1
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Zheng Z, Schmidt-Rohr K. Phenolic syringyl end groups in 13C-enriched hardwoods detected and quantified by solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 133:101947. [PMID: 39067393 DOI: 10.1016/j.ssnmr.2024.101947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/14/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
While syringyl units are the most abundant monolignols in hardwood lignin, their phenolic (i.e. hydroxyl) end group concentration has not been measured. In two uniformly 13C-enriched young hardwoods, from beech and oak, the syringyl units were quantitatively investigated by advanced solid-state 13C NMR. Small signals of OH-terminated syringyl units were resolved in spectrally edited two-dimensional 13C-13C NMR spectra of the two hardwoods. Their distinct peak positions predicted based on literature data were validated via the abundant OH-terminated syringyl units in hydrolyzed 13C-beechwood. In a two-dimensional 13C-13C exchange spectrum with diagonal-ridge suppression, a well-resolved peak of phenolic syringyl units was observed at the characteristic C-H peak position of syringyl rings, without significant overlap from guaiacyl peaks. Accurate 13C chemical shifts of regular and end-group syringyl units were obtained. Through spectrally edited 2D NMR after 1H inversion recovery, phenols of condensed tannin complexed with arginine were carefully analyzed and shown to overlap minimally with signals from phenolic syringyl units. The local structure and resulting spin dynamics of ether (chain) and hydroxyl (end-group) syringyl units are nearly the same, enabling quantification by peak integration or deconvolution, which shows that phenolic syringyl end groups account for 2 ± 1 % of syringyl units in beechwood and 5 ± 2 % in oakwood. The observed low end-group concentration needs to be taken into account in realistic molecular models of hardwood lignin structure.
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Affiliation(s)
- Zhaoxi Zheng
- Department of Chemistry, Brandeis University, Waltham, MA, 02453, United States
| | - Klaus Schmidt-Rohr
- Department of Chemistry, Brandeis University, Waltham, MA, 02453, United States.
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2
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Overall SA, Hartmann SJ, Luu-Nguyen QH, Judge P, Pinotsi D, Marti L, Sigurdsson ST, Wender PA, Barnes AB. Topological Heterogeneity of Protein Kinase C Modulators in Human T-Cells Resolved with In-Cell Dynamic Nuclear Polarization NMR Spectroscopy. J Am Chem Soc 2024. [PMID: 39322225 DOI: 10.1021/jacs.4c05704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Phorbol ester analogs are a promising class of anticancer therapeutics and HIV latency reversing agents that interact with cellular membranes to recruit and activate protein kinase C (PKC) isoforms. However, it is unclear how these esters interact with membranes and how this might correlate with the biological activity of different phorbol ester analogs. Here, we have employed dynamic nuclear polarization (DNP) NMR to characterize phorbol esters in a native cellular context. The enhanced NMR sensitivity afforded by DNP and cryogenic operation reveals topological heterogeneity of 13C-21,22-phorbol-myristate-acetate (PMA) within T cells utilizing 13C-13C correlation and double quantum filtered NMR spectroscopy. We demonstrate the detection of therapeutically relevant amounts of PMA in T cells down to an upper limit of ∼60.0 pmol per million cells and identify PMA to be primarily localized in cellular membranes. Furthermore, we observe distinct 13C-21,22-PMA chemical shifts under DNP conditions in cells compared to model membrane samples and homogenized cell membranes, that cannot be accounted for by differences in conformation. We provide evidence for distinct membrane topologies of 13C-21,22-PMA in cell membranes that are consistent with shallow binding modes. This is the first of its kind in-cell DNP characterization of small molecules dissolved in the membranes of living cells, establishing in-cell DNP-NMR as an important method for the characterization of drug-membrane interactions within the context of the complex heterogeneous environment of intact cellular membranes. This work sets the stage for the identification of the in-cell structural interactions that govern the biological activity of phorbol esters.
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Affiliation(s)
- Sarah A Overall
- Institute of Molecular Physical Science, ETH Zurich, 8093 Zurich, Switzerland
| | - Sina J Hartmann
- Institute of Molecular Physical Science, ETH Zurich, 8093 Zurich, Switzerland
| | - Quang H Luu-Nguyen
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Patrick Judge
- Department of Biochemistry, Biophysics, & Structural Biology, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, 8093 Zurich, Switzerland
| | - Lea Marti
- Institute of Molecular Physical Science, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Paul A Wender
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Alexander B Barnes
- Institute of Molecular Physical Science, ETH Zurich, 8093 Zurich, Switzerland
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3
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Harding BD, Barclay AM, Piehl DW, Hiett A, Warmuth OA, Han R, Henzler-Wildman K, Rienstra CM. Cross polarization stability in multidimensional NMR spectroscopy of biological solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107724. [PMID: 38991266 PMCID: PMC11364147 DOI: 10.1016/j.jmr.2024.107724] [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: 10/06/2023] [Revised: 06/03/2024] [Accepted: 06/16/2024] [Indexed: 07/13/2024]
Abstract
Magic-angle spinning (MAS) solid-state nuclear magnetic resonance (SSNMR) spectroscopy is a powerful and versatile technique for probing structure and dynamics in large, insoluble biological systems at atomic resolution. With many recent advances in instrumentation and polarization methods, technology development in SSNMR remains an active area of research and presents opportunities to further improve data collection, processing, and analysis of samples with low sensitivity and complex tertiary and quaternary structures. SSNMR spectra are often collected as multidimensional data, requiring stable experimental conditions to minimize signal fluctuations (t1 noise). In this work, we examine the factors adversely affecting signal stability as well as strategies used to mitigate them, considering laboratory environmental requirements, configuration of amplifiers, and pulse sequence parameter selection. We show that Thermopad® temperature variable attenuators (TVAs) can partially compensate for the changes in amplifier output power as a function of temperature and thereby ameliorate one significant source of instability for some spectrometers and pulse sequences. We also consider the selection of tangent ramped cross polarization (CP) waveform shapes, to balance the requirements of sensitivity and instrumental stability. These findings collectively enable improved stability and overall performance for CP-based multidimensional spectra of microcrystalline, membrane, and fibrous proteins performed at multiple magnetic field strengths.
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Affiliation(s)
- Benjamin D Harding
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Alexander M Barclay
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dennis W Piehl
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ashley Hiett
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Owen A Warmuth
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ruixian Han
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Katherine Henzler-Wildman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Chad M Rienstra
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706 USA; Morgridge Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706 USA.
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4
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Chávez M, Ernst M. Continuous Floquet theory in solid-state NMR. J Chem Phys 2024; 160:244111. [PMID: 38940539 DOI: 10.1063/5.0213078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
This article presents the application of continuous Floquet theory in solid-state nuclear magnetic resonance (NMR). Continuous Floquet theory extends the traditional Floquet theory to non-continuous Hamiltonians, enabling the description of observable effects not fully captured by the traditional Floquet theory due to its requirement for a periodic Hamiltonian. We present closed-form expressions for computing first- and second-order effective Hamiltonians, streamlining integration with the traditional Floquet theory and facilitating application in NMR experiments featuring multiple modulation frequencies. Subsequently, we show examples of the practical application of continuous Floquet theory by investigating several solid-state NMR experiments. These examples illustrate the importance of the duration of the pulse scheme regarding the width of the resonance conditions and the near-resonance behavior.
