compared to SPECIFIC CP, DBP is very simple to set up and highly robust to RF variations. Thus, it can reduce the efforts in experimental optimization, especially for low-sensitive samples, and is very suitable for long-time or quantitative experiments. The efficacy of DBP is demonstrated by the E. coli diacylglycerol kinase (DAGK) proteoliposome. We anticipate that DBP would be useful for (segments of) membrane proteins that undergo the μs-ms timescale motions in magic-angle spinning (MAS) solid-state NMR.
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Affiliation(s)
- Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Yanke Chen
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China.
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15
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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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16
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:9162-85. [PMID: 26136394 PMCID: PMC4943876 DOI: 10.1002/anie.201410653] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/26/2015] [Indexed: 11/07/2022]
Abstract
In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi-author interdisciplinary Review presents a state-of-the-art description of the primary approaches that were considered. Topics discussed included the future of ultrahigh-field NMR systems, emerging NMR detection technologies, new approaches to nuclear hyperpolarization, and progress in sample preparation. All of these are orthogonal efforts, whose gains could multiply and thereby enhance the sensitivity of solid- and liquid-state experiments. While substantial advances have been made in all these areas, numerous challenges remain in the quest of endowing NMR spectroscopy with the sensitivity that has characterized forms of spectroscopies based on electrical or optical measurements. These challenges, and the ways by which scientists and engineers are striving to solve them, are also addressed.
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Affiliation(s)
- Jan-Henrik Ardenkjaer-Larsen
- GE Healthcare, Broendby, Denmark; Department of Electrical Engineering, Technical University of Denmark, Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre (Denmark)
| | - Gregory S Boebinger
- U.S. National High Magnetic Field Lab, Florida State University, Tallahassee, FL 32310 (USA)
| | - Arnaud Comment
- Institute of Physics of Biological Systems, Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland)
| | - Simon Duckett
- Department of Chemistry, University of York, Heslington, York, YO10 5DD (UK)
| | - Arthur S Edison
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610 (USA)
| | | | | | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Lab, MIT, Cambridge, MA 02139-4703 (USA)
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, College Station (USA)
| | - Hidaeki Maeda
- Riken Center for Life Science Technologies, Yokohama, Kanagawa (Japan)
| | - Giacomo Parigi
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | - Thomas Prisner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Enrico Ravera
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | | | - Shimon Vega
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel)
| | - Andrew Webb
- Department of Radiology, C. J. Gorter Center for High Field MRI, Leiden University Medical Center (The Netherlands)
| | - Claudio Luchinat
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy).
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).
| | - Lucio Frydman
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel).
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17
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Neue Ansätze zur Empfindlichkeitssteigerung in der biomolekularen NMR-Spektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410653] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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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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19
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Fasshuber HK, Lakomek NA, Habenstein B, Loquet A, Shi C, Giller K, Wolff S, Becker S, Lange A. Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR. Protein Sci 2015; 24:592-8. [PMID: 25644665 DOI: 10.1002/pro.2654] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 01/07/2023]
Abstract
By applying [1-(13) C]- and [2-(13) C]-glucose labeling schemes to the folded globular protein ubiquitin, a strong reduction of spectral crowding and increase in resolution in solid-state NMR (ssNMR) spectra could be achieved. This allowed spectral resonance assignment in a straightforward manner and the collection of a wealth of long-range distance information. A high precision solid-state NMR structure of microcrystalline ubiquitin was calculated with a backbone rmsd of 1.57 to the X-ray structure and 1.32 Å to the solution NMR structure. Interestingly, we can resolve structural heterogeneity as the presence of three slightly different conformations. Structural heterogeneity is most significant for the loop region β1-β2 but also for β-strands β1, β2, β3, and β5 as well as for the loop connecting α1 and β3. This structural polymorphism observed in the solid-state NMR spectra coincides with regions that showed dynamics in solution NMR experiments on different timescales.
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Affiliation(s)
- Hannes Klaus Fasshuber
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany; Institut für Biologie, Humboldt-Universität, zu Berlin, Berlin, Germany
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20
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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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21
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Drabik E, Jeziorna A, Bienias U, Trzeciak-Karlikowska K, Pawlak T, Paluch P, Potrzebowski MJ. Study of the mechanism of thermal chemical processes in the crystals of YAF tripeptides by means of mass spectrometry and solid state NMR. J Phys Chem B 2013; 117:13481-9. [PMID: 24070178 DOI: 10.1021/jp407080q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thermal reactions in two Tyr-Ala-Phe (YAF) tripeptide crystals with different molecular packing (monoclinic and hexagonal), distinct stereochemistry of central amino acid (D or L alanine) and specific arrangement of molecules in the crystal lattice (head-to-tail) were investigated. Samples were heated up to 180 °C, while the melting point for YAF crystals is above the 220 °C. Below the melting temperature, in both cases the chemical reactions leading to formation of cyclic dipeptides (YA diketopiperazine) and leaving of phenylalanine were observed. Two possible mechanisms of chemical reaction in the crystal lattice assuming intra- and/or intermolecular pathways were considered. (13)C and (15)N enriched YAF samples were employed to study of mechanism of solid state reactivity using mass spectrometry and advanced solid state NMR techniques (2D DARR (Dipolar Assisted Rotational Resonance) and 2D Double CP (Cross-Polarization) correlations).
