1
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Scott FJ, Eddy S, Gullion T, Mentink-Vigier F. Sorbitol-Based Glass Matrices Enable Dynamic Nuclear Polarization beyond 200 K. J Phys Chem Lett 2024; 15:8743-8751. [PMID: 39162721 DOI: 10.1021/acs.jpclett.4c02054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
In magic angle spinning dynamic nuclear polarization (MAS-DNP) experiments, paramagnetic species are often dispersed in rigid glass-forming matrices such as glycerol/water mixtures, but their modest glass-transition temperature (Tg) restricts the viable temperature range for MAS-DNP. To expand applications of DNP at higher temperatures, new matrices and physical insights are required. Here we demonstrate that sorbitol, Tg ≈ 267 K, advantageously replaces glycerol, Tg ≈ 190 K, to carry out DNP at higher temperature while maintaining an identical 13C NMR spectrum footprint and thus minimizing spectral overlap. DNP stops being effective in glycerol/water at ∼180 K, but sorbitol/DMSO gives a significant enhancement at 230 K with AsymPol-POK biradicals at 600 MHz/395 GHz. For the first time, a simple analytical model is proposed that provides physical insights and explains the effect of biradical concentration, the temperature dependence of the enhancement, the signal buildup times, and the enhanced signal-to-noise ratio. The model reveals that electron spin relaxation is the limiting factor for high-temperature DNP in the case of AsymPol-POK. We showcase the efficacy of this new DNP formulation on an intriguing chitin sample extracted from cicada exoskeleton which allowed for the recording of rapid heteronuclear correlation spectra at 100 and 225 K.
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Affiliation(s)
- Faith J Scott
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuel Eddy
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Terry Gullion
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Drive, Tallahassee, Florida 32310, United States
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2
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Porat-Dahlerbruch G, Sergeyev IV, Quinn CM, Struppe J, Banks D, Dahlheim C, Johnson D, Murphy D, Ilott A, Abraham A, Polenova T. Spatial Organization of Lipid Nanoparticle siRNA Delivery Systems Revealed by an Integrated Magnetic Resonance Approach. SMALL METHODS 2024:e2400622. [PMID: 39021326 DOI: 10.1002/smtd.202400622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Indexed: 07/20/2024]
Abstract
Lipid nanoparticles (LNPs) are increasingly finding applications in targeted drug delivery, including for subcutaneous, intravenous, inhalation, and vaccine administration. While a variety of microscopy techniques are widely used for LNP characterization, their resolution does not allow for characterization of the spatial organization of different components, such as the excipients, targeting agents, or even the active ingredient. Herein, an approach is presented to probe the spatial organization of individual constituent groups of LNPs used for siRNA-based drug delivery, currently in clinical trials, by multinuclear solid-state magic-angle-spinning nuclear magnetic resonance (MAS NMR) spectroscopy. Dynamic nuclear polarization is exploited (DNP) for sensitivity enhancement, together with judicious 2H labeing, to detect functionally important LNP constituents, the siRNA and the targeting agent (<1-2 w/v%), respectively, and achieve a structural model of the LNP locating the siRNA in the core, the targeting agent below the surface, and the sugars above the lipid bilayer at the surface. The integrated approach presented here is applicable for structural analysis of LNPs and can be extended more generally to other multi-component biological formulations.
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Ivan V Sergeyev
- Bristol Myers Squibb, Drug Product Development, New Brunswick, NJ, 08901, USA
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, USA
| | - Daniel Banks
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, USA
| | - Charles Dahlheim
- Bristol Myers Squibb, Drug Product Development, New Brunswick, NJ, 08901, USA
| | - Donald Johnson
- Bristol Myers Squibb, Drug Product Development, New Brunswick, NJ, 08901, USA
| | - Denette Murphy
- Bristol Myers Squibb, Drug Product Development, New Brunswick, NJ, 08901, USA
| | - Andrew Ilott
- Bristol Myers Squibb, Drug Product Development, New Brunswick, NJ, 08901, USA
| | - Anuji Abraham
- Bristol Myers Squibb, Drug Product Development, New Brunswick, NJ, 08901, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
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3
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Sergeyev IV, Fritzsching K, Rogawski R, McDermott A. Resolution in cryogenic solid state NMR: Challenges and solutions. Protein Sci 2024; 33:e4803. [PMID: 37847566 PMCID: PMC11184935 DOI: 10.1002/pro.4803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023]
Abstract
NMR at cryogenic temperatures has the potential to provide rich site-specific details regarding biopolymer structure, function, and mechanistic intermediates. Broad spectral lines compared with room temperature NMR can sometimes present practical challenges. A number of hypotheses regarding the origins of line broadening are explored. One frequently considered explanation is the presence of inhomogeneous conformational distributions. Possibly these arise when the facile characteristic motions that occur near room temperature become dramatically slower or "frozen out" at temperatures below the solvent phase change. Recent studies of low temperature spectra harness the distributions in properties in these low temperature spectra to uncover information regarding the conformational ensembles that drive biological function.
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Affiliation(s)
| | | | - Rivkah Rogawski
- Columbia University, Department of ChemistryNew YorkNew YorkUSA
| | - Ann McDermott
- Columbia University, Department of ChemistryNew YorkNew YorkUSA
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4
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Costello WN, Xiao Y, Mentink-Vigier F, Kragelj J, Frederick KK. DNP-assisted solid-state NMR enables detection of proteins at nanomolar concentrations in fully protonated cellular milieu. JOURNAL OF BIOMOLECULAR NMR 2024; 78:95-108. [PMID: 38520488 DOI: 10.1007/s10858-024-00436-9] [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: 11/09/2023] [Accepted: 02/09/2024] [Indexed: 03/25/2024]
Abstract
With the sensitivity enhancements conferred by dynamic nuclear polarization (DNP), magic angle spinning (MAS) solid state NMR spectroscopy experiments can attain the necessary sensitivity to detect very low concentrations of proteins. This potentially enables structural investigations of proteins at their endogenous levels in their biological contexts where their native stoichiometries with potential interactors is maintained. Yet, even with DNP, experiments are still sensitivity limited. Moreover, when an isotopically-enriched target protein is present at physiological levels, which typically range from low micromolar to nanomolar concentrations, the isotope content from the natural abundance isotopes in the cellular milieu can outnumber the isotope content of the target protein. Using isotopically enriched yeast prion protein, Sup35NM, diluted into natural abundance yeast lysates, we optimized sample composition. We found that modest cryoprotectant concentrations and fully protonated environments support efficient DNP. We experimentally validated theoretical calculations of the limit of specificity for an isotopically enriched protein in natural abundance cellular milieu. We establish that, using pulse sequences that are selective for adjacent NMR-active nuclei, proteins can be specifically detected in cellular milieu at concentrations in the hundreds of nanomolar. Finally, we find that maintaining native stoichiometries of the protein of interest to the components of the cellular environment may be important for proteins that make specific interactions with cellular constituents.
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Affiliation(s)
- Whitney N Costello
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
| | | | - Jaka Kragelj
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
- Slovenian NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Kendra K Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA.
- Center for Alzheimer's and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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5
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Yi X, Fritzsching KJ, Rogawski R, Xu Y, McDermott AE. Contribution of protein conformational heterogeneity to NMR lineshapes at cryogenic temperatures. Proc Natl Acad Sci U S A 2024; 121:e2301053120. [PMID: 38346186 PMCID: PMC10895356 DOI: 10.1073/pnas.2301053120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/17/2023] [Indexed: 02/15/2024] Open
Abstract
While low-temperature Nuclear Magnetic Resonance (NMR) holds great promise for the analysis of unstable samples and for sensitizing NMR detection, spectral broadening in frozen protein samples is a common experimental challenge. One hypothesis explaining the additional linewidth is that a variety of conformations are in rapid equilibrium at room temperature and become frozen, creating an inhomogeneous distribution at cryogenic temperatures. Here, we investigate conformational heterogeneity by measuring the backbone torsion angle (Ψ) in Escherichia coli Dihydrofolate Reductase (DHFR) at 105 K. Motivated by the particularly broad N chemical shift distribution in this and other examples, we modified an established NCCN Ψ experiment to correlate the chemical shift of Ni+1 to Ψi. With selective 15N and 13C enrichment of Ile, only the unique I60-I61 pair was expected to be detected in 13C'-15N correlation spectrum. For this unique amide, we detected three different conformation basins based on dispersed chemical shifts. Backbone torsion angles Ψ were determined for each basin: 114 ± 7° for the major peak and 150 ± 8° and 164 ± 16° for the minor peaks as contrasted with 118° for the X-ray crystal structure (and 118° to 130° for various previously reported structures). These studies support the hypothesis that inhomogeneous distributions of protein backbone torsion angles contribute to the lineshape broadening in low-temperature NMR spectra.