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Affiliation(s)
- Matías Chávez
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Matthias Ernst
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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5
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Nimerovsky E, Kosteletos S, Lange S, Becker S, Lange A, Andreas LB. Homonuclear Simplified Preservation of Equivalent Pathways Spectroscopy. J Phys Chem Lett 2024; 15:6272-6278. [PMID: 38856103 PMCID: PMC11194807 DOI: 10.1021/acs.jpclett.4c00991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
Recently developed homonuclear transverse mixing optimal control pulses (hTROP) revealed an elegant way to enhance the detected signal in multidimensional magic-angle spinning (MAS) nuclear magnetic resonance experiments. Inspired by their work, we present two homonuclear simplified preservation of equivalent pathways spectroscopy (hSPEPS) sequences for recoupling CA-CO and CA-CB dipolar couplings under fast and ultrafast MAS rates, theoretically enabling a √2 improvement in sensitivity for each indirect dimension. The efficiencies of hSPEPS are evaluated for non-deuterated samples of influenza A M2 and bacterial rhomboid protease GlpG under two different external magnetic fields (600 and 1200 MHz) and MAS rates (55 and 100 kHz). Three-dimensional (H)CA(CO)NH, (H)CO(CA)NH, and (H)CB(CA)NH spectra demonstrate the high robustness of hSPEPS elements to excite carbon-carbon correlations, especially in the (H)CB(CA)NH spectrum, where hSPEPS outperforms the J-based sequence by a factor of, on average, 2.85.
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Affiliation(s)
- Evgeny Nimerovsky
- Department
of NMR-Based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Spyridon Kosteletos
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Sascha Lange
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Stefan Becker
- Department
of NMR-Based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Adam Lange
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Straße 10, Berlin 13125, Germany
| | - Loren B. Andreas
- Department
of NMR-Based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
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6
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Beriashvili D, Zhou J, Liu Y, Folkers GE, Baldus M. Cellular Applications of DNP Solid-State NMR - State of the Art and a Look to the Future. Chemistry 2024; 30:e202400323. [PMID: 38451060 DOI: 10.1002/chem.202400323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Sensitivity enhanced dynamic nuclear polarization solid-state NMR is emerging as a powerful technique for probing the structural properties of conformationally homogenous and heterogenous biomolecular species irrespective of size at atomic resolution within their native environments. Herein we detail advancements that have made acquiring such data, specifically within the confines of intact bacterial and eukaryotic cell a reality and further discuss the type of structural information that can presently be garnered by the technique's exploitation. Subsequently, we discuss bottlenecks that have thus far curbed cellular DNP-ssNMR's broader adoption namely due a lack of sensitivity and spectral resolution. We also explore possible solutions ranging from utilization of new pulse sequences, design of better performing polarizing agents, and application of additional biochemical/ cell biological methodologies.
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Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiaxin Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
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7
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Wilson CB, Yau WM, Tycko R. Experimental Evidence for Millisecond-Timescale Structural Evolution Following the Microsecond-Timescale Folding of a Small Protein. PHYSICAL REVIEW LETTERS 2024; 132:048402. [PMID: 38335342 PMCID: PMC11423860 DOI: 10.1103/physrevlett.132.048402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/27/2023] [Indexed: 02/12/2024]
Abstract
Prior work has shown that small proteins can fold (i.e., convert from unstructured to structured states) within 10 μs. Here we use time-resolved solid state nuclear magnetic resonance (ssNMR) methods to show that full folding of the 35-residue villin headpiece subdomain (HP35) requires a slow annealing process that has not been previously detected. ^{13}C ssNMR spectra of frozen HP35 solutions, acquired with a variable time τ_{e} at 30 °C after rapid cooling from 95 °C and before rapid freezing, show changes on the 3-10 ms timescale, attributable to slow rearrangements of protein sidechains during τ_{e}.
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Affiliation(s)
- C Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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8
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Bastos R, Marín-Montesinos I, Ferreira SS, Mentink-Vigier F, Sardo M, Mafra L, Coimbra MA, Coelho E. Covalent connectivity of glycogen in brewer's spent yeast cell walls revealed by enzymatic approaches and dynamic nuclear polarization NMR. Carbohydr Polym 2024; 324:121475. [PMID: 37985041 PMCID: PMC10695155 DOI: 10.1016/j.carbpol.2023.121475] [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: 08/04/2023] [Revised: 09/16/2023] [Accepted: 10/08/2023] [Indexed: 11/22/2023]
Abstract
Yeast cell walls undergo modifications during the brewing process, leading to a remodelling of their architecture. One significant change is the increased insolubility of the cell wall glycogen pool, likely due to the formation of covalent bonds between glycogen and cell wall polysaccharides. To verify this hypothesis, we extracted the brewer's spent yeast with 4 M KOH, obtaining an insoluble glucan fraction (AE.4 M) primarily composed of (α1 → 4)- and (1 → 3)-linked Glc residues. Dynamic nuclear polarization solid-state NMR of AE.4 M revealed distinct glucan resonances that helped to differentiate between α- and β glucosyl (1 → 4)-linked residues, and confirm covalent linkages between (β1 → 3)-glucans and glycogen through a (β1 → 4)-linkage. The hydrolysis with different endo-glucanases (zymolyase, cellulase, and lichenase) was used to obtain solubilized high molecular weight glycogen fractions. NMR analysis showed that covalent links between glycogen and (β1 → 6)-glucans through (α1 → 6) glycosidic linkage, with branching at the C6 position involving (β1 → 3), and (β1 → 6)-glucans. HPAEC-PAD analysis of the enzymatically released oligosaccharides confirmed covalent linkages of (β1 → 3), (β1 → 6)-, and (β1 → 4)-glucan motifs with (α1 → 4)-glucans. This combination of multiple enzymatic approaches and NMR methods shed light into the role of yeast cell wall glycogen as a structural core covalently linked to other cell wall components during the brewing process.
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Affiliation(s)
- Rita Bastos
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Ildefonso Marín-Montesinos
- CICECO-Aveiro Institute of Materials, Department of Chemistry University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Sónia S Ferreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, 32310, FL, United States.
| | - Mariana Sardo
- CICECO-Aveiro Institute of Materials, Department of Chemistry University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Luís Mafra
- CICECO-Aveiro Institute of Materials, Department of Chemistry University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Manuel A Coimbra
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Elisabete Coelho
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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9
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Duong NT, Viel S, Ziarelli F, Thureau P, Mollica G. A facile approach for estimating radio-frequency field strength of low-receptivity nuclei. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 358:107614. [PMID: 38141495 DOI: 10.1016/j.jmr.2023.107614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/03/2023] [Accepted: 12/15/2023] [Indexed: 12/25/2023]
Abstract
Radio-frequency (RF) field calibration is essential in NMR spectroscopy. A common practice is to collect a nutation curve by varying the pulse length in a direct single-pulse excitation experiment or in a cross-polarization magic-angle spinning with a flip-back pulse experiment. From the null points on this curve, one can calculate the RF field strength. Nevertheless, the practical implementation is not always straightforward or can even be unrealizable, especially for low-receptivity nuclei owing to their associated low sensitivity. Several researchers used an approach that involves utilizing other nuclei with more sensitivity but nearly identical Larmor frequencies to that of the nucleus of interest. However, such an approach has not been a common practice so far. In this work, we have systematically revisited this approach using 3.2 mm rotors on different sets of nuclei covering a Larmor frequency range up to 80 MHz. The effect of solid- and solution-states on RF field strength measurements has been investigated. The detection of each set of nuclei is then carried out with a resonant circuit in the NMR probe consisting of identical coils and capacitors. Our methodology is illustrated by recording 135/137Ba NMR spectra of BaTiO3 without prior 135/137Ba RF field calibration.