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Affiliation(s)
- Ewelina Drabik
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Sienkiewicza 112, 90-363 Lodz, Poland
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22
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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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23
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Bertini I, Luchinat C, Parigi G, Ravera E. SedNMR: on the edge between solution and solid-state NMR. Acc Chem Res 2013; 46:2059-69. [PMID: 23470055 DOI: 10.1021/ar300342f] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Solid-state NMR (SS-NMR) of proteins requires that those molecules be immobilized, usually by crystallization, freezing, or lyophilization. However, self-crowding can also slow molecular rotation sufficiently to prevent the nuclear interactions from averaging. To achieve self-crowding, researchers can use a centrifugal field to create a concentration gradient or use regular ultracentrifugation to produce highly concentrated, gel-like solutions. Thus sedimented solute NMR (SedNMR) provides a simple method to prepare biological samples for SS-NMR experiments with minimal perturbation. This method may also give researchers a way to investigate species that are not otherwise accessible by NMR. We induce the sedimentation in one of two ways: (1) by the extreme centrifugal force exerted during magic angle spinning (MAS-induced sedimentation or in situ) or (2) by an ultracentrifuge (UC-induced sedimentation or ex situ). Sedimentation is particularly useful in situations where it is difficult to obtain protein crystals. Furthermore, because the proteins remain in a largely hydrated state, the sedimented samples may provide SS-NMR spectra that have better resolution than the spectra from frozen solutions or lyophilized powders. If sedimentation is induced in situ, the same protein sample can be used for both solution and SS-NMR studies. Finally, we show that in situ SedNMR can be used to detect the NMR signals of large molecular adducts that have binding constants that are too weak to allow for the selective isolation and crystallization of the complexed species. We can selectively induce sedimentation for the heaviest molecular species. Because the complexed molecules are subtracted from the bulk solution, the reaction proceeds further toward the formation of complexes.
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Affiliation(s)
- Ivano Bertini
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy, and Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy, and Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy, and Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy, and Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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24
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Cukkemane A, Baldus M. Characterization of a cyclic nucleotide-activated K(+) channel and its lipid environment by using solid-state NMR spectroscopy. Chembiochem 2013; 14:1789-98. [PMID: 23956185 DOI: 10.1002/cbic.201300182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Indexed: 01/31/2023]
Abstract
Voltage-gated ion channels are large tetrameric multidomain membrane proteins that play crucial roles in various cellular transduction pathways. Because of their large size and domain-related mobility, structural characterization has proved challenging. We analyzed high-resolution solid-state NMR data on different isotope-labeled protein constructs of a bacterial cyclic nucleotide-activated K(+) channel (MlCNG) in lipid bilayers. We could identify the different subdomains of the 4×355 residue protein, such as the voltage-sensing domain and the cyclic nucleotide binding domain. Comparison to ssNMR data obtained on isotope-labeled cell membranes suggests a tight association of negatively charged lipids to the channel. We detected spectroscopic polymorphism that extends beyond the ligand binding site, and the corresponding protein segments have been associated with mutant channel types in eukaryotic systems. These findings illustrate the potential of ssNMR for structural investigations on large membrane-embedded proteins, even in the presence of local disorder.
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Affiliation(s)
- Abhishek Cukkemane
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht (The Netherlands)
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25
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Chevelkov V, Shi C, Fasshuber HK, Becker S, Lange A. Efficient band-selective homonuclear CO-CA cross-polarization in protonated proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 56:303-11. [PMID: 23925478 DOI: 10.1007/s10858-013-9767-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/30/2013] [Indexed: 05/10/2023]
Abstract
Previously introduced for highly deuterated proteins, band-selective magnetization transfer between CO and CA spins by dipolar-based homonuclear cross polarization is applied here to a protonated protein. Robust and efficient recoupling is achieved when the sum of effective radio-frequency fields on CO and CA resonances equals two times the spinning rate, yielding up to 33% of magnetization transfer efficiency in protonated ubiquitin. The approach is designed for moderate magic-angle spinning rates and high external magnetic fields when the isotropic chemical shift difference of CO and CA considerably exceeds the spinning rate. This method has been implemented in NiCOi-1CAi-1 and CAi(Ni)COi-1CAi-1 two-dimensional interresidual correlation experiments for fast and efficient resonance assignment of ubiquitin by solid-state NMR spectroscopy.