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Affiliation(s)
- Xu Yi
- Department of Chemistry, Columbia University, New York, NY 1002
| | | | - Rivkah Rogawski
- Department of Chemistry, Columbia University, New York, NY 1002
| | - Yunyao Xu
- Department of Chemistry, Columbia University, New York, NY 1002
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, NY 1002
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6
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Qiang W, Kengwerere M, Zhao W, Scott FJ, Wutoh-Hughes X, Wang T, Mentink-Vigier F. Heterotypic Interactions between the 40- and 42-Residue Isoforms of β-Amyloid Peptides on Lipid Bilayer Surfaces. ACS Chem Neurosci 2023; 14:4153-4162. [PMID: 37991929 PMCID: PMC10867818 DOI: 10.1021/acschemneuro.3c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
Co-aggregation involving different amyloidogenic sequences has been emphasized recently in the modified amyloid cascade hypothesis. Yet, molecular-level interactions between two predominant β-amyloid peptide sequences, Aβ40 and Aβ42, in the fibrillation process in membrane-mimicked environments remain unclear. Here, we report biophysical evidence that demonstrates the molecular-level interactions between Aβ40 and Aβ42 at the membrane-associated conucleation stage using dynamic nuclear polarization-enhanced solid-state NMR spectroscopy. These residue-specific contacts are distinguished from those reported in mature fibrils formed by either Aβ40 or Aβ42. Meanwhile, site-specific interactions between Aβ and lipid molecules and modulation of microsecond-time-scale lipid dynamics are observed, which may be responsible for the more rapid and significant membrane content leakage compared to that with Aβ40 alone.
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Affiliation(s)
- Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA
| | - Maurine Kengwerere
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA
| | - Wancheng Zhao
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Faith J. Scott
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Xyomara Wutoh-Hughes
- Department of Chemistry, Binghamton University, State University of New York, Binghamton, NY 13902, USA
| | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
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7
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Dervişoğlu R, Antonschmidt L, Nimerovsky E, Sant V, Kim M, Ryazanov S, Leonov A, Carlos Fuentes-Monteverde J, Wegstroth M, Giller K, Mathies G, Giese A, Becker S, Griesinger C, Andreas LB. Anle138b interaction in α-synuclein aggregates by dynamic nuclear polarization NMR. Methods 2023; 214:18-27. [PMID: 37037308 DOI: 10.1016/j.ymeth.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/22/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
Small molecules that bind to oligomeric protein species such as membrane proteins and fibrils are of clinical interest for development of therapeutics and diagnostics. Definition of the binding site at atomic resolution via NMR is often challenging due to low binding stoichiometry of the small molecule. For fibrils and aggregation intermediates grown in the presence of lipids, we report atomic-resolution contacts to the small molecule at sub nm distance via solid-state NMR using dynamic nuclear polarization (DNP) and orthogonally labelled samples of the protein and the small molecule. We apply this approach to α-synuclein (αS) aggregates in complex with the small molecule anle138b, which is a clinical drug candidate for disease modifying therapy. The small central pyrazole moiety of anle138b is detected in close proximity to the protein backbone and differences in the contacts between fibrils and early intermediates are observed. For intermediate species, the 100 K condition for DNP helps to preserve the aggregation state, while for both fibrils and oligomers, the DNP enhancement is essential to obtain sufficient sensitivity.
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Affiliation(s)
- Rıza Dervişoğlu
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Leif Antonschmidt
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Evgeny Nimerovsky
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Vrinda Sant
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Myeongkyu Kim
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sergey Ryazanov
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | - Andrei Leonov
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | | | - Melanie Wegstroth
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karin Giller
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University, Munich, Germany
| | - Stefan Becker
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR based structural Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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8
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Yi X, Fritzsching KJ, Rogawski R, Xu Y, McDermott AE. Contribution of protein conformational heterogeneity to NMR lineshapes at cryogenic temperatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525358. [PMID: 36747795 PMCID: PMC9900807 DOI: 10.1101/2023.01.24.525358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
While low temperature NMR holds great promise for the analysis of unstable samples and for sensitizing NMR detection, spectral broadening in frozen protein samples is a common experimental challenge. One hypothesis explaining the additional linewidth is that a variety of conformations are in rapid equilibrium at room temperature and become frozen, creating an inhomogeneous distribution at cryogenic temperatures. Here we investigate conformational heterogeneity by measuring the backbone torsion angle (Ψ) in E. coli DHFR at 105K. Motivated by the particularly broad N chemical shift distribution in this and other examples, we modified an established NCCN Ψ experiment to correlate the chemical shift of N i+1 to Ψ i . With selective 15 N and 13 C enrichment of Ile, only the unique I60-I61 pair was expected to be detected in 13 C'- 15 N correlation spectrum. For this unique amide we detected three different conformation basins based on dispersed chemical shifts. Backbone torsion angles Ψ were determined for each basin 114 ± 7 for the major peak, and 150 ± 8 and 164 ± 16° for the minor peak as contrasted with 118 for the X-ray crystal structure (and 118-130 for various previously reported structures). These studies support the hypothesis that inhomogeneous distributions of protein backbone torsion angles contribute to the lineshape broadening in low temperature NMR spectra. Significance Statement Understanding protein conformational flexibility is essential for insights into the molecular basis of protein function and the thermodynamics of proteins. Here we investigate the ensemble of protein backbone conformations in a frozen protein freezing, which is likely a close representation for the ensemble in rapid equilibrium at room temperature. Various conformers are spectrally resolved due to the exquisite sensitivity of NMR shifts to local conformations, and NMR methods allow us to directly probe the torsion angles corresponding to each band of chemical shifts.
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9
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Döller SC, Gutmann T, Hoffmann M, Buntkowsky G. A case study on the influence of hydrophilicity on the signal enhancement by dynamic nuclear polarization. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101829. [PMID: 36116176 DOI: 10.1016/j.ssnmr.2022.101829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/25/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
In this work, the behavior of four different commercially available polarizing agents is investigated employing the non-ionic model surfactant 1-octanol as analyte. A relative method for the comparison of the proportion of the direct and indirect polarization transfer pathways is established, allowing a direct comparison of the polarization efficacy for different radicals and different parts of the 1-octanol molecule despite differences in radical concentration or sample amount. With this approach, it could be demonstrated that the hydrophilicity is a key factor in the way polarization is transferred from the polarizing agent to the analyte. These findings are confirmed by the determination of buildup times Tb, illustrating that the choice of polarizing agent plays an essential role in ensuring an optimal polarization transfer and therefore the maximum amount of enhancement possible for DNP enhanced NMR measurements.
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Affiliation(s)
- Sonja C Döller
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287, Darmstadt, Germany
| | - Torsten Gutmann
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287, Darmstadt, Germany
| | - Markus Hoffmann
- Department of Chemistry and Biochemistry, State University of New York College at Brockport, Brockport, NY, 14420, USA
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287, Darmstadt, Germany.
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10
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Michaelis VK, Keeler EG, Bahri S, Ong TC, Daviso E, Colvin MT, Griffin RG. Biradical Polarizing Agents at High Fields. J Phys Chem B 2022; 126:7847-7856. [PMID: 36194539 PMCID: PMC9886493 DOI: 10.1021/acs.jpcb.2c03985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The sensitivity enhancements available from dynamic nuclear polarization (DNP) are rapidly reshaping the research landscape and expanding the field of nuclear magnetic resonance (NMR) spectroscopy as a tool for solving complex chemical and structural problems. The past decade has seen considerable advances in this burgeoning method, while efforts to further improve its capabilities continue along many avenues. In this report, we examine the influence of static magnetic field strength and temperature on the reported 1H DNP enhancements from three conventional organic biradicals: TOTAPOL, AMUPol, and SPIROPOL. In contrast to the conventional wisdom, our findings show that at liquid nitrogen temperatures and 700 MHz/460.5 GHz, these three bisnitroxides all provide similar 1H DNP enhancements, ε ≈ 60. Furthermore, we investigate the influence of temperature, microwave power, magnetic field strength, and protein sample deuteration on the NMR experimental results.
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Affiliation(s)
- Vladimir K. Michaelis
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Department of Chemistry, University of Alberta, Edmonton T6G 2G2 Alberta, Canada
| | - Eric G. Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; New York Structural Biology Center, New York 10027, New York, United States
| | - Salima Bahri
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584CH, The Netherlands
| | - Ta-Chung Ong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles 90095 California, United States
| | - Eugenio Daviso
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Department of Scientific Support and Applications Development, Covaris LLC, Woburn 01801 Massachusetts, United States
| | - Michael T. Colvin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Ortho Clinical Diagnostics, Rochester 14626 New York, United States
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States
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11
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Deligey F, Frank MA, Cho SH, Kirui A, Mentink-Vigier F, Swulius MT, Nixon BT, Wang T. Structure of In Vitro-Synthesized Cellulose Fibrils Viewed by Cryo-Electron Tomography and 13C Natural-Abundance Dynamic Nuclear Polarization Solid-State NMR. Biomacromolecules 2022; 23:2290-2301. [PMID: 35341242 PMCID: PMC9198983 DOI: 10.1021/acs.biomac.1c01674] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/16/2022] [Indexed: 12/25/2022]
Abstract
Cellulose, the most abundant biopolymer, is a central source for renewable energy and functionalized materials. In vitro synthesis of cellulose microfibrils (CMFs) has become possible using purified cellulose synthase (CESA) isoforms from Physcomitrium patens and hybrid aspen. The exact nature of these in vitro fibrils remains unknown. Here, we characterize in vitro-synthesized fibers made by CESAs present in membrane fractions of P. patens over-expressing CESA5 by cryo-electron tomography and dynamic nuclear polarization (DNP) solid-state NMR. DNP enabled measuring two-dimensional 13C-13C correlation spectra without isotope-labeling of the fibers. Results show structural similarity between in vitro fibrils and native CMF in plant cell walls. Intensity quantifications agree with the 18-chain structural model for plant CMF and indicate limited fibrillar bundling. The in vitro system thus reveals insights into cell wall synthesis and may contribute to novel cellulosic materials. The integrated DNP and cryo-electron tomography methods are also applicable to structural studies of other carbohydrate-based biomaterials.