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Affiliation(s)
| | - Stéphane Viel
- Aix Marseille Univ, CNRS, ICR, Marseille, France; Institut Universitaire de France, Paris, France
| | - Fabio Ziarelli
- Aix Marseille Univ, CNRS, Centrale Méditerranée, FSCM, Marseille, France
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10
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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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11
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Maji A, Soutar CP, Zhang J, Lewandowska A, Uno BE, Yan S, Shelke Y, Murhade G, Nimerovsky E, Borcik CG, Arango AS, Lange JD, Marin-Toledo JP, Lyu Y, Bailey KL, Roady PJ, Holler JT, Khandelwal A, SantaMaria AM, Sanchez H, Juvvadi PR, Johns G, Hageman MJ, Krise J, Gebremariam T, Youssef EG, Bartizal K, Marr KA, Steinbach WJ, Ibrahim AS, Patterson TF, Wiederhold NP, Andes DR, Pogorelov TV, Schwieters CD, Fan TM, Rienstra CM, Burke MD. Tuning sterol extraction kinetics yields a renal-sparing polyene antifungal. Nature 2023; 623:1079-1085. [PMID: 37938782 PMCID: PMC10883201 DOI: 10.1038/s41586-023-06710-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
Decades of previous efforts to develop renal-sparing polyene antifungals were misguided by the classic membrane permeabilization model1. Recently, the clinically vital but also highly renal-toxic small-molecule natural product amphotericin B was instead found to kill fungi primarily by forming extramembraneous sponge-like aggregates that extract ergosterol from lipid bilayers2-6. Here we show that rapid and selective extraction of fungal ergosterol can yield potent and renal-sparing polyene antifungals. Cholesterol extraction was found to drive the toxicity of amphotericin B to human renal cells. Our examination of high-resolution structures of amphotericin B sponges in sterol-free and sterol-bound states guided us to a promising structural derivative that does not bind cholesterol and is thus renal sparing. This derivative was also less potent because it extracts ergosterol more slowly. Selective acceleration of ergosterol extraction with a second structural modification yielded a new polyene, AM-2-19, that is renal sparing in mice and primary human renal cells, potent against hundreds of pathogenic fungal strains, resistance evasive following serial passage in vitro and highly efficacious in animal models of invasive fungal infections. Thus, rational tuning of the dynamics of interactions between small molecules may lead to better treatments for fungal infections that still kill millions of people annually7,8 and potentially other resistance-evasive antimicrobials, including those that have recently been shown to operate through supramolecular structures that target specific lipids9.
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Affiliation(s)
- Arun Maji
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Corinne P Soutar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jiabao Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Agnieszka Lewandowska
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Brice E Uno
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Su Yan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Yogesh Shelke
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ganesh Murhade
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Evgeny Nimerovsky
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department for NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Collin G Borcik
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Andres S Arango
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Justin D Lange
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Yinghuan Lyu
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Keith L Bailey
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patrick J Roady
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jordan T Holler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anuj Khandelwal
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anna M SantaMaria
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Hiram Sanchez
- Department of Medicine, Section of Infectious Disease, University of Wisconsin-Madison, Madison, WI, USA
| | - Praveen R Juvvadi
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Michael J Hageman
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Joanna Krise
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | | | - Eman G Youssef
- Division of Infectious Diseases, The Lundquist Institute, Torrance, CA, USA
| | | | | | - William J Steinbach
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Ashraf S Ibrahim
- Division of Infectious Diseases, The Lundquist Institute, Torrance, CA, USA
- David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Thomas F Patterson
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Nathan P Wiederhold
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - David R Andes
- Department of Medicine, Section of Infectious Disease, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Taras V Pogorelov
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy M Fan
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chad M Rienstra
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA.
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA.
| | - Martin D Burke
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
- Molecule Maker Lab Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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12
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Johann C, Wegner S, Althoff G, Struppe J. Automation in solid state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 355:107554. [PMID: 37717302 DOI: 10.1016/j.jmr.2023.107554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Automation in solid state NMR (ssNMR) requires appropriate hardware, from rotor loading mechanisms over highly stable rf-transmitters and probe circuitry to automatic tuning and matching capabilities including automatic magic angle adjustment for ssNMR probes. While these hardware capabilities are highly desirable and are, to various degrees, provided by manufacturers, we focus herein on automating experiment setup using radio frequency (rf) fields, which are key parameters in solid state NMR experiments. Specifically, these include spinlock fields during cross polarization (CP), or rf-fields for homo- or heteronuclear spin recoupling or decoupling. Often, these fields have specific relationships to the magic angle spinning (MAS) frequency. Relying on a well-maintained spectrometer, the experiment setup shifts from traditionally required optimization of rf-power values for each element of an experiment sequence to automatically setting all parameters correctly without any need for optimization. The proposed approach allows executing an experiment by reading its rf-amplitude requirements based on the actual MAS rotation frequency just before starting data acquisition, while all other hardware-related parameters are automatically provided through global tables and scripts. Under modest MAS frequencies, no further rf-power optimization is required while providing optimal sensitivity of better than 90% of the optimal signal to noise. Any optional parameter optimization relates only to adjusting rf-nutation frequencies to the requirements of the sample and the sample rotation frequency rather than the spectrometer hardware. Fast MAS CP experiments with MAS frequencies above 40 kHz require a semi-automated setup by optimizing Hartmann-Hahn (HH) matched rf-fields that are synchronously varied relative to the MAS-frequency. This allows for a significant reduction of setup steps by up to one order of magnitude for such experiments, avoiding the traditional grid search for optimal CPMAS conditions. The approach presented here can also be applied to decoupling or recoupling sequences, requiring rotor synchronized rf-fields, reducing the setup to a few steps addressing the spin system's properties rather than the spectrometer hardware. Our approach permits automating all basic solid state NMR experiments for high throughput analytical tasks.
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Affiliation(s)
- Christof Johann
- Buker Biospin Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | | | - Gerhard Althoff
- Buker Biospin Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States.
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13
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Xiao H, Zhang Z, Kang H, Yang J. Solid-State NMR Double-Quantum Dipolar Recoupling Enhanced by Additional Phase Modulation. Chemphyschem 2023; 24:e202300141. [PMID: 37309720 DOI: 10.1002/cphc.202300141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Additional phase modulation (APM) is proposed to generally enhance the theoretical efficiency of homonuclear double-quantum (DQ) recoupling in solid-state NMR. APM applies an additional phase list to DQ recoupling in steps of an entire block. The sine-based phase list can enhance the theoretical efficiency by 15-30 %, from 0.52 to 0.68 (non-γ-encoded recoupling) or from 0.73 to 0.84 (γ-encoded recoupling), with doubled recoupling time. The genetic-algorithm (GA) optimized APM can adiabatically enhance the efficiency to ∼1.0 at longer times. The concept of APM has been tested on SPR-51 , BaBa, and SPR-31 , which represent γ-encoded recoupling, non-γ-encoded recoupling, and another kind beyond the former two, respectively. Simulations reveal that enhancements from APM are due to the activation of more crystallites in the powder. Experiments on 2,3-13 C labeled alanine are used to validate the APM recoupling. This new concept shall shed light on developing more efficient homonuclear recoupling methods.
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Affiliation(s)
- Hang Xiao
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Huimin Kang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
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14
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Jeon J, Yau WM, Tycko R. Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering. Nat Commun 2023; 14:2964. [PMID: 37221174 DOI: 10.1038/s41467-023-38494-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer's disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers that form on time scales from 0.7 ms to 1.0 h after initiation of self-assembly by a rapid pH drop. Low-temperature ssNMR spectra of freeze-trapped intermediates indicate that β-strand conformations within and contacts between the two main hydrophobic segments of Aβ40 develop within 1 ms, while light scattering data imply a primarily monomeric state up to 5 ms. Intermolecular contacts involving residues 18 and 33 develop within 0.5 s, at which time Aβ40 is approximately octameric. These contacts argue against β-sheet organizations resembling those found previously in protofibrils and fibrils. Only minor changes in the Aβ40 conformational distribution are detected as larger assemblies develop.
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Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland/National Institute of Standards and Technology, Rockville, MD, 20850, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
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15
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Nimerovsky E, Najbauer EÉ, Becker S, Andreas LB. Great Offset Difference Internuclear Selective Transfer. J Phys Chem Lett 2023; 14:3939-3945. [PMID: 37078685 PMCID: PMC10150390 DOI: 10.1021/acs.jpclett.3c00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Carbon-carbon dipolar recoupling sequences are frequently used building blocks in routine magic-angle spinning NMR experiments. While broadband homonuclear first-order dipolar recoupling sequences mainly excite intra-residue correlations, selective methods can detect inter-residue transfers and long-range correlations. Here, we present the great offset difference internuclear selective transfer (GODIST) pulse sequence optimized for selective carbonyl or aliphatic recoupling at fast magic-angle spinning, here, 55 kHz. We observe a 3- to 5-fold increase in intensities compared with broadband RFDR recoupling for perdeuterated microcrystalline SH3 and for the membrane protein influenza A M2 in lipid bilayers. In 3D (H)COCO(N)H and (H)CO(CO)NH spectra, inter-residue carbonyl-carbonyl correlations up to about 5 Å are observed in uniformly 13C-labeled proteins.