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26
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Schneider R, Odronitz F, Hammesfahr B, Hellkamp M, Kollmar M. Peakr: simulating solid-state NMR spectra of proteins. ACTA ACUST UNITED AC 2013; 29:1134-40. [PMID: 23493322 DOI: 10.1093/bioinformatics/btt125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
MOTIVATION When analyzing solid-state nuclear magnetic resonance (NMR) spectra of proteins, assignment of resonances to nuclei and derivation of restraints for 3D structure calculations are challenging and time-consuming processes. Simulated spectra that have been calculated based on, for example, chemical shift predictions and structural models can be of considerable help. Existing solutions are typically limited in the type of experiment they can consider and difficult to adapt to different settings. RESULTS Here, we present Peakr, a software to simulate solid-state NMR spectra of proteins. It can generate simulated spectra based on numerous common types of internuclear correlations relevant for assignment and structure elucidation, can compare simulated and experimental spectra and produces lists and visualizations useful for analyzing measured spectra. Compared with other solutions, it is fast, versatile and user friendly. AVAILABILITY AND IMPLEMENTATION Peakr is maintained under the GPL license and can be accessed at http://www.peakr.org. The source code can be obtained on request from the authors.
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Affiliation(s)
- Robert Schneider
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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27
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Lv G, Faßhuber HK, Loquet A, Demers JP, Vijayan V, Giller K, Becker S, Lange A. A straightforward method for stereospecific assignment of val and leu prochiral methyl groups by solid-state NMR: Scrambling in the [2-13C]Glucose labeling scheme. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 228:45-49. [PMID: 23354009 DOI: 10.1016/j.jmr.2012.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 06/01/2023]
Abstract
The unambiguous stereospecific assignment of the prochiral methyl groups in Val and Leu plays an important role in the structural investigation of proteins by NMR. Here, we present a straightforward method for their stereospecific solid-state NMR assignment based on [2-(13)C]Glucose ([2-(13)C]Glc) as the sole carbon source during protein expression. The approach is fundamentally based on the stereo-selective biosynthetic pathway of Val and Leu, and the co-presence of [2-(13)C]pyruvate produced mainly by glycolysis and [3-(13)C]/[1,3-(13)C]pyruvate most probably formed through scrambling in the pentose phosphate pathway. As a consequence, the isotope spin pairs (13)Cβ-(13)Cγ2 and (13)Cα-(13)Cγ1 in Val, and (13)Cγ-(13)Cδ2 and (13)Cβ-(13)Cδ1 in Leu are obtained. The approach is successfully demonstrated with the stereospecific assignment of the methyl groups of Val and Leu of type 3 secretion system PrgI needles and microcrystalline ubiquitin.
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Affiliation(s)
- Guohua Lv
- Max Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany
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28
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Ikeda K, Egawa A, Fujiwara T. Secondary structural analysis of proteins based on (13)C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database. JOURNAL OF BIOMOLECULAR NMR 2013; 55:189-200. [PMID: 23271376 DOI: 10.1007/s10858-012-9701-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 12/21/2012] [Indexed: 06/01/2023]
Abstract
Magic-angle-spinning solid-state (13)C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-(13)C,(15)N labeled samples. To overcome this problem, we present a method for assigning (13)C chemical shifts and secondary structures from unresolved two-dimensional (13)C-(13)C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to (13)C(α), (13)C(β), and (13)C' chemical shifts and cross-peak intensities. The experimental (13)C-(13)C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific C(α), C(β), and C' chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50-200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved (13)C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.