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Affiliation(s)
- Fabien Deligey
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Mark A. Frank
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, University
Park, Pennsylvania 16802, United States
| | - Sung Hyun Cho
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, University
Park, Pennsylvania 16802, United States
| | - Alex Kirui
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Matthew T. Swulius
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, Hershey, Pennsylvania 17033, United States
| | - B. Tracy Nixon
- Department
of Biochemistry and Molecular Biology, Pennsylvania
State University, University
Park, Pennsylvania 16802, United States
| | - Tuo Wang
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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12
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Elathram N, Ackermann BE, Debelouchina GT. DNP-enhanced solid-state NMR spectroscopy of chromatin polymers. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100057. [PMID: 35707629 PMCID: PMC9191766 DOI: 10.1016/j.jmro.2022.100057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chromatin is a DNA-protein polymer that represents the functional form of the genome. The main building block of chromatin is the nucleosome, a structure that contains 147 base pairs of DNA and two copies each of the histone proteins H2A, H2B, H3 and H4. Previous work has shown that magic angle spinning (MAS) NMR spectroscopy can capture the nucleosome at high resolution although studies have been challenging due to low sensitivity, the presence of dynamic and rigid components, and the complex interaction networks of nucleosomes within the chromatin polymer. Here, we use dynamic nuclear polarization (DNP) to enhance the sensitivity of MAS NMR experiments of nucleosome arrays at 100 K and show that well-resolved 13C-13C MAS NMR correlations can be obtained much more efficiently. We evaluate the effect of temperature on the chemical shifts and linewidths in the spectra and demonstrate that changes are relatively minimal and clustered in regions of histone-DNA or histone-histone contacts. We also compare samples prepared with and without DNA and show that the low temperature 13C-13C correlations exhibit sufficient resolution to detect chemical shift changes and line broadening for residues that form the DNA-histone interface. On the other hand, we show that the measurement of DNP-enhanced 15N-13C histone-histone interactions within the nucleosome core is complicated by the natural 13C abundance network in the sample. Nevertheless, the enhanced sensitivity afforded by DNP can be used to detect long-range correlations between histone residues and DNA. Overall, our experiments demonstrate that DNP-enhanced MAS NMR spectroscopy of chromatin samples yields spectra with high resolution and sensitivity and can be used to capture functionally relevant protein-DNA interactions that have implications for gene regulation and genome organization.
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Affiliation(s)
| | | | - Galia T. Debelouchina
- Corresponding author: Galia Debelouchina, University of California, San Diego, Natural Sciences Building 4322, 9500 Gilman Dr., La Jolla, CA 92093, 858-534-3038,
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13
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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14
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Ghosh R, Dumarieh R, Xiao Y, Frederick KK. Stability of the nitroxide biradical AMUPol in intact and lysed mammalian cells. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 336:107150. [PMID: 35151975 PMCID: PMC8961433 DOI: 10.1016/j.jmr.2022.107150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Dynamic Nuclear Polarization (DNP) enhanced solid state NMR increases experimental sensitivity, potentially enabling detection of biomolecules at their physiological concentrations. The sensitivity of DNP experiments is due to the transfer of polarization from electron spins of free radicals to the nuclear spins of interest. Here, we investigate the reduction of AMUPol in both lysed and intact HEK293 cells. We find that nitroxide radicals are reduced with first order reduction kinetics by cell lysates at a rate of ∼ 12% of the added nitroxide radical concentration per hour. We also found that electroporation delivered a consistent amount of AMUPol to intact cells and that nitroxide radicals are reduced just slightly more rapidly (∼15% per hour) by intact cells than by cell lysates. The two nitroxide radicals of AMUPol are reduced independently and this leads to considerable accumulation of the DNP-silent monoradical form of AMUPol, particularly in preparations of intact cells where nearly half of the AMUPol is already reduced to the DNP silent monoradical form at the earliest experimental time points. This confirms that the loss of the DNP-active biradical form of AMUPol is faster than the nitroxide reduction rate. Finally, we investigate the effect of adding N-ethyl maleimide, a well-known inhibitor of thiol (-SH) group-based reduction of nitroxide biradicals in cells, on AMUPol reduction, cellular viability, and DNP performance. Although pre-treatment of cells with NEM effectively inhibited the reduction of AMUPol, exposure to NEM compromised cellular viability and, surprisingly, did not improve DNP performance. Collectively, these results indicate that, currently, the most effective strategy to obtain high DNP enhancements for DNP-assisted in-cell NMR is to minimize room temperature contact times with cellular constituents and suggest that the development of bio-resistant polarization agents for DNP could considerably increase the sensitivity of DNP-assisted in-cell NMR experiments.
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Affiliation(s)
- Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States
| | - Rania Dumarieh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States
| | - Kendra K Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States; Center for Neurodegenerative and Alzheimer's Disease, UT Southwestern Medical Center, Dallas 75390, United States.
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15
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Li M, Reichert P, Narasimhan C, Sorman B, Xu W, Cote A, Su Y. Investigating Crystalline Protein Suspension Formulations of Pembrolizumab from MAS NMR Spectroscopy. Mol Pharm 2022; 19:936-952. [PMID: 35107019 DOI: 10.1021/acs.molpharmaceut.1c00915] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Developing biological formulations to maintain the chemical and structural integrity of therapeutic antibodies remains a significant challenge. Monoclonal antibody (mAb) crystalline suspension formulation is a promising alternative for high concentration subcutaneous drug delivery. It demonstrates many merits compared to the solution formulation to reach a high concentration at the reduced viscosity and enhanced stability. One main challenge in drug development is the lack of high-resolution characterization of the crystallinity and stability of mAb microcrystals in the native formulations. Conventional analytical techniques often cannot evaluate structural details of mAb microcrystals in the native suspension due to the presence of visible particles, relatively small crystal size, high protein concentration, and multicomponent nature of a liquid formulation. This study demonstrates the first high-resolution characterization of mAb microcrystalline suspension using magic angle spinning (MAS) NMR spectroscopy. Crystalline suspension formulation of pembrolizumab (Keytruda, Merck & Co., Inc., Kenilworth, NJ 07033, U.S.) is utilized as a model system. Remarkably narrow 13C spectral linewidth of approximately 29 Hz suggests a high order of crystallinity and conformational homogeneity of pembrolizumab crystals. The impact of thermal stress and dehydration on the structure, dynamics, and stability of these mAb crystals in the formulation environment is evaluated. Moreover, isotopic labeling and heteronuclear 13C and 15N spectroscopies have been utilized to identify the binding of caffeine in the pembrolizumab crystal lattice, providing molecular insights into the cocrystallization of the protein and ligand. Our study provides valuable structural details for facilitating the design of crystalline suspension formulation of Keytruda and demonstrates the high potential of MAS NMR as an advanced tool for biophysical characterization of biological therapeutics.
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Affiliation(s)
- Mingyue Li
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Paul Reichert
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Bradley Sorman
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Aaron Cote
- Biologics Process Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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16
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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17
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Overall SA, Barnes AB. Biomolecular Perturbations in In-Cell Dynamic Nuclear Polarization Experiments. Front Mol Biosci 2021; 8:743829. [PMID: 34751246 PMCID: PMC8572051 DOI: 10.3389/fmolb.2021.743829] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022] Open
Abstract
In-cell DNP is a growing application of NMR to the study of biomolecular structure and function within intact cells. An important unresolved question for in-cell DNP spectroscopy is the integrity of cellular samples under the cryogenic conditions of DNP. Despite the rich literature around cryopreservation of cells in the fields of stem cell/embryonic cell therapeutics, cell line preservation and in cryo-EM applications, the effect of cryopreservation procedures on DNP parameters is unclear. In this report we investigate cell survival and apoptosis in the presence of cryopreserving agents and DNP radicals. We also assess the effects of these reagents on cellular enhancements. We show that the DNP radical AMUPol has no effect on membrane permeability and does not induce apoptosis. Furthermore, the standard aqueous glass forming reagent, comprised of 60/30/10 d8-glycerol/D2O/H2O (DNP juice), rapidly dehydrates cells and induces apoptosis prior to freezing, reducing structural integrity of the sample prior to DNP analysis. Preservation with d6-DMSO at 10% v/v provided similar DNP enhancements per √unit time compared to glycerol preservation with superior maintenance of cell size and membrane integrity prior to freezing. DMSO preservation also greatly enhanced post-thaw survival of cells slow-frozen at 1°C/min. We therefore demonstrate that in-cell DNP-NMR studies should be done with d6-DMSO as cryoprotectant and raise important considerations for the progression of in-cell DNP-NMR towards the goal of high quality structural studies.