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Affiliation(s)
- Evgeny Nimerovsky
- Department of NMR-based Structural
Biology, Max Planck Institute for Multidisciplinary
Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Eszter Éva Najbauer
- Department of NMR-based Structural
Biology, Max Planck Institute for Multidisciplinary
Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Stefan Becker
- Department of NMR-based Structural
Biology, Max Planck Institute for Multidisciplinary
Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Loren B. Andreas
- Department of NMR-based Structural
Biology, Max Planck Institute for Multidisciplinary
Sciences, Am Fassberg 11, Göttingen 37077, Germany
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16
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Arunachalam V, Sharma K, Mote KR, Madhu PK. Asynchronising five-fold symmetry sequence for better homonuclear polarisation transfer in magic-angle-spinning solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 124:101858. [PMID: 36796278 DOI: 10.1016/j.ssnmr.2023.101858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Recoupling, decoupling, and multidimensional correlation experiments in magic-angle-spinning (MAS) solid-state NMR can be designed by exploiting the symmetry of internal spin interactions. One such scheme, namely, C521, and its supercycled version SPC521, notated as a five-fold symmetry sequence, is widely used for double-quantum dipole-dipole recoupling. Such schemes are generally rotor synchronised by design. We demonstrate an asynchronous implementation of the SPC521 sequence leading to higher double-quantum homonuclear polarisation transfer efficiency compared to the normal synchronous implementation. Rotor-synchronisation is broken in two different ways: lengthening the duration of one of the pulses, denoted as pulse-width variation (PWV), and mismatching the MAS frequency denoted as MAS variation (MASV). The application of this asynchronous sequence is shown on three different samples, namely, U-13C-alanine and 1,4-13C-labelled ammonium phthalate which include 13Cα-13Cβ, 13Cα-13Co, and 13Co-13Co spin systems, and adenosine 5'- triphosphate disodium salt trihydrate (ATP⋅3H2O). We show that the asynchronous version performs better for spin pairs with small dipole-dipole couplings and large chemical-shift anisotropies, for example, 13Co-13Co. Simulations and experiments are shown to corroborate the results.
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Affiliation(s)
- Vaishali Arunachalam
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - Kshama Sharma
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - P K Madhu
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
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17
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Duma L, Senicourt L, Rigaud B, Papadopoulos V, Lacapère JJ. Solid-state NMR study of structural heterogeneity of the apo WT mouse TSPO reconstituted in liposomes. Biochimie 2023; 205:73-85. [PMID: 36029902 DOI: 10.1016/j.biochi.2022.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/08/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
In the last decades, ligand binding to human TSPO has been largely used in clinical neuroimaging, but little is known about the interaction mechanism. Protein conformational mobility plays a key role in the ligand recognition and both, ligand-free and ligand-bound structures, are mandatory for characterizing the molecular binding mechanism. In the absence of crystals for mammalian TSPO, we have exploited solid-state nuclear magnetic resonance (ssNMR) spectroscopy under magic-angle spinning (MAS) to study the apo form of recombinant mouse TSPO (mTSPO) reconstituted in lipids. This environment has been previously described to permit binding of its high-affinity drug ligand PK11195 and appears therefore favourable for the study of molecular dynamics. We have optimized the physical conditions to get the best resolution for MAS ssNMR spectra of the ligand-free mTSPO. We have compared and combined various ssNMR spectra to get dynamical information either for the lipids or for the mTSPO. Partial assignment of residue types suggests few agreements with the published solution NMR assignment of the PK11195-bound mTSPO in DPC detergent. Moreover, we were able to observe some lateral chains of aromatic residues that were not assigned in solution. 13C double-quantum NMR spectroscopy shows remarkable dynamics for ligand-free mTSPO in lipids which may have significant implications on the recognition of the ligand and/or other protein partners.
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Affiliation(s)
- Luminita Duma
- Champagne-Ardenne University, CNRS, ICMR UMR, 7312, Reims, France.
| | - Lucile Senicourt
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 4 Place Jussieu, F-75005, Paris, France
| | - Baptiste Rigaud
- CNRS Institut des Matériaux de Paris Centre (FR2482), 4 Place Jussieu, 75005, Paris, France
| | - Vassilios Papadopoulos
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jean-Jacques Lacapère
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 4 Place Jussieu, F-75005, Paris, France
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18
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Safeer A, Kleijburg F, Bahri S, Beriashvili D, Veldhuizen EJA, van Neer J, Tegelaar M, de Cock H, Wösten HAB, Baldus M. Probing Cell-Surface Interactions in Fungal Cell Walls by High-Resolution 1 H-Detected Solid-State NMR Spectroscopy. Chemistry 2023; 29:e202202616. [PMID: 36181715 PMCID: PMC10099940 DOI: 10.1002/chem.202202616] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/05/2022]
Abstract
Solid-state NMR (ssNMR) spectroscopy facilitates the non-destructive characterization of structurally heterogeneous biomolecules in their native setting, for example, comprising proteins, lipids and polysaccharides. Here we demonstrate the utility of high and ultra-high field 1 H-detected fast MAS ssNMR spectroscopy, which exhibits increased sensitivity and spectral resolution, to further elucidate the atomic-level composition and structural arrangement of the cell wall of Schizophyllum commune, a mushroom-forming fungus from the Basidiomycota phylum. These advancements allowed us to reveal that Cu(II) ions and the antifungal peptide Cathelicidin-2 mainly bind to cell wall proteins at low concentrations while glucans are targeted at high metal ion concentrations. In addition, our data suggest the presence of polysaccharides containing N-acetyl galactosamine (GalNAc) and proteins, including the hydrophobin proteins SC3, shedding more light on the molecular make-up of cells wall as well as the positioning of the polypeptide layer. Obtaining such information may be of critical relevance for future research into fungi in material science and biomedical contexts.
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Affiliation(s)
- Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Fleur Kleijburg
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Salima Bahri
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Edwin J A Veldhuizen
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Utrecht University, Yalelaan 1, 3584 CL, Utrecht (The, Netherlands
| | - Jacq van Neer
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Martin Tegelaar
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Hans de Cock
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
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19
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Yao R, Beriashvili D, Zhang W, Li S, Safeer A, Gurinov A, Rockenbauer A, Yang Y, Song Y, Baldus M, Liu Y. Highly bioresistant, hydrophilic and rigidly linked trityl-nitroxide biradicals for cellular high-field dynamic nuclear polarization. Chem Sci 2022; 13:14157-14164. [PMID: 36540821 PMCID: PMC9728575 DOI: 10.1039/d2sc04668g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/16/2022] [Indexed: 09/23/2023] Open
Abstract
Cellular dynamic nuclear polarization (DNP) has been an effective means of overcoming the intrinsic sensitivity limitations of solid-state nuclear magnetic resonance (ssNMR) spectroscopy, thus enabling atomic-level biomolecular characterization in native environments. Achieving DNP signal enhancement relies on doping biological preparations with biradical polarizing agents (PAs). Unfortunately, PA performance within cells is often limited by their sensitivity to the reductive nature of the cellular lumen. Herein, we report the synthesis and characterization of a highly bioresistant and hydrophilic PA (StaPol-1) comprising the trityl radical OX063 ligated to a gem-diethyl pyrroline nitroxide via a rigid piperazine linker. EPR experiments in the presence of reducing agents such as ascorbate and in HeLa cell lysates demonstrate the reduction resistance of StaPol-1. High DNP enhancements seen in small molecules, proteins and cell lysates at 18.8 T confirm that StaPol-1 is an excellent PA for DNP ssNMR investigations of biomolecular systems at high magnetic fields in reductive environments.