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Affiliation(s)
- Keisuke Ikeda
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan
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29
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Herbert-Pucheta JE, Chan-Huot M, Duma L, Abergel D, Bodenhausen G, Assairi L, Blouquit Y, Charbonnier JB, Tekely P. Probing Structural and Motional Features of the C-Terminal Part of the Human Centrin 2/P17-XPC Microcrystalline Complex by Solid-State NMR Spectroscopy. J Phys Chem B 2012. [DOI: 10.1021/jp3099472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jose-Enrique Herbert-Pucheta
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
| | - Monique Chan-Huot
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
- Institut Curie - Centre de Recherche, 91405 Orsay, France
- INSERM U759, 91405 Orsay, France
| | - Luminita Duma
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
| | - Daniel Abergel
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
| | - Geoffrey Bodenhausen
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
| | - Liliane Assairi
- Institut Curie - Centre de Recherche, 91405 Orsay, France
- INSERM U759, 91405 Orsay, France
| | - Yves Blouquit
- Institut Curie - Centre de Recherche, 91405 Orsay, France
- INSERM U759, 91405 Orsay, France
| | - Jean-Baptiste Charbonnier
- UMR 8221,
Laboratoire de Biologie Structurale
et Radiobiologie, iBiTec-S, CEA, 91191
Gif-sur-Yvette, France
| | - Piotr Tekely
- Ecole Normale Supérieure, Département
de Chimie, 24 rue Lhomond, 75231 Paris, France
- Université Pierre-et-Marie Curie, Paris, France
- UMR 7203, Laboratoire des Biomolécules, CNRS/UPMC/ENS, Paris, France
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30
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Cukkemane A, Nand D, Gradmann S, Weingarth M, Kaupp UB, Baldus M. Solid-state NMR [13C,15N] resonance assignments of the nucleotide-binding domain of a bacterial cyclic nucleotide-gated channel. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:225-9. [PMID: 22302441 PMCID: PMC3438399 DOI: 10.1007/s12104-012-9363-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/17/2012] [Indexed: 05/21/2023]
Abstract
Channels regulated by cyclic nucleotides are key signalling proteins in several biological pathways. The regulatory aspect is conferred by a C-terminal cyclic nucleotide-binding domain (CNBD). We report resonance assignments of the CNBD of a bacterial mlCNG channel obtained using 2D and 3D solid-state NMR under Magic-angle Spinning conditions. A secondary chemical shift analysis of the 141 residue protein suggests a three-dimensional fold seen in earlier X-ray and solution-state NMR work and points to spectroscopic polymorphism for a selected set of resonances.
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Affiliation(s)
- Abhishek Cukkemane
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Deepak Nand
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sabine Gradmann
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Markus Weingarth
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - U. Benjamin Kaupp
- Center of Advanced European Studies and Research (Caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Marc Baldus
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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31
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Banigan JR, Traaseth NJ. Utilizing afterglow magnetization from cross-polarization magic-angle-spinning solid-state NMR spectroscopy to obtain simultaneous heteronuclear multidimensional spectra. J Phys Chem B 2012; 116:7138-44. [PMID: 22582831 PMCID: PMC3418334 DOI: 10.1021/jp303269m] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The time required for data acquisition and subsequent spectral assignment are limiting factors for determining biomolecular structure and dynamics using solid-state NMR spectroscopy. While strong magnetic dipolar couplings give rise to relatively broad spectra lines, the couplings also mediate the coherent magnetization transfer via the Hartmann-Hahn cross-polarization (HH-CP) experiment. This mechanism is used in nearly all backbone assignment experiments for carrying out polarization transfer between (1)H, (15)N, and (13)C. In this Article, we describe a general spectroscopic approach to use the residual or "afterglow" magnetization from the (15)N to (13)C selective HH-CP experiment to collect a second multidimensional heteronuclear data set. This approach allowed for the collection of two commonly used sequential assignment experiments (2D NCA and NCO or 3D NCACX and NCOCX) at the same time. Our "afterglow" technique was demonstrated with uniformly [(13)C,(15)N] and [1,3-(13)C] glycerol-labeled ubiquitin using instrumentation available on all standard solid-state NMR spectrometers configured for magic-angle-spinning. This method is compatible with several other sensitivity enhancement experiments and can be used as an isotopic filtering tool to reduce the spectral complexity and decrease the time needed for assignment.
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Affiliation(s)
- James R. Banigan
- Department of Chemistry, New York University, New York, NY 10003
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32
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Structural characterization of polyglutamine fibrils by solid-state NMR spectroscopy. J Mol Biol 2011; 412:121-36. [PMID: 21763317 DOI: 10.1016/j.jmb.2011.06.045] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 06/21/2011] [Accepted: 06/27/2011] [Indexed: 01/21/2023]
Abstract
Protein aggregation via polyglutamine stretches occurs in a number of severe neurodegenerative diseases such as Huntington's disease. We have investigated fibrillar aggregates of polyglutamine peptides below, at, and above the toxicity limit of around 37 glutamine residues using solid-state NMR and electron microscopy. Experimental data are consistent with a dry fibril core of at least 70-80 Å in width for all constructs. Solid-state NMR dipolar correlation experiments reveal a largely β-strand character of all samples and point to tight interdigitation of hydrogen-bonded glutamine side chains from different sheets. Two approximately equally frequent populations of glutamine residues with distinct sets of chemical shifts are found, consistent with local backbone dihedral angles compensating for β-strand twist or with two distinct sets of side-chain conformations. Peptides comprising 15 glutamine residues are present as single extended β-strands. Data obtained for longer constructs are most compatible with a superpleated arrangement with individual molecules contributing β-strands to more than one sheet and an antiparallel assembly of strands within β-sheets.