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Affiliation(s)
- Sarah A Overall
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
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18
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Zhu S, Kachooei E, Harmer JR, Brown LJ, Separovic F, Sani MA. TOAC spin-labeled peptides tailored for DNP-NMR studies in lipid membrane environments. Biophys J 2021; 120:4501-4511. [PMID: 34480924 DOI: 10.1016/j.bpj.2021.08.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/08/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
The benefit of combining in-cell solid-state dynamic nuclear polarization (DNP) NMR and cryogenic temperatures is providing sufficient signal/noise and preservation of bacterial integrity via cryoprotection to enable in situ biophysical studies of antimicrobial peptides. The radical source required for DNP was delivered into cells by adding a nitroxide-tagged peptide based on the antimicrobial peptide maculatin 1.1 (Mac1). In this study, the structure, localization, and signal enhancement properties of a single (T-MacW) and double (T-T-MacW) TOAC (2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxylic acid) spin-labeled Mac1 analogs were determined within micelles or lipid vesicles. The solution NMR and circular dichroism results showed that the spin-labeled peptides adopted helical structures in contact with micelles. The peptides behaved as an isolated radical source in the presence of multilamellar vesicles, and the electron paramagnetic resonance (EPR) electron-electron distance for the doubly spin-labeled peptide was ∼1 nm. The strongest paramagnetic relaxation enhancement (PRE) was observed for the lipid NMR signals near the glycerol-carbonyl backbone and was stronger for the doubly spin-labeled peptide. Molecular dynamics simulation of the T-T-MacW radical source in phospholipid bilayers supported the EPR and PRE observations while providing further structural insights. Overall, the T-T-MacW peptide achieved better 13C and 15N signal NMR enhancements and 1H spin-lattice T1 relaxation than T-MacW.
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Affiliation(s)
- Shiying Zhu
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Ehsan Kachooei
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - Louise J Brown
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
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19
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Solid state NMR of membrane proteins: methods and applications. Biochem Soc Trans 2021; 49:1505-1513. [PMID: 34397082 DOI: 10.1042/bst20200070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/17/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
Abstract
Membranes of cells are active barriers, in which membrane proteins perform essential remodelling, transport and recognition functions that are vital to cells. Membrane proteins are key regulatory components of cells and represent essential targets for the modulation of cell function and pharmacological intervention. However, novel folds, low molarity and the need for lipid membrane support present serious challenges to the characterisation of their structure and interactions. We describe the use of solid state NMR as a versatile and informative approach for membrane and membrane protein studies, which uniquely provides information on structure, interactions and dynamics of membrane proteins. High resolution approaches are discussed in conjunction with applications of NMR methods to studies of membrane lipid and protein structure and interactions. Signal enhancement in high resolution NMR spectra through DNP is discussed as a tool for whole cell and interaction studies.
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20
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Sergeyev IV, Quinn CM, Struppe J, Gronenborn A, Polenova T. Competing Transfer Pathways in Direct and Indirect Dynamic Nuclear Polarization MAS NMR Experiments on HIV-1 Capsid Assemblies: Implications for Sensitivity and Resolution. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:239-249. [PMID: 34136885 PMCID: PMC8203495 DOI: 10.5194/mr-2-239-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/23/2021] [Indexed: 04/25/2023]
Abstract
Dynamic nuclear polarization-enhanced (DNP) magic angle spinning (MAS) NMR of biological systems is a rapidly growing field. Large signal enhancements make the technique particularly attractive for signal-limited cases, such as studies of complex biological assemblies or at natural isotopic abundance. However, spectral resolution is considerably reduced compared to ambient-temperature non-DNP spectra. Herein, we report a systematic investigation into sensitivity and resolution of 1D and 2D 13C-detected DNP MAS NMR experiments on HIV-1 CA tubular assemblies. We show that the magnitude and sign of signal enhancement as well as the homogeneous line width are strongly dependent on the biradical concentration, the dominant polarization transfer pathway, and the enhancement buildup time. Our findings provide guidance for optimal choice of sample preparation and experimental conditions in DNP experiments.
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Affiliation(s)
- Ivan V. Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
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21
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Gauto D, Dakhlaoui O, Marin-Montesinos I, Hediger S, De Paëpe G. Targeted DNP for biomolecular solid-state NMR. Chem Sci 2021; 12:6223-6237. [PMID: 34084422 PMCID: PMC8115112 DOI: 10.1039/d0sc06959k] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/18/2021] [Indexed: 12/23/2022] Open
Abstract
High-field dynamic nuclear polarization is revolutionizing the scope of solid-state NMR with new applications in surface chemistry, materials science and structural biology. In this perspective article, we focus on a specific DNP approach, called targeted DNP, in which the paramagnets introduced to polarize are not uniformly distributed in the sample but site-specifically located on the biomolecular system. After reviewing the various targeting strategies reported to date, including a bio-orthogonal chemistry-based approach, we discuss the potential of targeted DNP to improve the overall NMR sensitivity while avoiding the use of glass-forming DNP matrix. This is especially relevant to the study of diluted biomolecular systems such as, for instance, membrane proteins within their lipidic environment. We also discuss routes towards extracting structural information from paramagnetic relaxation enhancement (PRE) induced by targeted DNP at cryogenic temperature, and the possibility to recover site-specific information in the vicinity of the paramagnetic moieties using high-resolution selective DNP spectra. Finally, we review the potential of targeted DNP for in-cell NMR studies and how it can be used to extract a given protein NMR signal from a complex cellular background.
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Affiliation(s)
- Diego Gauto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Ons Dakhlaoui
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- Univ. Grenoble Alpes, CNRS, CERMAV Grenoble France
| | - Ildefonso Marin-Montesinos
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- University of Aveiro, CICECO Chem. Dept. Aveiro Portugal
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
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22
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Deo T, Cheng Q, Paul S, Qiang W, Potapov A. Application of DNP-enhanced solid-state NMR to studies of amyloid-β peptide interaction with lipid membranes. Chem Phys Lipids 2021; 236:105071. [PMID: 33716023 DOI: 10.1016/j.chemphyslip.2021.105071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/13/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022]
Abstract
The cellular membrane disruption induced by the aggregation of Aβ peptide has been proposed as a plausible cause of neuronal cell death during Alzheimer's disease. The molecular-level details of the Aβ interaction with cellular membranes were previously probed using solid state NMR (ssNMR), however, due to the limited sensitivity of the latter, studies were limited to samples with high Aβ-to-lipid ratio. The dynamic nuclear polarization (DNP) is a technique for increasing the sensitivity of NMR. In this work we demonstrate the feasibility of DNP-enhanced ssNMR studies of Aβ40 peptide interacting with various model liposomes: (1) a mixture of zwitterionic 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) and negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG); (2) a mixture of POPC, POPG, cholesterol, sphingomyelin and ganglioside GM1; (3) the synaptic plasma membrane vesicles (SPMVs) extracted from rat brain tissues. In addition, DNP-ssNMR was applied to capturing changes in Aβ40 conformation taking place upon the peptide insertion into POPG liposomes. The signal enhancements under conditions of DNP allow carrying out informative 2D ssNMR experiments with about 0.25 mg of Aβ40 peptides (i.e. reaching Aβ40-to-lipid ratio of 1:200). In the studied liposome models, the 13C NMR chemical shifts at many 13C-labelled sites of Aβ40 are characteristic of β-sheets. In addition, in POPG liposomes the peptide forms hydrophobic contacts F19-L34 and F19-I32. Both the chemical shifts and hydrophobic contacts of Aβ40 in POPG remain the same before and after 8 h of incubation. This suggests that conformation at the 13C-labelled sites of the peptide is similar before and after the insertion process. Overall, our results demonstrate that DNP helps to overcome the sensitivity limitation of ssNMR, and thereby expand the applicability of ssNMR for charactering the Aβ peptide interacting with lipids.
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Affiliation(s)
- Thomas Deo
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Qinghui Cheng
- Department of Chemistry, Binghamton University, the State University of New York, Binghamton, NY, 13902, USA
| | - Subhadip Paul
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Wei Qiang
- Department of Chemistry, Binghamton University, the State University of New York, Binghamton, NY, 13902, USA
| | - Alexey Potapov
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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23
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Nevzorov AA, Marek A, Milikisiyants S, Smirnov AI. Characterization of photonic band resonators for DNP NMR of thin film samples at 7 T magnetic field. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 323:106893. [PMID: 33418455 PMCID: PMC8362290 DOI: 10.1016/j.jmr.2020.106893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Polarization of nuclear spins via Dynamic Nuclear Polarization (DNP) relies on generating sufficiently high mm-wave B1e fields over the sample, which could be achieved by developing suitable resonance structures. Recently, we have introduced one-dimensional photonic band gap (1D PBG) resonators for DNP and reported on prototype devices operating at ca. 200 GHz electron resonance frequency. Here we systematically compare the performance of five (5) PBG resonators constructed from various alternating dielectric layers by monitoring the DNP effect on natural-abundance 13C spins in synthetic diamond microparticles embedded into a commercial polyester-based lapping film of just 3 mil (76 μm) thickness. An odd-numbered configuration of dielectric layers for 1D PBG resonator was introduced to achieve further B1e enhancements. Among the PBG configurations tested, combinations of high-ε perovskite LiTaO3 together with AlN as well as AlN with optical quartz wafers have resulted in ca. 40 to over 50- fold gains in the average mm-wave power over the sample vs. the mirror-only configuration. The results are rationalized in terms of the electromagnetic energy distribution inside the resonators obtained analytically and from COMSOL simulations. It was found that average of B1e2 over the sample strongly depends on the arrangement of the dielectric layers that are the closest to the sample, which favors odd-numbered PBG resonator configurations for their use in DNP.