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Affiliation(s)
- Ru Yao
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - David Beriashvili
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Wenxiao Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Shuai Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Adil Safeer
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Antal Rockenbauer
- Institute of Materials and Environmental Chemistry, Hungarian Academy of Sciences And, Department of Physics, Budapest University of Technology and Economics Budafoki Ut 8 1111 Budapest Hungary
| | - Yin Yang
- State Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University Tianjin 300071 China
| | - Yuguang Song
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, 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 Group, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Yangping Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, 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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20
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Mentink-Vigier F, Eddy S, Gullion T. MAS-DNP enables NMR studies of insect wings. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101838. [PMID: 36410100 PMCID: PMC9722638 DOI: 10.1016/j.ssnmr.2022.101838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
NMR is a valuable tool for studying insects. Solid-state NMR has been used to obtain the chemical composition and gain insight into the sclerotization process of exoskeletons. There is typically little difficulty in obtaining sufficient sample quantity for exoskeletons. However, obtaining enough sample of other insect components for solid-state NMR experiments can be problematic while isotopically enriching them is near impossible. This is especially the case for insect wing membranes which is of interest to us. Issues with obtaining sufficient sample are the thickness of wing membranes is on the order of microns, each membrane region is surrounded by veins and occupies a small area, and the membranes are separated from the wing by physical dissection. Accordingly, NMR signal enhancement methods are needed. MAS-DNP has a track record of providing significant signal enhancements for a wide variety of materials. Here we demonstrate that MAS-DNP is useful for providing high quality one-dimensional and two-dimensional solid-state NMR spectra on cicada wing membrane at natural isotopic abundance.
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Affiliation(s)
- Frédéric Mentink-Vigier
- CIMAR/NMR National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL, 32310, USA.
| | - Samuel Eddy
- Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Terry Gullion
- Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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21
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Pokorný V, Touš P, Štejfa V, Růžička K, Rohlíček J, Czernek J, Brus J, Červinka C. Anisotropy, segmental dynamics and polymorphism of crystalline biogenic carboxylic acids. Phys Chem Chem Phys 2022; 24:25904-25917. [PMID: 36260017 DOI: 10.1039/d2cp03698c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Carboxylic acids of the Krebs cycle possess invaluable biochemical significance. Still, there are severe gaps in the availability of thermodynamic and crystallographic data, as well as ambiguities prevailing in the literature on the thermodynamic characterization and polymorph ranking. Providing an unambiguous description of the structure, thermodynamics and polymorphism of their neat crystalline phases requires a complex multidisciplinary approach. This work presents results of an extensive investigation of the structural anisotropy of the thermal expansion and local dynamics within these crystals, obtained from a beneficial cooperation of NMR crystallography and ab initio calculations of non-covalent interactions. The observed structural anisotropy and spin-lattice relaxation times are traced to large spatial variations in the strength of molecular interactions in the crystal lattice, especially in the orientation of the hydrogen bonds. A completely resolved crystal structure for oxaloacetic acid is reported for the first time. Thanks to multi-instrumental calorimetric effort, this work clarifies phase behavior, determines third-law entropies of the crystals, and states definitive polymorph ranking for succinic and fumaric acids. These thermodynamic observations are then interpreted in terms of first-principles quasi-harmonic calculations of cohesive properties. A sophisticated model capturing electronic, thermal, and configurational-entropic effects on the crystal structure approaches captures the subtle Gibbs energy differences governing polymorph ranking for succinic and fumaric acids, representing another success story of computational chemistry.
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Affiliation(s)
- Václav Pokorný
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic
| | - Petr Touš
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Vojtěch Štejfa
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Květoslav Růžička
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
| | - Jan Rohlíček
- Institute of Physics, Czech Academy of Sciences, Na Slovance 2, CZ-182 21 Prague 8, Czech Republic
| | - Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic
| | - Jiří Brus
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic
| | - Ctirad Červinka
- Department of Physical Chemistry, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
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22
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Aguion PI, Marchanka A, Carlomagno T. Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy. J Struct Biol X 2022; 6:100072. [PMID: 36090770 PMCID: PMC9449856 DOI: 10.1016/j.yjsbx.2022.100072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Solid-state NMR (ssNMR) has become a well-established technique to study large and insoluble protein assemblies. However, its application to nucleic acid-protein complexes has remained scarce, mainly due to the challenges presented by overlapping nucleic acid signals. In the past decade, several efforts have led to the first structure determination of an RNA molecule by ssNMR. With the establishment of these tools, it has become possible to address the problem of structure determination of nucleic acid-protein complexes by ssNMR. Here we review first and more recent ssNMR methodologies that study nucleic acid-protein interfaces by means of chemical shift and peak intensity perturbations, direct distance measurements and paramagnetic effects. At the end, we review the first structure of an RNA-protein complex that has been determined from ssNMR-derived intermolecular restraints.
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Affiliation(s)
- Philipp Innig Aguion
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Alexander Marchanka
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Teresa Carlomagno
- School of Biosciences/College of Life and Enviromental Sciences, Institute of Cancer and Genomic Sciences/College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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23
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Wi S, Dwivedi N, Dubey R, Mentink-Vigier F, Sinha N. Dynamic nuclear polarization-enhanced, double-quantum filtered 13C- 13C dipolar correlation spectroscopy of natural 13C abundant bone-tissue biomaterial. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 335:107144. [PMID: 35085899 PMCID: PMC8823282 DOI: 10.1016/j.jmr.2022.107144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 05/03/2023]
Abstract
Here, we describe a method for obtaining a dynamic nuclear polarization (DNP)-enhanced double-quantum filtered (DQF) two-dimensional (2D) dipolar 13C-13C correlation spectra of bone-tissue material at natural 13C abundance. DNP-enhanced DQF 2D dipolar 13C-13C spectra were obtained using a few different mixing times of the dipolar-assisted rotational resonance (DARR) scheme and these spectra were compared to a conventional 2D through-space double-quantum (DQ)-single-quantum (SQ) correlation spectrum. While this scheme can only be used for an assignment purpose to reveal the carbon-carbon connectivity within a residue, the DQF 13C-13C dipolar correlation scheme introduced here can be used to obtain longer distance carbon-carbon constraints. A DQF pulse block is placed before the DARR mixing scheme for removing dominant 13C single-quantum (SQ) signals because these SQ 13C signals are overwhelmingly large compared to those 13C-13C dipolar cross-peaks generated and therefore saturate the dynamic range of the NMR detection. This approach exhibits strong enough 2D cross-peaks in a dipolar 13C-13C correlation spectrum and potentially provides pairwise 13C-13C dipolar constraints because the dipolar truncation effect as well as multi-step signal propagations involving a spin cluster that contains more than two spins can be ignored probabilistically. To obtain fast signal averaging, AsymPolPOK was used to provide a short 1H DNP signal build-up time (1.3 s) and to expedite our MAS DNP NMR acquisitions while still maintaining a satisfactory DNP enhancement factor (ε = 50). Under long DARR mixing, a t1-noise-like artifact was observed at a site that possesses a large chemical shift anisotropy (CSA) and a few different strategies to address this problem were discussed.
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Affiliation(s)
- Sungsool Wi
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32304, USA.
| | - Navneet Dwivedi
- Department of Advanced Spectroscopy and Imaging, Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow 226014, India; Department of Physics, Integral University, Lucknow 226026, India
| | - Richa Dubey
- Department of Advanced Spectroscopy and Imaging, Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow 226014, India
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32304, USA
| | - Neeraj Sinha
- Department of Advanced Spectroscopy and Imaging, Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow 226014, India
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24
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Solid-state NMR analysis of unlabeled fungal cell walls from Aspergillus and Candida species. J Struct Biol X 2022; 6:100070. [PMID: 35899175 PMCID: PMC9310124 DOI: 10.1016/j.yjsbx.2022.100070] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/10/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022] Open
Abstract
An NMR investigation strategy with atomic resolution for unlabeled fungal cell walls. Conserved carbohydrate core revealed in conidia and mycelia of Aspergillus fumigatus. Confirmation of the structural function of α-glucans in A. fumigatus. Carbohydrate fingerprints preserved in liquid and solid cultures of Candida albicans.