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33
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Ciesielski W, Kassassir H, Potrzebowski MJ. A practical guide for the setup of a 1H-31P-13C double cross-polarization (DCP) experiment. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2011; 39:151-157. [PMID: 21440422 DOI: 10.1016/j.ssnmr.2010.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 11/30/2010] [Accepted: 12/02/2010] [Indexed: 05/30/2023]
Abstract
O-phospho-L-threonine is a convenient sample to setup a (1)H-(31)P-(13)C double cross-polarization (DCP) Hartmann-Hahn match. The (1)H-(31)P-(13)C technique is extremely sensitive to the rate of the sample spinning. Both zero-quantum (ZQ) and double-quantum (DQ) cross-polarization operate at an average spinning rate (6-7 kHz). At higher spinning rates (10 kHz), the DQCP mechanism dominates and leads to a reduction of signal intensity, in particular for lower (31)P RF field strength. The application of two shape pulses during the second cross-polarization greatly improves the signal to noise ratio allowing the recording of better quality spectra. (31)P-(13)C spectrally induced filtering in combination with cross-polarization (SPECIFIC-CP) experiments can be carried out under ZQCP and DQCP conditions if careful attention is paid to the choice of RF field amplitudes and carriers Ω. Application of 1D and 2D (1)H-(31)P-(13)C experiments is demonstrated on model samples; disodium ATP hydrate and O-phospho-L-tyrosine.
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Affiliation(s)
- Wlodzimierz Ciesielski
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, 90-363 Lodz, Poland
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34
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Huang KY, Amodeo GA, Tong L, McDermott A. The structure of human ubiquitin in 2-methyl-2,4-pentanediol: a new conformational switch. Protein Sci 2011; 20:630-9. [PMID: 21432937 PMCID: PMC3064841 DOI: 10.1002/pro.584] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A new crystal structure of human ubiquitin is reported at 1.8 Å resolution. Compared with the other known crystal structure or the solution NMR structure of monomeric human ubiquitin, this new structure is similar in its overall fold but differs with respect to the conformation of the backbone in a surface-exposed region. The conformation reported here resembles conformations previously seen in complex with deubiquinating enzymes, wherein the Asp52/Gly53 main chain and Glu24 side chain move. This movement exposes the backbone carbonyl of Asp52 to the exterior of the molecule, making it possible to engage in hydrogen-bond contacts with neighboring molecules, rather than in an internal hydrogen bond with the backbone of Glu24. This particular crystal form of ubiquitin has been used in a large number of solid state NMR studies. The structure described here elucidates the origin of many of the chemical shift differences comparing solution and solid state studies.
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Affiliation(s)
- Kuo Ying Huang
- Department of Chemistry, Columbia UniversityNew York, New York 10027
| | - Gabriele A Amodeo
- Department of Biological Science, Columbia UniversityNew York, New York 10027
| | - Liang Tong
- Department of Biological Science, Columbia UniversityNew York, New York 10027
| | - Ann McDermott
- Department of Chemistry, Columbia UniversityNew York, New York 10027,*Correspondence to: Ann McDermott, Columbia University, Department of Chemistry, MC3113, New York, NY 10027. E-mail:
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35
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Chan JCC. Solid-state NMR techniques for the structural determination of amyloid fibrils. Top Curr Chem (Cham) 2011; 306:47-88. [PMID: 21630137 DOI: 10.1007/128_2011_154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review discusses the solid-state NMR techniques developed for the study of amyloid fibrils. Literature up to the end of 2010 has been surveyed and the materials are organized according to five categories, viz. homonuclear dipolar recoupling and polarization transfer via J-coupling, heteronuclear dipolar recoupling, correlation spectroscopy, recoupling of chemical shift anisotropy, and tensor correlation. Our emphasis is on the NMR techniques and their practical aspects. The biological implications of the results obtained for amyloid fibrils are only briefly discussed. Our main objective is to showcase the power of NMR in the study of biological unoriented solids.
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Affiliation(s)
- Jerry C C Chan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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36
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Andreas LB, Eddy MT, Pielak RM, Chou J, Griffin RG. Magic angle spinning NMR investigation of influenza A M2(18-60): support for an allosteric mechanism of inhibition. J Am Chem Soc 2010; 132:10958-60. [PMID: 20698642 DOI: 10.1021/ja101537p] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The tetrameric M2 proton channel from influenza A virus conducts protons at low pH and is inhibited by aminoadamantyl drugs such as amantadine and rimantadine (Rmt). We report magic angle spinning NMR spectra of POPC and DPhPC membrane-embedded M2(18-60), both apo and in the presence of Rmt. Similar line widths in the spectra of apo and bound M2 indicate that Rmt does not have a significant impact on the dynamics or conformational heterogeneity of this construct. Substantial chemical shift changes for many residues in the transmembrane region support an allosteric mechanism of inhibition. An Rmt titration supports a binding stoichiometry of >1 Rmt molecule per channel and shows that nonspecific binding or changes in membrane composition are unlikely sources of the chemical shift changes. In addition, doubling of spectral lines in all of the observed samples provides evidence that the channel assembles with twofold symmetry.