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Affiliation(s)
- Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
| | - Antonin Marek
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
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24
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Miao Y, Lam D, Zhuang J, Zhu J, Poget SF, Tang M. Membrane Topology of an Ion Channel Detected by Solid-State Nuclear Magnetic Resonance and Paramagnetic Effects. J Phys Chem Lett 2020; 11:9795-9801. [PMID: 33151058 DOI: 10.1021/acs.jpclett.0c02014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ion channels are often targeted by toxins or other ligands to modify their channel activities and alter ion conductance. Interactions between toxins and ion channels could result in changes in membrane insertion depth for residues close to the binding site. Paramagnetic solid-state nuclear magnetic resonance (SSNMR) has shown great potential in providing structural information on membrane samples. We used KcsA as a model ion channel to investigate how the paramagnetic effects of Mn2+ and Dy3+ ions with headgroup-modified chelator lipids would influence the SSNMR signals of membrane proteins in proteoliposomes. Spectral comparisons have shown significant changes of peak intensities for the residues in the loop or terminal regions due to paramagnetic effects corresponding to the close proximity to the membrane surface. Hence, these results demonstrate that paramagnetic SSNMR can be used to detect surface residues based on the topology and membrane insertion properties for integral membrane proteins.
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Affiliation(s)
- Yimin Miao
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Dennis Lam
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Jianqin Zhuang
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Jing Zhu
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Sebastien F Poget
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Ming Tang
- Department of Chemistry, College of Staten Island-Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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25
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Zhai W, Lucini Paioni A, Cai X, Narasimhan S, Medeiros-Silva J, Zhang W, Rockenbauer A, Weingarth M, Song Y, Baldus M, Liu Y. Postmodification via Thiol-Click Chemistry Yields Hydrophilic Trityl-Nitroxide Biradicals for Biomolecular High-Field Dynamic Nuclear Polarization. J Phys Chem B 2020; 124:9047-9060. [PMID: 32961049 DOI: 10.1021/acs.jpcb.0c08321] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dynamic nuclear polarization (DNP) is a powerful method to enhance nuclear magnetic resonance (NMR) signal intensities, enabling unprecedented applications in life and material science. An ultimate goal is to expand the use of DNP-enhanced solid-state NMR to ultrahigh magnetic fields where optimal spectral resolution and sensitivity are integrated. Trityl-nitroxide (TN) biradicals have attracted significant interest in high-field DNP, but their application to complex (bio)molecules has so far been limited. Here we report a novel postmodification strategy for synthesis of hydrophilic TN biradicals in order to improve their use in biomolecular applications. Initially, three TN biradicals (referred to as NATriPols 1-3) with amino-acid linkers were synthesized. EPR studies showed that the α-position of the amino-acid linkers is an ideal modification site for these biradicals since their electron-electron magnetic interactions are marginally affected by the substituents at this position. On the basis of this finding, we synthesized NATriPol-4 with pyridine disulfide appended at the α-position. Postmodification of NATriPol-4 via thiol-click chemistry resulted in various TN biradicals including hydrophilic NATriPol-5 in a quantitative manner. Interestingly, DNP enhancements at 18.8 T of NATriPols for 13C,15N-proline in a glycerol/water matrix are inversely correlated with their hydrophobicity. Importantly, applications of hydrophilic NATriPol-5 and NATriPol-3 to biomolecules including a globular soluble protein and a membrane targeting peptide reveal significantly improved performance compared to TEMTriPol-1 and AMUPol. Our work provides an efficient approach for one-step synthesis of new polarizing agents with tunable physicochemical properties, thus expediting optimization of new biradicals for biomolecular applications at ultrahigh magnetic fields.
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Affiliation(s)
- Weixiang Zhai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Wenxiao Zhang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Hungarian Academy of Sciences, and Department of Physics, Budapest University of Technology and Economics, Budafokiut 8, 1111 Budapest, Hungary
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Yuguang Song
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, P. R. China
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26
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Tran NT, Mentink-Vigier F, Long JR. Dynamic Nuclear Polarization of Biomembrane Assemblies. Biomolecules 2020; 10:E1246. [PMID: 32867275 PMCID: PMC7565305 DOI: 10.3390/biom10091246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 01/02/2023] Open
Abstract
While atomic scale structural and dynamic information are hallmarks of nuclear magnetic resonance (NMR) methodologies, sensitivity is a fundamental limitation in NMR studies. Fully exploiting NMR capabilities to study membrane proteins is further hampered by their dilution within biological membranes. Recent developments in dynamic nuclear polarization (DNP), which can transfer the relatively high polarization of unpaired electrons to nuclear spins, show promise for overcoming the sensitivity bottleneck and enabling NMR characterization of membrane proteins under native-like conditions. Here we discuss fundamental aspects of DNP-enhanced solid-state NMR spectroscopy, experimental details relevant to the study of lipid assemblies and incorporated proteins, and sensitivity gains which can be realized in biomembrane-based samples. We also present unique insights which can be gained from DNP measurements and prospects for further development of the technique for elucidating structures and orientations of membrane proteins in native lipid environments.
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Affiliation(s)
- Nhi T. Tran
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA;
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA;
| | - Joanna R. Long
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA;
- Department of Biochemistry & Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
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27
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Chakraborty A, Deligey F, Quach J, Mentink-Vigier F, Wang P, Wang T. Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy. Biochem Soc Trans 2020; 48:1089-1099. [PMID: 32379300 PMCID: PMC7565284 DOI: 10.1042/bst20191084] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 01/07/2023]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing technique magic-angle spinning dynamic nuclear polarization (MAS-DNP) have substantially expanded the territory of ssNMR investigations and enabled the detection of polymer interfaces in a cellular environment. This article highlights the emerging MAS-DNP approaches and their applications to the analysis of biomolecular composites and intact cells to determine the folding pathway and ligand binding of proteins, the structural polymorphism of low-populated biopolymers, as well as the physical interactions between carbohydrates, proteins, and lignin. These structural features provide an atomic-level understanding of many cellular processes, promoting the development of better biomaterials and inhibitors. It is anticipated that the capabilities of MAS-DNP in biomolecular and biomaterial research will be further enlarged by the rapid development of instrumentation and methodology.
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Affiliation(s)
- Arnab Chakraborty
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jenny Quach
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Ping Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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28
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Kaminker I. Recent Advances in Magic Angle Spinning‐Dynamic Nuclear Polarization Methodology. Isr J Chem 2019. [DOI: 10.1002/ijch.201900092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ilia Kaminker
- School of ChemistryTel Aviv University Ramat Aviv 6997801 Tel Aviv Israel
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29
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Tang M, Lam D. Paramagnetic solid-state NMR of proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 103:9-16. [PMID: 31585788 DOI: 10.1016/j.ssnmr.2019.101621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
The paramagnetic properties of metal ions and stable radicals can affect NMR spectra, which can lead to changes in peak intensities, relaxation times and chemical shifts. The changes from paramagnetic effects provide intriguing opportunities for solid-state NMR studies of proteins. In this review, we summarized the trends and progress of paramagnetic solid-state NMR of proteins in the past decade, and showed that paramagnetic effects have great potential applications for sensitivity enhancement, structure determination and topological analysis for microcrystalline proteins, protein complexes, protein aggregates and membrane proteins.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Dennis Lam
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
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30
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Mandala VS, Hong M. High-sensitivity protein solid-state NMR spectroscopy. Curr Opin Struct Biol 2019; 58:183-190. [PMID: 31031067 PMCID: PMC6778492 DOI: 10.1016/j.sbi.2019.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 03/17/2019] [Accepted: 03/21/2019] [Indexed: 10/27/2022]
Abstract
The sensitivity of solid-state nuclear magnetic resonance (SSNMR) spectroscopy for structural biology is significantly increased by 1H detection under fast magic-angle spinning (MAS) and by dynamic nuclear polarization (DNP) from electron spins to nuclear spins. The former allows studies of the structure and dynamics of small quantities of proteins under physiological conditions, while the latter permits studies of large biomolecular complexes in lipid membranes and cells, protein intermediates, and protein conformational distributions. We highlight recent applications of these two emerging SSNMR technologies and point out areas for future development.
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Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States.
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31
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Application of millisecond time-resolved solid state NMR to the kinetics and mechanism of melittin self-assembly. Proc Natl Acad Sci U S A 2019; 116:16717-16722. [PMID: 31387974 DOI: 10.1073/pnas.1908006116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Common experimental approaches for characterizing structural conversion processes such as protein folding and self-assembly do not report on all aspects of the evolution from an initial state to the final state. Here, we demonstrate an approach that is based on rapid mixing, freeze-trapping, and low-temperature solid-state NMR (ssNMR) with signal enhancements from dynamic nuclear polarization (DNP). Experiments on the folding and tetramerization of the 26-residue peptide melittin following a rapid pH jump show that multiple aspects of molecular structure can be followed with millisecond time resolution, including secondary structure at specific isotopically labeled sites, intramolecular and intermolecular contacts between specific pairs of labeled residues, and overall structural order. DNP-enhanced ssNMR data reveal that conversion of conformationally disordered melittin monomers at low pH to α-helical conformations at neutral pH occurs on nearly the same timescale as formation of antiparallel melittin dimers, about 6 to 9 ms for 0.3 mM melittin at 24 °C in aqueous solution containing 20% (vol/vol) glycerol and 75 mM sodium phosphate. Although stopped-flow fluorescence data suggest that melittin tetramers form quickly after dimerization, ssNMR spectra show that full structural order within melittin tetramers develops more slowly, in ∼60 ms. Time-resolved ssNMR is likely to find many applications to biomolecular structural conversion processes, including early stages of amyloid formation, viral capsid formation, and protein-protein recognition.