Fungal infections cause high mortality in immunocompromised individuals, which has emerged as a significant threat to human health. The efforts devoted to the development of antifungal agents targeting the cell wall polysaccharides have been hindered by our incomplete picture of the assembly and remodeling of fungal cell walls. High-resolution solid-state nuclear magnetic resonance (ss NMR) studies have substantially revised our understanding of the polymorphic structure of polysaccharides and the nanoscale organization of cell walls in Aspergillus fumigatus and multiple other fungi. However, this approach requires 13C/15N-enrichment of the sample being studied, severely restricting its application. Here we employ the dynamic nuclear polarization (DNP) technique to compare the unlabeled cell wall materials of A. fumigatus and C. albicans prepared using both liquid and solid media. For each fungus, we have identified a highly conserved carbohydrate core for the cell walls of conidia and mycelia, and from liquid and solid cultures. Using samples prepared in different media, the recently identified function of α-glucan, which packs with chitin to form the mechanical centers, has been confirmed through conventional ss NMR measurements of polymer dynamics. These timely efforts not only validate the structural principles recently discovered for A. fumigatus cell walls in different morphological stages, but also open up the possibility of extending the current investigation to other fungal materials and cellular systems that are challenging to label.
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25
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Fungicidal amphotericin B sponges are assemblies of staggered asymmetric homodimers encasing large void volumes. Nat Struct Mol Biol 2021; 28:972-981. [PMID: 34887566 PMCID: PMC9336184 DOI: 10.1038/s41594-021-00685-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 10/12/2021] [Indexed: 12/16/2022]
Abstract
Amphotericin B (AmB) is a powerful but toxic fungicide that operates via enigmatic small molecule-small molecule interactions. This mechanism has challenged the frontiers of structural biology for half a century. We recently showed AmB primarily forms extramembranous aggregates that kill yeast by extracting ergosterol from membranes. Here, we report key structural features of these antifungal 'sponges' illuminated by high-resolution magic-angle spinning solid-state NMR, in concert with simulated annealing and molecular dynamics computations. The minimal unit of assembly is an asymmetric head-to-tail homodimer: one molecule adopts an all-trans C1-C13 motif, the other a C6-C7-gauche conformation. These homodimers are staggered in a clathrate-like lattice with large void volumes similar to the size of sterols. These results illuminate the atomistic interactions that underlie fungicidal assemblies of AmB and suggest this natural product may form biologically active clathrates that host sterol guests.
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26
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Xiao H, Zhang Z, Yang J. Theory of frequency-selective homonuclear dipolar recoupling in solid-state NMR. J Chem Phys 2021; 155:174105. [PMID: 34742189 DOI: 10.1063/5.0065396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In solid-state nuclear magnetic resonance, frequency-selective homonuclear dipolar recoupling is key to quantitative distance measurement or selective enhancement of correlations between atoms of interest in multiple-spin systems, which are not amenable to band-selective or broadband recoupling. Previous frequency-selective recoupling is mostly based on the so-called rotational resonance (R2) condition that restricts the application to spin pairs with resonance frequencies differing in integral multiples of the magic-angle spinning (MAS) frequency. Recently, we have proposed a series of frequency-selective homonuclear recoupling sequences called SPR (short for Selective Phase-optimized Recoupling), which have been successfully applied for selective 1H-1H or 13C-13C recoupling under from moderate (∼10 kHz) to ultra-fast (150 kHz) MAS frequencies. In this study, we fully analyze the average Hamiltonian theory of SPR sequences and reveal the origin of frequency selectivity in recoupling. The theoretical description, as well as numerical simulations and experiments, demonstrates that the frequency selectivity can be easily controlled by the flip angle (p) in the (p)ϕk(p)ϕk+π unit in the pSPR-Nn sequences. Small flip angles lead to frequency-selective recoupling, while large flip angles may lead to broadband recoupling in principle. The result shall shed new light on the design of homonuclear recoupling sequences with arbitrary frequency bandwidths.
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Affiliation(s)
- Hang Xiao
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, People's Republic of China
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27
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Chakraborty A, Fernando LD, Fang W, Dickwella Widanage MC, Wei P, Jin C, Fontaine T, Latgé JP, Wang T. A molecular vision of fungal cell wall organization by functional genomics and solid-state NMR. Nat Commun 2021; 12:6346. [PMID: 34732740 PMCID: PMC8566572 DOI: 10.1038/s41467-021-26749-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/21/2021] [Indexed: 12/16/2022] Open
Abstract
Vast efforts have been devoted to the development of antifungal drugs targeting the cell wall, but the supramolecular architecture of this carbohydrate-rich composite remains insufficiently understood. Here we compare the cell wall structure of a fungal pathogen Aspergillus fumigatus and four mutants depleted of major structural polysaccharides. High-resolution solid-state NMR spectroscopy of intact cells reveals a rigid core formed by chitin, β-1,3-glucan, and α-1,3-glucan, with galactosaminogalactan and galactomannan present in the mobile phase. Gene deletion reshuffles the composition and spatial organization of polysaccharides, with significant changes in their dynamics and water accessibility. The distribution of α-1,3-glucan in chemically isolated and dynamically distinct domains supports its functional diversity. Identification of valines in the alkali-insoluble carbohydrate core suggests a putative function in stabilizing macromolecular complexes. We propose a revised model of cell wall architecture which will improve our understanding of the structural response of fungal pathogens to stresses. The fungal cell wall is a complex structure composed mainly of glucans, chitin and glycoproteins. Here, the authors use solid-state NMR spectroscopy to assess the cell wall architecture of Aspergillus fumigatus, comparing wild-type cells and mutants lacking major structural polysaccharides, with insights into the distinct functions of these components.
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Affiliation(s)
- Arnab Chakraborty
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, USA
| | | | - Wenxia Fang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| | | | - Pingzhen Wei
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| | - Cheng Jin
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Thierry Fontaine
- Unité de Biologie et pathogénicité fongiques, INRAE, USC2019, Institut Pasteur, Paris, France
| | - Jean-Paul Latgé
- Institute of Molecular biology and Biotechnology (IMBBFORTH), University of Crete, Heraklion, Greece.
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, USA.
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28
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Zhang J, Sakai H, Suzuki K, Hasobe T, Tkachenko NV, Chang IY, Hyeon-Deuk K, Kaji H, Teranishi T, Sakamoto M. Near-Unity Singlet Fission on a Quantum Dot Initiated by Resonant Energy Transfer. J Am Chem Soc 2021; 143:17388-17394. [PMID: 34647732 DOI: 10.1021/jacs.1c04731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conversion of a high-energy photon into two excitons using singlet fission (SF) has stimulated a variety of studies in fields from fundamental physics to device applications. However, efficient SF has only been achieved in limited systems, such as solid crystals and covalent dimers. Here, we established a novel system by assembling 4-(6,13-bis(2-(triisopropylsilyl)ethynyl)pentacen-2-yl)benzoic acid (Pc) chromophores on nanosized CdTe quantum dots (QDs). A near-unity SF (198 ± 5.7%) initiated by interfacial resonant energy transfer from CdTe to surface Pc was obtained. The unique arrangement of Pc determined by the surface atomic configuration of QDs is the key factor realizing unity SF. The triplet-triplet annihilation was remarkably suppressed due to the rapid dissociation of triplet pairs, leading to long-lived free triplets. In addition, the low light-harvesting ability of Pc in the visible region was promoted by the efficient energy transfer (99 ± 5.8%) from the QDs to Pc. The synergistically enhanced light-harvesting ability, high triplet yield, and long-lived triplet lifetime of the SF system on nanointerfaces could pave the way for an unmatched advantage of SF.