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Affiliation(s)
- Loren B Andreas
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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37
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Demers JP, Vijayan V, Becker S, Lange A. Tailored low-power cross-polarization under fast magic-angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 205:216-23. [PMID: 20570194 DOI: 10.1016/j.jmr.2010.04.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 04/29/2010] [Indexed: 05/10/2023]
Abstract
High static magnetic fields and very fast magic-angle spinning (MAS) promise to improve resolution and sensitivity of solid-state NMR experiments. The fast MAS regime has permitted the development of low-power cross-polarization schemes, such as second-order cross-polarization (SOCP), which prevent heat deposition in the sample. Those schemes are however limited in bandwidth, as weak radio-frequency (RF) fields only cover a small chemical shift range for rare nuclei (e.g. (13)C). Another consideration is that the efficiency of cross-polarization is very sensitive to magnetization decay that occurs during the spin-lock pulse on the abundant nuclei (e.g. (1)H). Having characterized this decay in glutamine at 60 kHz MAS, we propose two complementary strategies to tailor cross-polarization to desired spectral regions at low RF power. In the case of multiple sites with small chemical shift dispersion, a larger bandwidth for SOCP is obtained by slightly increasing the RF power while avoiding recoupling conditions that lead to fast spin-lock decay. In the case of two spectral regions with large chemical shift offset, an extension of the existing low-power schemes, called MOD-CP, is introduced. It consists of a spin-lock on (1)H and an amplitude-modulated spin-lock on the rare nucleus. The range of excited chemical shifts is assessed by experimental excitation profiles and numerical simulation of an I(2)S spin system. All SOCP-based schemes exhibit higher sensitivity than high-power CP schemes, as demonstrated on solid (glutamine) and semi-solid (hydrated, micro-crystalline ubiquitin) samples.
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Affiliation(s)
- Jean-Philippe Demers
- Max Planck Institute for Biophysical Chemistry, Solid-state NMR, Göttingen 37077, Germany
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38
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Abstract
The prion hypothesis states that the prion and non-prion form of a protein differ only in their 3D conformation and that different strains of a prion differ by their 3D structure. Recent technical developments have enabled solid-state NMR to address the atomic-resolution structures of full-length prions, and a first comparative study of two of them, HET-s and Ure2p, in fibrillar form, has recently appeared as a pair of companion papers. Interestingly, the two structures are rather different: HET-s features an exceedingly well-ordered prion domain and a partially disordered globular domain. Ure2p in contrast features a very well ordered globular domain with a conserved fold, and-most probably-a partially ordered prion domain. For HET-s, the structure of the prion domain is characterized at atomic-resolution. For Ure2p, structure determination is under way, but the highly resolved spectra clearly show that information at atomic resolution should be achievable.
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Affiliation(s)
- Anja Böckmann
- IBCP UMR 5086 CNRS/Université de Lyon, Lyon, France.
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39
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Loquet A, Gardiennet C, Böckmann A. Protein 3D structure determination by high-resolution solid-state NMR. CR CHIM 2010. [DOI: 10.1016/j.crci.2010.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Schneider R, Seidel K, Etzkorn M, Lange A, Becker S, Baldus M. Probing Molecular Motion by Double-Quantum (13C,13C) Solid-State NMR Spectroscopy: Application to Ubiquitin. J Am Chem Soc 2009; 132:223-33. [DOI: 10.1021/ja906283h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert Schneider
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Karsten Seidel
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Manuel Etzkorn
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Adam Lange
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marc Baldus
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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41
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Aluas M, Tripon C, Griffin JM, Filip X, Ladizhansky V, Griffin RG, Brown SP, Filip C. CHHC and (1)H-(1)H magnetization exchange: analysis by experimental solid-state NMR and 11-spin density-matrix simulations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 199:173-87. [PMID: 19467890 PMCID: PMC2706310 DOI: 10.1016/j.jmr.2009.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 04/20/2009] [Indexed: 05/03/2023]
Abstract
A protocol is presented for correcting the effect of non-specific cross-polarization in CHHC solid-state MAS NMR experiments, thus allowing the recovery of the (1)H-(1)H magnetization exchange functions from the mixing-time dependent buildup of experimental CHHC peak intensity. The presented protocol also incorporates a scaling procedure to take into account the effect of multiplicity of a CH(2) or CH(3) moiety. Experimental CHHC buildup curves are presented for l-tyrosine.HCl samples where either all or only one in 10 molecules are U-(13)C labeled. Good agreement between experiment and 11-spin SPINEVOLUTION simulation (including only isotropic (1)H chemical shifts) is demonstrated for the initial buildup (t(mix)<100micros) of CHHC peak intensity corresponding to an intramolecular close (2.5A) H-H proximity. Differences in the initial CHHC buildup are observed between the one in 10 dilute and 100% samples for cases where there is a close intermolecular H-H proximity in addition to a close intramolecular H-H proximity. For the dilute sample, CHHC cross-peak intensities tended to significantly lower values for long mixing times (500micros) as compared to the 100% sample. This difference is explained as being due to the dependence of the limiting total magnetization on the ratio N(obs)/N(tot) between the number of protons that are directly attached to a (13)C nucleus and hence contribute significantly to the observed (13)C CHHC NMR signal, and the total number of (1)H spins into the system. (1)H-(1)H magnetization exchange curves extracted from CHHC spectra for the 100% l-tyrosine.HCl sample exhibit a clear sensitivity to the root sum squared dipolar coupling, with fast buildup being observed for the shortest intramolecular distances (2.5A) and slower, yet observable buildup for the longer intermolecular distances (up to 5A).