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32
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Good DB, Voinov MA, Bolton D, Ward ME, Sergeyev IV, Caporini M, Scheffer P, Lo A, Rosay M, Marek A, Brown LS, I Smirnov A, Ladizhansky V. A biradical-tagged phospholipid as a polarizing agent for solid-state MAS Dynamic Nuclear Polarization NMR of membrane proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 100:92-101. [PMID: 31029957 PMCID: PMC6709687 DOI: 10.1016/j.ssnmr.2019.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/29/2019] [Accepted: 04/12/2019] [Indexed: 06/01/2023]
Abstract
A novel Dynamic Nuclear Polarization (DNP) NMR polarizing agent ToSMTSL-PTE representing a phospholipid with a biradical TOTAPOL tethered to the polar head group has been synthesized, characterized, and employed to enhance solid-state Nuclear Magnetic Resonance (SSNMR) signal of a lipid-reconstituted integral membrane protein proteorhodopsin (PR). A matrix-free PR formulation for DNP improved the absolute sensitivity of NMR signal by a factor of ca. 4 compared to a conventional preparation with TOTAPOL dispersed in a glassy glycerol/water matrix. DNP enhancements measured at 400 MHz/263 GHz and 600 MHz/395 GHz showed a strong field dependence but remained moderate at both fields, and comparable to those obtained for PR covalently modified with ToSMTSL. Additional continuous wave (CW) X-band electron paramagnetic resonance (EPR) experiments with ToSMTSL-PTE in solutions and in lipid bilayers revealed that an unfavorable conformational change of the linker connecting mononitroxides could be one of the reasons for moderate DNP enhancements. Further, differential scanning calorimetry (DSC) and CW EPR experiments indicated an inhomogeneous distribution and/or a possibility of a partial aggregation of ToSMTSL-PTE in DMPC:DMPA bilayers when the concentration of the polarizing agent was increased to 20 mol% to maximize the DNP enhancement. Thus, conformational changes and an inhomogeneous distribution of the lipid-based biradicals in lipid bilayers emerged as important factors to consider for further development of this matrix-free approach for DNP of membrane proteins.
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Affiliation(s)
- Daryl B Good
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Maxim A Voinov
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - David Bolton
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Meaghan E Ward
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Peter Scheffer
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Andy Lo
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | | | - Antonin Marek
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA; Bruker Biospin, Billerica, MA, USA.
| | - Vlad Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada; Bruker Biospin, Billerica, MA, USA.
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33
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Salnikov ES, Aussenac F, Abel S, Purea A, Tordo P, Ouari O, Bechinger B. Dynamic Nuclear Polarization / solid-state NMR of membranes. Thermal effects and sample geometry. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 100:70-76. [PMID: 30995597 DOI: 10.1016/j.ssnmr.2019.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Whereas specially designed dinitroxide biradicals, reconstitution protocols, oriented sample geometries and NMR probes have helped to much increase the DNP enhancement factors of membrane samples they still lag considerably behind those obtained from glasses made of protein solutions. Here we show that not only the MAS rotor material but also the distribution of the membrane samples within the NMR rotor have a pronounced effect on the DNP enhancement. These observations are rationalized with the cooling efficiency and the internal properties of the sample, monitored by their T1 relaxation, microwave ON versus OFF signal intensities and DNP effect. The data are suggestive that for membranes the speed of cooling has a pronounced effect on the membrane properties and concomitantly the distribution of biradicals within the sample.
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Affiliation(s)
| | | | - Sebastian Abel
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | | | - Paul Tordo
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | - Olivier Ouari
- Aix-Marseille University, CNRS, UMR 7273, Institut de Chimie Radicalaire, 13013, Marseille, France
| | - Burkhard Bechinger
- Institute of Chemistry, University of Strasbourg / CNRS, UMR7177, 67070, Strasbourg, France.
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34
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Wang X, Caulkins BG, Riviere G, Mueller LJ, Mentink-Vigier F, Long JR. Direct dynamic nuclear polarization of 15N and 13C spins at 14.1 T using a trityl radical and magic angle spinning. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 100:85-91. [PMID: 31026722 PMCID: PMC6604067 DOI: 10.1016/j.ssnmr.2019.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 05/05/2023]
Abstract
We investigate solid-state dynamic nuclear polarization of 13C and 15N nuclei using monoradical trityl OX063 as a polarizing agent in a magnetic field of 14.1 T with magic angle spinning at ∼100 K. We monitored the field dependence of direct 13C and 15N polarization for frozen [13C, 15N] urea and achieved maximum absolute enhancement factors of 240 and 470, respectively. The field profiles are consistent with polarization of 15N spins via either the solid effect or the cross effect, and polarization of 13C spins via a combination of cross effect and solid effect. For microcrystalline, 15N-enriched tryptophan synthase sample containing trityl radical, a 1500-fold increase in 15N signal was observed under microwave irradiation. These results show the promise of trityl radicals and their derivatives for direct polarization of low gamma, spin-½ nuclei at high magnetic fields and suggest a novel approach for selectively polarizing specific moieties or for polarizing systems which have low levels of protonation.
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Affiliation(s)
- Xiaoling Wang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32310, USA
| | - Bethany G Caulkins
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Gwladys Riviere
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute and National High Magnetic Field Laboratory, University of Florida, Gainesville, FL, 32610-0245, USA
| | - Leonard J Mueller
- Department of Chemistry, University of California Riverside, Riverside, CA, 92521, USA
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32310, USA
| | - Joanna R Long
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute and National High Magnetic Field Laboratory, University of Florida, Gainesville, FL, 32610-0245, USA.
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35
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Solid-State NMR Approaches to Study Protein Structure and Protein-Lipid Interactions. Methods Mol Biol 2019. [PMID: 31218633 DOI: 10.1007/978-1-4939-9512-7_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Solid-state NMR spectroscopy has been developed for the investigation of membrane-associated polypeptides and remains one of the few techniques to reveal high-resolution structural information in liquid-disordered phospholipid bilayers. In particular, oriented samples have been used to investigate the structure, dynamics and topology of membrane polypeptides. Much of the previous solid-state NMR work has been developed and performed on peptides but the technique is constantly expanding towards larger membrane proteins. Here, a number of protocols are presented describing among other the reconstitution of membrane proteins into oriented membranes, monitoring membrane alignment by 31P solid-state NMR spectroscopy, investigations of the protein by one- and two-dimensional 15N solid-state NMR and measurements of the lipid order parameters using 2H solid-state NMR spectroscopy. Using such methods solid-state NMR spectroscopy has revealed a detailed picture of the ensemble of both lipids and proteins and their mutual interdependence in the bilayer environment.
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36
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Al-Harthi S, Lachowicz JI, Nowakowski ME, Jaremko M, Jaremko Ł. Towards the functional high-resolution coordination chemistry of blood plasma human serum albumin. J Inorg Biochem 2019; 198:110716. [PMID: 31153112 DOI: 10.1016/j.jinorgbio.2019.110716] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 12/11/2022]
Abstract
Human serum albumin (HSA) is a monomeric, globular, multi-carrier and the most abundant protein in the blood. HSA displays multiple ligand binding sites with extraordinary binding capacity for a wide range of ions and molecules. For decades, HSA's ability to bind to various ligands has led many scientists to study its physiological properties and protein structure; indeed, a better understanding of HSA-ligand interactions in human blood, at the atomic level, will likely foster the development of more potent, and overall more performant, diagnostic and therapeutic tools against serious human disorders such as diabetes, cardiovascular disorders, and cancer. Here, we present a concise overview of the current knowledge of HSA's structural characteristics, and its coordination chemistry with transition metal ions, within the scope and limitations of current techniques and biophysical methods to reach atomic resolution in solution and in blood serum. We also highlight the overwhelming need of a detailed atomistic understanding of HSA dynamic structures and interactions that are transient, weak, multi-site and multi-step, and allosterically affected by each other. Considering the fact that HSA is a current clinical tool for drug delivery systems and a potential contender as molecular cargo and nano-vehicle used in biophysical, clinical and industrial fields, we underline the emerging need for novel approaches to target the dynamic functional coordination chemistry of the human blood serum albumin in solution, at the atomic level.
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Affiliation(s)
- Samah Al-Harthi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), 23955-6900 Thuwal, Saudi Arabia
| | - Joanna Izabela Lachowicz
- Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria, I-09042 Monserrato, Cagliari, Italy
| | - Michal Eligiusz Nowakowski
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), 23955-6900 Thuwal, Saudi Arabia; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Mariusz Jaremko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), 23955-6900 Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), 23955-6900 Thuwal, Saudi Arabia.
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37
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Bolla JR, Agasid MT, Mehmood S, Robinson CV. Membrane Protein-Lipid Interactions Probed Using Mass Spectrometry. Annu Rev Biochem 2019; 88:85-111. [PMID: 30901263 DOI: 10.1146/annurev-biochem-013118-111508] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins that exist in lipid bilayers are not isolated molecular entities. The lipid molecules that surround them play crucial roles in maintaining their full structural and functional integrity. Research directed at investigating these critical lipid-protein interactions is developing rapidly. Advancements in both instrumentation and software, as well as in key biophysical and biochemical techniques, are accelerating the field. In this review, we provide a brief outline of structural techniques used to probe protein-lipid interactions and focus on the molecular aspects of these interactions obtained from native mass spectrometry (native MS). We highlight examples in which lipids have been shown to modulate membrane protein structure and show how native MS has emerged as a complementary technique to X-ray crystallography and cryo-electron microscopy. We conclude with a short perspective on future developments that aim to better understand protein-lipid interactions in the native environment.