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Affiliation(s)
- Jie Zhang
- Department of Chemistry, Graduate School of Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Hayato Sakai
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Katsuaki Suzuki
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Taku Hasobe
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Nikolai V Tkachenko
- Chemistry and Advanced Materials Group, Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, FI33720 Tampere, Finland
| | - I-Ya Chang
- Department of Chemistry, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Kim Hyeon-Deuk
- Department of Chemistry, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Hironori Kaji
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Toshiharu Teranishi
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Masanori Sakamoto
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
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29
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Li J, Sae Her A, Traaseth NJ. Asymmetric protonation of glutamate residues drives a preferred transport pathway in EmrE. Proc Natl Acad Sci U S A 2021; 118:e2110790118. [PMID: 34607959 PMCID: PMC8521673 DOI: 10.1073/pnas.2110790118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 11/18/2022] Open
Abstract
EmrE is an Escherichia coli multidrug efflux pump and member of the small multidrug resistance (SMR) family that transports drugs as a homodimer by harnessing energy from the proton motive force. SMR family transporters contain a conserved glutamate residue in transmembrane 1 (Glu14 in EmrE) that is required for binding protons and drugs. Yet the mechanism underlying proton-coupled transport by the two glutamate residues in the dimer remains unresolved. Here, we used NMR spectroscopy to determine acid dissociation constants (pKa ) for wild-type EmrE and heterodimers containing one or two Glu14 residues in the dimer. For wild-type EmrE, we measured chemical shifts of the carboxyl side chain of Glu14 using solid-state NMR in lipid bilayers and obtained unambiguous evidence on the existence of asymmetric protonation states. Subsequent measurements of pKa values for heterodimers with a single Glu14 residue showed no significant differences from heterodimers with two Glu14 residues, supporting a model where the two Glu14 residues have independent pKa values and are not electrostatically coupled. These insights support a transport pathway with well-defined protonation states in each monomer of the dimer, including a preferred cytoplasmic-facing state where Glu14 is deprotonated in monomer A and protonated in monomer B under pH conditions in the cytoplasm of E. coli Our findings also lead to a model, hop-free exchange, which proposes how exchangers with conformation-dependent pKa values reduce proton leakage. This model is relevant to the SMR family and transporters comprised of inverted repeat domains.
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Affiliation(s)
- Jianping Li
- Department of Chemistry, New York University, New York, NY 10003
| | - Ampon Sae Her
- Department of Chemistry, New York University, New York, NY 10003
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30
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Mathew R, Stevensson B, Edén M. Refined Structures of O-Phospho-l-serine and Its Calcium Salt by New Multinuclear Solid-State NMR Crystallography Methods. J Phys Chem B 2021; 125:10985-11004. [PMID: 34553936 PMCID: PMC8503883 DOI: 10.1021/acs.jpcb.1c05587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Indexed: 12/17/2022]
Abstract
O-phospho-l-serine (Pser) and its Ca salt, Ca[O-phospho-l-serine]·H2O (CaPser), play important roles for bone mineralization and were recently also proposed to account for the markedly improved bone-adhesive properties of Pser-doped calcium phosphate-based cements for biomedical implants. However, the hitherto few proposed structural models of Pser and CaPser were obtained by X-ray diffraction, thereby leaving the proton positions poorly defined. Herein, we refine the Pser and CaPser structures by density functional theory (DFT) calculations and contrast them with direct interatomic-distance constraints from two-dimensional (2D) nuclear magnetic resonance (NMR) correlation experimentation at fast magic-angle spinning (MAS), encompassing double-quantum-single-quantum (2Q-1Q) 1H NMR along with heteronuclear 13C{1H} and 31P{1H} correlation NMR experiments. The Pser and CaPser structures before and after refinements by DFT were validated against sets of NMR-derived effective 1H-1H, 1H-31P, and 1H-13C distances, which confirmed the improved accuracy of the refined structures. Each distance set was derived from one sole 2D NMR experiment applied to a powder without isotopic enrichment. The distances were extracted without invoking numerical spin-dynamics simulations or approximate phenomenological models. We highlight the advantages and limitations of the new distance-extraction procedure. Isotropic 1H, 13C, and 31P chemical shifts obtained by DFT calculations using the gauge including projector augmented wave (GIPAW) method agreed very well with the experimental results. We discuss the isotropic and anisotropic 13C and 31P chemical-shift parameters in relation to the previous literature, where most data on CaPser are reported herein for the first time.
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Affiliation(s)
- Renny Mathew
- Department of Materials and Environmental
Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Baltzar Stevensson
- Department of Materials and Environmental
Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mattias Edén
- Department of Materials and Environmental
Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden
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31
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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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32
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Matsuura BS, Huss S, Zheng Z, Yuan S, Wang T, Chen B, Badding JV, Trauner D, Elacqua E, van Duin ACT, Crespi VH, Schmidt-Rohr K. Perfect and Defective 13C-Furan-Derived Nanothreads from Modest-Pressure Synthesis Analyzed by 13C NMR. J Am Chem Soc 2021; 143:9529-9542. [PMID: 34130458 DOI: 10.1021/jacs.1c03671] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The molecular structure of nanothreads produced by the slow compression of 13C4-furan was studied by advanced solid-state NMR. Spectral editing showed that >95% of carbon atoms were bonded to one hydrogen (C-H) and that there were 2-4% CH2, 0.6% C═O, and <0.3% CH3 groups. Alkenes accounted for 18% of the CH moieties, while trapped, unreacted furan made up 7%. Two-dimensional (2D) 13C-13C and 1H-13C NMR identified 12% of all carbon in asymmetric O-CH═CH-CH-CH- and 24% in symmetric O-CH-CH═CH-CH- rings. While the former represented defects or chain ends, some of the latter appeared to form repeating thread segments. Around 10% of carbon atoms were found in highly ordered, fully saturated nanothread segments. Unusually slow 13C spin-exchange with sites outside the perfect thread segments documented a length of at least 14 bonds; the small width of the perfect-thread signals also implied a fairly long, regular structure. Carbons in the perfect threads underwent relatively slow spin-lattice relaxation, indicating slow spin exchange with other threads and smaller amplitude motions. Through partial inversion recovery, the signals of the perfect threads were observed and analyzed selectively. Previously considered syn-threads with four different C-H bond orientations were ruled out by centerband-only detection of exchange NMR, which was, on the contrary, consistent with anti-threads. The observed 13C chemical shifts were matched well by quantum-chemical calculations for anti-threads but not for more complex structures like syn/anti-threads. These observations represent the first direct determination of the atomic-level structure of fully saturated nanothreads.
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Affiliation(s)
- Bryan S Matsuura
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Steven Huss
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Zhaoxi Zheng
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Shichen Yuan
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Tao Wang
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bo Chen
- Donostia International Physics Center, Paseo Manuel de Lardizabal, 4, 20018 Donostia-San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - John V Badding
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Dirk Trauner
- Department of Chemistry, New York University, New York, New York 10003, United States
- Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016, United States
- NYU Neuroscience Institute, New York University School of Medicine, New York, New York 10016, United States
| | - Elizabeth Elacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Adri C T van Duin
- Department of Mechanical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Vincent H Crespi
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Klaus Schmidt-Rohr
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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33
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Duan P, Kaser SJ, Lyczakowski JJ, Phyo P, Tryfona T, Dupree P, Hong M. Xylan Structure and Dynamics in Native Brachypodium Grass Cell Walls Investigated by Solid-State NMR Spectroscopy. ACS OMEGA 2021; 6:15460-15471. [PMID: 34151124 PMCID: PMC8210444 DOI: 10.1021/acsomega.1c01978] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/21/2021] [Indexed: 05/07/2023]
Abstract
The polysaccharide composition and dynamics of the intact stem and leaf cell walls of the model grass Brachypodium distachyon are investigated to understand how developmental stage affects the polysaccharide structure of grass cell walls. 13C enrichment of the entire plant allowed detailed analysis of the xylan structure, side-chain functionalization, dynamics, and interaction with cellulose using magic-angle-spinning solid-state NMR spectroscopy. Quantitative one-dimensional 13C NMR spectra and two-dimensional 13C-13C correlation spectra indicate that stem and leaf cell walls contain less pectic polysaccharides compared to previously studied seedling primary cell walls. Between the stem and the leaf, the secondary cell wall-rich stem contains more xylan and more cellulose compared to the leaf. Moreover, the xylan chains are about twofold more acetylated and about 60% more ferulated in the stem. These highly acetylated and ferulated xylan chains adopt a twofold conformation more prevalently and interact more extensively with cellulose. These results support the notion that acetylated xylan is found more in the twofold screw conformation, which preferentially binds cellulose. This in turn promotes cellulose-lignin interactions that are essential for the formation of the secondary cell wall.