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Affiliation(s)
- Mihaela Aluas
- Physics Department, Babes-Bolyai University, 400084 Cluj, Romania
| | - Carmen Tripon
- National Institute for R&D of Isotopic and Molecular Technologies, P.O. Box 700, 400293 Cluj, Romania
| | - John M. Griffin
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Xenia Filip
- Physics Department, Babes-Bolyai University, 400084 Cluj, Romania
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1
| | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Steven P. Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Claudiu Filip
- National Institute for R&D of Isotopic and Molecular Technologies, P.O. Box 700, 400293 Cluj, Romania
- Corresponding Author, Fax.: ++40 264 420042, e-mail:
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42
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Nielsen AB, Bjerring M, Nielsen JT, Nielsen NC. Symmetry-based dipolar recoupling by optimal control: Band-selective experiments for assignment of solid-state NMR spectra of proteins. J Chem Phys 2009; 131:025101. [DOI: 10.1063/1.3157737] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Seidel K, Etzkorn M, Schneider R, Ader C, Baldus M. Comparative analysis of NMR chemical shift predictions for proteins in the solid phase. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2009; 35:235-242. [PMID: 19231140 DOI: 10.1016/j.ssnmr.2008.12.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 12/10/2008] [Accepted: 12/11/2008] [Indexed: 05/27/2023]
Abstract
A comparative analysis of nuclear chemical shift predictions of proteins in the solid state by rapid algorithms trained on and verified with solution-state NMR assignments is presented. The precision of predictions by four dedicated computer programs (SHIFTS, PROSHIFTS, SHIFTX and SPARTA) was found to be close to values obtained for proteins in solution. Correlation coefficients depend on the NMR nucleus (N, C', C(alpha) and C(beta)) and on secondary structure (beta-strand, random coil and alpha-helix), but also on the molecular environment (membrane-integral or not). The findings establish a quantitative basis for using chemical shift prediction programs for solid-state NMR applications. On the other hand, prediction inaccuracies identified for certain resonance kind, residue type, and molecular environment point to possible areas of methodological improvement.
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Affiliation(s)
- Karsten Seidel
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Lewandowski JR, De Paëpe G, Eddy MT, Griffin RG. (15)N-(15)N proton assisted recoupling in magic angle spinning NMR. J Am Chem Soc 2009; 131:5769-76. [PMID: 19334788 PMCID: PMC2754755 DOI: 10.1021/ja806578y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a new magic angle spinning (MAS) NMR experiment for obtaining (15)N-(15)N correlation spectra. The approach yields direct information about the secondary and tertiary structure of proteins, including identification of alpha-helical stretches and interstrand connectivity in antiparallel beta-sheets, which are of major interest for structural studies of membrane proteins and amyloid fibrils. The method, (15)N-(15)N proton assisted recoupling (PAR), relies on a second-order mechanism, third spin assisted recoupling (TSAR), used previously in the context of (15)N-(13)C and (13)C-(13)C polarization transfer schemes. In comparison to (15)N-(15)N proton-driven spin diffusion experiments, the PAR technique accelerates polarization transfer between (15)N's by a factor of approximately 10(2)-10(3) and is furthermore applicable over the entire range of currently available MAS frequencies (10-70 kHz).