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Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Mark T Agasid
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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38
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Mandala VS, Liao SY, Gelenter MD, Hong M. The Transmembrane Conformation of the Influenza B Virus M2 Protein in Lipid Bilayers. Sci Rep 2019; 9:3725. [PMID: 30842530 PMCID: PMC6403292 DOI: 10.1038/s41598-019-40217-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Influenza A and B viruses cause seasonal flu epidemics. The M2 protein of influenza B (BM2) is a membrane-embedded tetrameric proton channel that is essential for the viral lifecycle. BM2 is a functional analog of AM2 but shares only 24% sequence identity for the transmembrane (TM) domain. The structure and function of AM2, which is targeted by two antiviral drugs, have been well characterized. In comparison, much less is known about the structure of BM2 and no drug is so far available to inhibit this protein. Here we use solid-state NMR spectroscopy to investigate the conformation of BM2(1-51) in phospholipid bilayers at high pH, which corresponds to the closed state of the channel. Using 2D and 3D correlation NMR experiments, we resolved and assigned the 13C and 15N chemical shifts of 29 residues of the TM domain, which yielded backbone (φ, ψ) torsion angles. Residues 6-28 form a well-ordered α-helix, whereas residues 1-5 and 29-35 display chemical shifts that are indicative of random coil or β-sheet conformations. The length of the BM2-TM helix resembles that of AM2-TM, despite their markedly different amino acid sequences. In comparison, large 15N chemical shift differences are observed between bilayer-bound BM2 and micelle-bound BM2, indicating that the TM helix conformation and the backbone hydrogen bonding in lipid bilayers differ from the micelle-bound conformation. Moreover, HN chemical shifts of micelle-bound BM2 lack the periodic trend expected for coiled coil helices, which disagree with the presence of a coiled coil structure in micelles. These results establish the basis for determining the full three-dimensional structure of the tetrameric BM2 to elucidate its proton-conduction mechanism.
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Affiliation(s)
- Venkata S Mandala
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Shu-Yu Liao
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA.
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Lacabanne D, Fogeron ML, Wiegand T, Cadalbert R, Meier BH, Böckmann A. Protein sample preparation for solid-state NMR investigations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 110:20-33. [PMID: 30803692 DOI: 10.1016/j.pnmrs.2019.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
Preparation of a protein sample for solid-state NMR is in many aspects similar to solution-state NMR approaches, mainly with respect to the need for stable isotope labeling. But the possibility of using solid-state NMR to investigate membrane proteins in (native) lipids adds the important requirement of adapted membrane-reconstitution schemes. Also, dynamic nuclear polarization and paramagnetic NMR in solids need specific schemes using metal ions and radicals. Sample sedimentation has enabled structural investigations of objects inaccessible to other structural techniques, but rotor filling using sedimentation has become increasingly complex with smaller and smaller rotors, as needed for higher and higher magic-angle spinning (MAS) frequencies. Furthermore, solid-state NMR can investigate very large proteins and their complexes without the concomitant increase in line widths, motivating the use of selective labeling and unlabeling strategies, as well as segmental labeling, to decongest spectra. The possibility of investigating sub-milligram amounts of protein today using advanced fast MAS techniques enables alternative protein synthesis schemes such as cell-free expression. Here we review these specific aspects of solid-state NMR sample preparation.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France; Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France.
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40
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Nevzorov AA, Milikisiyants S, Marek AN, Smirnov AI. Multi-resonant photonic band-gap/saddle coil DNP probehead for static solid state NMR of microliter volume samples. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 297:113-123. [PMID: 30380458 PMCID: PMC6894392 DOI: 10.1016/j.jmr.2018.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/18/2018] [Accepted: 10/20/2018] [Indexed: 05/04/2023]
Abstract
The most critical condition for performing Dynamic Nuclear Polarization (DNP) NMR experiments is achieving sufficiently high electronic B1e fields over the sample at the matched EPR frequencies, which for modern high-resolution NMR instruments fall into the millimeter wave (mmW) range. Typically, mmWs are generated by powerful gyrotrons and/or extended interaction klystrons (EIKs) sources and then focused onto the sample by dielectric lenses. However, further development of DNP methods including new DNP pulse sequences may require B1e fields higher than one could achieve with the current mmW technology. In order to address the challenge of significantly enhancing the mmW field at the sample, we have constructed and tested one-dimensional photonic band-gap (PBG) mmW resonator that was incorporated inside a double-tuned radiofrequency (rf) NMR saddle coil. The photonic crystal is formed by stacking ceramic discs with alternating high and low dielectric constants and thicknesses of λ/4 or 3λ/4, where λ is the wavelength of the incident mmW field in the corresponding dielectric material. When the mmW frequency is within the band gap of the photonic crystal, a defect created in the middle of the crystal confines the mmW energy, thus forming a resonant structure. An aluminum mirror in the middle of the defect has been used to substitute one-half of the structure with its mirror image in order to reduce the resonator size and simplify its tuning. The latter is achieved by adjusting the width of the defect by moving the aluminum mirror with respect to the dielectric stack using a gear mechanism. The 1D PBG resonator was the key element for constructing a multi-resonant integrated DNP/NMR probehead operating at 190-199 GHz EPR/300 MHz 1H/75.5 MHz 13C NMR frequencies. Initial tests of the multi-resonant DNP/NMR probehead were carried out using a quasioptical mmW bridge and a Bruker Biospin Avance II spectrometer equipped with a standard Bruker 7 T wide-bore 89 mm magnet parked at 300.13 MHz 1H NMR frequency. The mmW bridge built with all solid-state active components allows for the frequency tuning between ca. 190 and ca. 199 GHz with the output power up to 27 dBm (0.5 W) at 192 GHz and up to 23 dBm (0.2 W) at 197.5 GHz. Room temperature DNP experiments with a synthetic single crystal high-pressure high-temperature (HPHT) diamond (0.3 × 0.3 × 3.0 mm3) demonstrated dramatic 1500-fold enhancement of 13C natural abundance NMR signal at full incident mmW power. Significant 13C DNP enhancement (of about 90) have been obtained at incident mmW powers of as low as <100 μW. Further tests of the resonator performance have been carried out with a thin (ca. 100 μm thickness) composite polystyrene-microdiamond film by controlling the average mmW power at the optimal DNP conditions via a gated mode of operation. From these experiments, the PBG resonator with loaded Q ≃ 250 and finesse F≈75 provides up to 12-fold or 11 db gain in the average mmW power vs. the non-resonant probehead configuration employing only a reflective mirror.
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Affiliation(s)
- Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
| | - Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Antonin N Marek
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
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41
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Medeiros-Silva J, Jekhmane S, Paioni AL, Gawarecka K, Baldus M, Swiezewska E, Breukink E, Weingarth M. High-resolution NMR studies of antibiotics in cellular membranes. Nat Commun 2018; 9:3963. [PMID: 30262913 PMCID: PMC6160437 DOI: 10.1038/s41467-018-06314-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/23/2018] [Indexed: 01/12/2023] Open
Abstract
The alarming rise of antimicrobial resistance requires antibiotics with unexploited mechanisms. Ideal templates could be antibiotics that target the peptidoglycan precursor lipid II, known as the bacterial Achilles heel, at an irreplaceable pyrophosphate group. Such antibiotics would kill multidrug-resistant pathogens at nanomolecular concentrations without causing antimicrobial resistance. However, due to the challenge of studying small membrane-embedded drug–receptor complexes in native conditions, the structural correlates of the pharmaceutically relevant binding modes are unknown. Here, using advanced highly sensitive solid-state NMR setups, we present a high-resolution approach to study lipid II-binding antibiotics directly in cell membranes. On the example of nisin, the preeminent lantibiotic, we show that the native antibiotic-binding mode strongly differs from previously published structures, and we demonstrate that functional hotspots correspond to plastic drug domains that are critical for the cellular adaptability of nisin. Thereby, our approach provides a foundation for an improved understanding of powerful antibiotics. Antibiotics that target the peptidoglycan precursor lipid II are promising templates for next-generation antibiotics. Here authors use solid-state NMR and monitor lipid II-binding antibiotics, such as nisin, directly in cell membranes.