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Affiliation(s)
- Józef R Lewandowski
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Jehle S, van Rossum B, Stout JR, Noguchi SM, Falber K, Rehbein K, Oschkinat H, Klevit RE, Rajagopal P. alphaB-crystallin: a hybrid solid-state/solution-state NMR investigation reveals structural aspects of the heterogeneous oligomer. J Mol Biol 2008; 385:1481-97. [PMID: 19041879 DOI: 10.1016/j.jmb.2008.10.097] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 09/24/2008] [Accepted: 10/29/2008] [Indexed: 10/21/2022]
Abstract
Atomic-level structural information on alphaB-Crystallin (alphaB), a prominent member of the small heat-shock protein family, has been a challenge to obtain due its polydisperse oligomeric nature. We show that magic-angle spinning solid-state NMR can be used to obtain high-resolution information on an approximately 580-kDa human alphaB assembled from 175-residue 20-kDa subunits. An approximately 100-residue alpha-crystallin domain is common to all small heat-shock proteins, and solution-state NMR was performed on two different alpha-crystallin domain constructs isolated from alphaB. In vitro, the chaperone-like activities of full-length alphaB and the isolated alpha-crystallin domain are identical. Chemical shifts of the backbone and C(beta) resonances have been obtained for residues 64-162 (alpha-crystallin domain plus part of the C-terminus) in alphaB and the isolated alpha-crystallin domain by solid-state and solution-state NMR, respectively. Both sets of data strongly predict six beta-strands in the alpha-crystallin domain. A majority of residues in the alpha-crystallin domain have similar chemical shifts in both solid-state and solution-state, indicating similar structures for the domain in its isolated and oligomeric forms. Sites of intersubunit interaction are identified from chemical shift differences that cluster to specific regions of the alpha-crystallin domain. Multiple signals are observed for the resonances of M68 in the oligomer, identifying the region containing this residue as existing in heterogeneous environments within alphaB. Evidence for a novel dimerization motif in the human alpha-crystallin domain is obtained by a comparison of (i) solid-state and solution-state chemical shift data and (ii) (1)H-(15)N heteronuclear single quantum coherence spectra as a function of pH. The isolated alpha-crystallin domain undergoes a dimer-monomer transition over the pH range 7.5-6.8. This steep pH-dependent switch may be important for alphaB to function optimally (e.g., to preserve the filament integrity of cardiac muscle proteins such as actin and desmin during cardiac ischemia, which is accompanied by acidosis).
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Etzkorn M, Kneuper H, Dünnwald P, Vijayan V, Krämer J, Griesinger C, Becker S, Unden G, Baldus M. Plasticity of the PAS domain and a potential role for signal transduction in the histidine kinase DcuS. Nat Struct Mol Biol 2008; 15:1031-9. [DOI: 10.1038/nsmb.1493] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Accepted: 08/29/2008] [Indexed: 11/09/2022]
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Affiliation(s)
- Cecil Dybowski*
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Shi Bai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
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48
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Schneider R, Ader C, Lange A, Giller K, Hornig S, Pongs O, Becker S, Baldus M. Solid-State NMR Spectroscopy Applied to a Chimeric Potassium Channel in Lipid Bilayers. J Am Chem Soc 2008; 130:7427-35. [DOI: 10.1021/ja800190c] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Robert Schneider
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Christian Ader
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Adam Lange
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Karin Giller
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Sönke Hornig
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Olaf Pongs
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
| | - Marc Baldus
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, and Institut für Neurale Signalverarbeitung, Zentrum für Molekulare Neurobiologie, Universität Hamburg, Falkenried 94, 20251 Hamburg, Germany
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Andronesi OC, Bergen MV, Biernat J, Seidel K, Griesinger C, Mandelkow E, Baldus M. Characterization of Alzheimer’s-like Paired Helical Filaments from the Core Domain of Tau Protein Using Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:5922-8. [DOI: 10.1021/ja7100517] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Gardiennet C, Loquet A, Etzkorn M, Heise H, Baldus M, Böckmann A. Structural constraints for the Crh protein from solid-state NMR experiments. JOURNAL OF BIOMOLECULAR NMR 2008; 40:239-50. [PMID: 18320329 PMCID: PMC2579321 DOI: 10.1007/s10858-008-9229-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Accepted: 02/06/2008] [Indexed: 05/11/2023]
Abstract
We demonstrate that short, medium and long-range constraints can be extracted from proton mediated, rare-spin detected correlation solid-state NMR experiments for the microcrystalline 10.4 x 2 kDa dimeric model protein Crh. Magnetization build-up curves from cross signals in NHHC and CHHC spectra deliver detailed information on side chain conformers and secondary structure for interactions between spin pairs. A large number of medium and long-range correlations can be observed in the spectra, and an analysis of the resolved signals reveals that the constraints cover the entire sequence, also including inter-monomer contacts between the two molecules forming the domain-swapped Crh dimer. Dynamic behavior is shown to have an impact on cross signals intensities, as indicated for mobile residues or regions by contacts predicted from the crystal structure, but absent in the spectra. Our work validates strategies involving proton distance measurements for large and complex proteins as the Crh dimer, and confirms the magnetization transfer properties previously described for small molecules in solid protein samples.
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Affiliation(s)
- Carole Gardiennet
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
| | - Antoine Loquet
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
| | - Manuel Etzkorn
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Henrike Heise
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Marc Baldus
- Max-Planck-Institute for Biophysical Chemistry, Solid-state NMR, Am Fassberg 11, 37077 Gottingen, Germany
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 C.N.R.S./Université de Lyon, 7, passage du Vercors, 69367 Lyon Cedex 07, France
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