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Affiliation(s)
- João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shehrazade Jekhmane
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Katarzyna Gawarecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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42
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Jaudzems K, Bertarello A, Chaudhari SR, Pica A, Cala-De Paepe D, Barbet-Massin E, Pell AJ, Akopjana I, Kotelovica S, Gajan D, Ouari O, Tars K, Pintacuda G, Lesage A. Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kristaps Jaudzems
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Bertarello
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Sachin R. Chaudhari
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia I-80126 Naples Italy
| | - Diane Cala-De Paepe
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Emeline Barbet-Massin
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrew J. Pell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
- Present address: Department of Materials and Environmental Chemistry; Arrhenius Laboratory; Stockholm University; Svante Arrhenius Väg 16 C SE-106 91 Stockholm Sweden
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | | | - David Gajan
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273; 13397 Marseille cedex 20 France
| | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | - Guido Pintacuda
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Anne Lesage
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
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43
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Jaudzems K, Bertarello A, Chaudhari SR, Pica A, Cala-De Paepe D, Barbet-Massin E, Pell AJ, Akopjana I, Kotelovica S, Gajan D, Ouari O, Tars K, Pintacuda G, Lesage A. Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning. Angew Chem Int Ed Engl 2018; 57:7458-7462. [DOI: 10.1002/anie.201801016] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/06/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Kristaps Jaudzems
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Bertarello
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Sachin R. Chaudhari
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia I-80126 Naples Italy
| | - Diane Cala-De Paepe
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Emeline Barbet-Massin
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrew J. Pell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
- Present address: Department of Materials and Environmental Chemistry; Arrhenius Laboratory; Stockholm University; Svante Arrhenius Väg 16 C SE-106 91 Stockholm Sweden
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | | | - David Gajan
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273; 13397 Marseille cedex 20 France
| | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | - Guido Pintacuda
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Anne Lesage
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
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44
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Itin B, Sergeyev IV. Strategies for Efficient Sample Preparation for Dynamic Nuclear Polarization Solid-State NMR of Biological Macromolecules. Methods Mol Biol 2018; 1688:133-154. [PMID: 29151208 DOI: 10.1007/978-1-4939-7386-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Solid-state NMR (SSNMR) is a powerful tool for the elucidation of structure and dynamics in biological macromolecules. Over the years, SSNMR spectroscopists have developed an array of techniques enabling the measurement of internuclear correlations, distances, and torsional angles; these have been applied to the study of a number of biological systems that are difficult to study by X-ray crystallography and solution NMR, including key biological targets such as membrane proteins and amyloid fibrils. Applications of SSNMR to other topic areas, including materials science, pharmaceuticals, and small molecules, have also flourished in recent years. These studies, however, have always been hampered by the low inherent sensitivity of SSNMR, requiring large amounts of both sample and time for data collection. By taking advantage of unpaired electrons doped into a sample as a ready source of additional nuclear polarization, dynamic nuclear polarization (DNP) has brought about large improvements in SSNMR sensitivity. These, in turn, have enabled structural studies of previously inaccessible targets, such as large protein complexes, nucleic acids, viral capsids, and membrane proteins in vivo. Herein, we focus on sample preparation strategies and considerations for scientists interested in applying DNP to challenging systems.
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Affiliation(s)
- Boris Itin
- New York Structural Biology Center, 89 Convent Avenue, New York, NY, 10027, USA.
| | - Ivan V Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, USA
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45
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Elkins MR, Williams JK, Gelenter MD, Dai P, Kwon B, Sergeyev IV, Pentelute BL, Hong M. Cholesterol-binding site of the influenza M2 protein in lipid bilayers from solid-state NMR. Proc Natl Acad Sci U S A 2017; 114:12946-12951. [PMID: 29158386 PMCID: PMC5724280 DOI: 10.1073/pnas.1715127114] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The influenza M2 protein not only forms a proton channel but also mediates membrane scission in a cholesterol-dependent manner to cause virus budding and release. The atomic interaction of cholesterol with M2, as with most eukaryotic membrane proteins, has long been elusive. We have now determined the cholesterol-binding site of the M2 protein in phospholipid bilayers using solid-state NMR spectroscopy. Chain-fluorinated cholesterol was used to measure cholesterol proximity to M2 while sterol-deuterated cholesterol was used to measure bound-cholesterol orientation in lipid bilayers. Carbon-fluorine distance measurements show that at a cholesterol concentration of 17 mol%, two cholesterol molecules bind each M2 tetramer. Cholesterol binds the C-terminal transmembrane (TM) residues, near an amphipathic helix, without requiring a cholesterol recognition sequence motif. Deuterium NMR spectra indicate that bound cholesterol is approximately parallel to the bilayer normal, with the rough face of the sterol rings apposed to methyl-rich TM residues. The distance- and orientation-restrained cholesterol-binding site structure shows that cholesterol is stabilized by hydrophobic interactions with the TM helix and polar and aromatic interactions with neighboring amphipathic helices. At the 1:2 binding stoichiometry, lipid 31P spectra show an isotropic peak indicative of high membrane curvature. This M2-cholesterol complex structure, together with previously observed M2 localization at phase boundaries, suggests that cholesterol mediates M2 clustering to the neck of the budding virus to cause the necessary curvature for membrane scission. The solid-state NMR approach developed here is generally applicable for elucidating the structural basis of cholesterol's effects on membrane protein function.
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Affiliation(s)
- Matthew R Elkins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jonathan K Williams
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139;
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46
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Lilly Thankamony AS, Wittmann JJ, Kaushik M, Corzilius B. Dynamic nuclear polarization for sensitivity enhancement in modern solid-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:120-195. [PMID: 29157490 DOI: 10.1016/j.pnmrs.2017.06.002] [Citation(s) in RCA: 273] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/03/2017] [Accepted: 06/08/2017] [Indexed: 05/03/2023]
Abstract
The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.
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Affiliation(s)
- Aany Sofia Lilly Thankamony
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Johannes J Wittmann
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Monu Kaushik
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany.
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47
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Visscher KM, Medeiros-Silva J, Mance D, Rodrigues JPGLM, Daniëls M, Bonvin AMJJ, Baldus M, Weingarth M. Supramolekulare Organisation und funktionale Auswirkungen von Ballungen von K +
-Kanälen in Membranen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Koen M. Visscher
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - João P. G. L. M. Rodrigues
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Mark Daniëls
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Alexandre M. J. J. Bonvin
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry; Utrecht University; Pandualaan 8 3584 CH Utrecht Niederlande
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48
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Visscher KM, Medeiros‐Silva J, Mance D, Rodrigues JPGLM, Daniëls M, Bonvin AMJJ, Baldus M, Weingarth M. Supramolecular Organization and Functional Implications of K + Channel Clusters in Membranes. Angew Chem Int Ed Engl 2017; 56:13222-13227. [PMID: 28685953 PMCID: PMC5655921 DOI: 10.1002/anie.201705723] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/29/2017] [Indexed: 11/19/2022]
Abstract
The segregation of cellular surfaces in heterogeneous patches is considered to be a common motif in bacteria and eukaryotes that is underpinned by the observation of clustering and cooperative gating of signaling membrane proteins such as receptors or channels. Such processes could represent an important cellular strategy to shape signaling activity. Hence, structural knowledge of the arrangement of channels or receptors in supramolecular assemblies represents a crucial step towards a better understanding of signaling across membranes. We herein report on the supramolecular organization of clusters of the K+ channel KcsA in bacterial membranes, which was analyzed by a combination of DNP-enhanced solid-state NMR experiments and MD simulations. We used solid-state NMR spectroscopy to determine the channel-channel interface and to demonstrate the strong correlation between channel function and clustering, which suggests a yet unknown mechanism of communication between K+ channels.
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Affiliation(s)
- Koen M. Visscher
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - João Medeiros‐Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - João P. G. L. M. Rodrigues
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Mark Daniëls
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Alexandre M. J. J. Bonvin
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of ChemistryUtrecht UniversityPandualaan 83584CHUtrechtThe Netherlands
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49
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Ni QZ, Yang F, Can TV, Sergeyev IV, D’Addio SM, Jawla SK, Li Y, Lipert MP, Xu W, Williamson RT, Leone A, Griffin RG, Su Y. In Situ Characterization of Pharmaceutical Formulations by Dynamic Nuclear Polarization Enhanced MAS NMR. J Phys Chem B 2017; 121:8132-8141. [PMID: 28762740 PMCID: PMC5592962 DOI: 10.1021/acs.jpcb.7b07213] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A principal advantage of magic angle spinning (MAS) NMR spectroscopy lies in its ability to determine molecular structure in a noninvasive and quantitative manner. Accordingly, MAS should be widely applicable to studies of the structure of active pharmaceutical ingredients (API) and formulations. However, the low sensitivity encountered in spectroscopy of natural abundance APIs present at low concentration has limited the success of MAS experiments. Dynamic nuclear polarization (DNP) enhances NMR sensitivity and can be used to circumvent this problem provided that suitable paramagnetic polarizing agent can be incorporated into the system without altering the integrity of solid dosages. Here, we demonstrate that DNP polarizing agents can be added in situ during the preparation of amorphous solid dispersions (ASDs) via spray drying and hot-melt extrusion so that ASDs can be examined during drug development. Specifically, the dependence of DNP enhancement on sample composition, radical concentration, relaxation properties of the API and excipients, types of polarizing agents and proton density, has been thoroughly investigated. Optimal enhancement values are obtained from ASDs containing 1% w/w radical concentration. Both polarizing agents TOTAPOL and AMUPol provided reasonable enhancements. Partial deuteration of the excipient produced 3× higher enhancement values. With these parameters, an ASD containing posaconazole and vinyl acetate yields a 32-fold enhancement which presumably results in a reduction of NMR measurement time by ∼1000. This boost in signal intensity enables the full assignment of the natural abundance pharmaceutical formulation through multidimensional correlation experiments.
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Affiliation(s)
- Qing Zhe Ni
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Fengyuan Yang
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Thach V. Can
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ivan V. Sergeyev
- Bruker BioSpin Corporation, Billerica, Massachusetts 01821, United States
| | - Suzanne M. D’Addio
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Sudheer K. Jawla
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yongjun Li
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Maya P. Lipert
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - R. Thomas Williamson
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Anthony Leone
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yongchao Su
- Merck Research Laboratories, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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50
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Rogawski R, McDermott AE. New NMR tools for protein structure and function: Spin tags for dynamic nuclear polarization solid state NMR. Arch Biochem Biophys 2017; 628:102-113. [PMID: 28623034 PMCID: PMC5815514 DOI: 10.1016/j.abb.2017.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/05/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022]
Abstract
Magic angle spinning solid state NMR studies of biological macromolecules [1-3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University, NY, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, NY, NY 10027, United States.
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