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Affiliation(s)
- Pu Duan
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Samuel J. Kaser
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Jan J. Lyczakowski
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1QW, U.K.
| | - Pyae Phyo
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - Theodora Tryfona
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1QW, U.K.
| | - Paul Dupree
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1QW, U.K.
| | - Mei Hong
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
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Tiwari N, Wi S, Mentink-Vigier F, Sinha N. Mechanistic Insights into the Structural Stability of Collagen-Containing Biomaterials Such as Bones and Cartilage. J Phys Chem B 2021; 125:4757-4766. [PMID: 33929847 PMCID: PMC8151626 DOI: 10.1021/acs.jpcb.1c01431] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structural stability of various collagen-containing biomaterials such as bones and cartilage is still a mystery. Despite the spectroscopic development of several decades, the detailed mechanism of collagen interaction with citrate in bones and glycosaminoglycans (GAGs) in the cartilage extracellular matrix (ECM) in its native state is unobservable. We present a significant advancement to probe the collagen interactions with citrate and GAGs in the ECM of native bones and cartilage along with specific/non-specific interactions inside the collagen assembly at the nanoscopic level through natural-abundance dynamic nuclear polarization-based solid-state nuclear magnetic resonance spectroscopy. The detected molecular-level interactions between citrate-collagen and GAG-collagen inside the native bone and cartilage matrices and other backbone and side-chain interactions in the collagen assembly are responsible for the structural stability and other biomechanical properties of these important classes of biomaterials.
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Affiliation(s)
- Nidhi Tiwari
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow – 226014, INDIA
- Department of Chemistry, Institute of Sciences, Banaras Hindu University, Varanasi – 221005, INDIA
| | - Sungsool Wi
- National High Magnetic Field Laboratory, Tallahassee, Florida 32304, USA
| | | | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow – 226014, INDIA
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35
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Xiao H, Zhang Z, Zhao Y, Yang J. Spectral editing of alanine, serine, and threonine in uniformly labeled proteins based on frequency-selective homonuclear recoupling in solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2021; 75:193-202. [PMID: 33890210 DOI: 10.1007/s10858-021-00367-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Spectral editing is crucial to simplify the crowded solid-state NMR spectra of proteins. New techniques are introduced to edit 13C-13C correlations of uniformly labeled proteins under moderate magic-angle spinning (MAS), based on our recent frequency-selective homonuclear recoupling sequences [Zhang et al., J. Phys. Chem. Lett. 2020, 11, 8077-8083]. The signals of alanine, serine, or threonine residues are selected out by selective 13Cα-13Cβ double-quantum filtering (DQF). The 13Cα-13Cβ correlations of alanine residues are selectively established with efficiency up to ~ 1.8 times that by dipolar-assisted rotational resonance (DARR). The techniques are shown in 2D/3D NCCX experiments and applied to the uniformly 13C, 15N labeled Aquaporin Z (AqpZ) membrane protein, demonstrating their potential to simplify spectral analyses in biological solid-state NMR.
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Affiliation(s)
- Hang Xiao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhengfeng Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China.
| | - Yongxiang Zhao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
| | - Jun Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P. R. China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China.
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36
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Using Solid-State 13C NMR Spectroscopy to Study the Molecular Organization of Primary Plant Cell Walls. Methods Mol Biol 2021. [PMID: 32617937 DOI: 10.1007/978-1-0716-0621-6_12] [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
A knowledge of the mobilities of the polysaccharides or parts of polysaccharides in a cell-wall preparation provides information about possible molecular interactions among the polysaccharides in the cell wall and the relative locations of polysaccharides within the cell wall. A number of solid-state 13C NMR techniques have been developed that can be used to investigate different types of polysaccharide mobilities: rigid, semirigid, mobile, and highly mobile. In this chapter techniques are described for obtaining spectra from primary cell-wall preparations using CP/MAS, proton-rotating frame, proton spin-spin, spin-echo relaxation spectra and single-pulse excitation. We also describe how proton spin relaxation editing can be used to obtain subspectra for cell-wall polysaccharides of different mobilities, and how 2D and 3D solid-state NMR experiments have recently been applied to plant cell walls.
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37
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Structural details of amyloid β oligomers in complex with human prion protein as revealed by solid-state MAS NMR spectroscopy. J Biol Chem 2021; 296:100499. [PMID: 33667547 PMCID: PMC8042448 DOI: 10.1016/j.jbc.2021.100499] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
Human PrP (huPrP) is a high-affinity receptor for oligomeric amyloid β (Aβ) protein aggregates. Binding of Aβ oligomers to membrane-anchored huPrP has been suggested to trigger neurotoxic cell signaling in Alzheimer’s disease, while an N-terminal soluble fragment of huPrP can sequester Aβ oligomers and reduce their toxicity. Synthetic oligomeric Aβ species are known to be heterogeneous, dynamic, and transient, rendering their structural investigation particularly challenging. Here, using huPrP to preserve Aβ oligomers by coprecipitating them into large heteroassemblies, we investigated the conformations of Aβ(1–42) oligomers and huPrP in the complex by solid-state MAS NMR spectroscopy. The disordered N-terminal region of huPrP becomes immobilized in the complex and therefore visible in dipolar spectra without adopting chemical shifts characteristic of a regular secondary structure. Most of the well-defined C-terminal part of huPrP is part of the rigid complex, and solid-state NMR spectra suggest a loss in regular secondary structure in the two C-terminal α-helices. For Aβ(1–42) oligomers in complex with huPrP, secondary chemical shifts reveal substantial β-strand content. Importantly, not all Aβ(1–42) molecules within the complex have identical conformations. Comparison with the chemical shifts of synthetic Aβ fibrils suggests that the Aβ oligomer preparation represents a heterogeneous mixture of β-strand-rich assemblies, of which some have the potential to evolve and elongate into different fibril polymorphs, reflecting a general propensity of Aβ to adopt variable β-strand-rich conformers. Taken together, our results reveal structural changes in huPrP upon binding to Aβ oligomers that suggest a role of the C terminus of huPrP in cell signaling. Trapping Aβ(1–42) oligomers by binding to huPrP has proved to be a useful tool for studying the structure of these highly heterogeneous β-strand-rich assemblies.
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38
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Jain SK, Tabassum T, Li L, Ren L, Fan W, Tsapatsis M, Caratzoulas S, Han S, Scott SL. P-Site Structural Diversity and Evolution in a Zeosil Catalyst. J Am Chem Soc 2021; 143:1968-1983. [PMID: 33491456 DOI: 10.1021/jacs.0c11768] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphorus-modified siliceous zeolites, or P-zeosils, catalyze the selective dehydration of biomass derivatives to platform chemicals such as p-xylene and 1,3-butadiene. Water generated during these reactions is a critical factor in catalytic activity, but the effects of hydrolysis on the structure, acidity, and distribution of the active sites are largely unknown. In this study, the P-sites in an all-silica self-pillared pentasil (P-SPP) with a low P-loading (Si/P = 27) were identified by solid-state 31P NMR using frequency-selective detection. This technique resolves overlapping signals for P-sites that are covalently bound to the solid phase, as well as oligomers confined in the zeolite but not attached to the zeolite. Dynamic Nuclear Polarization provides the sensitivity necessary to conduct 29Si-filtered 31P detection and 31P-31P correlation experiments. The aforementioned techniques allow us to distinguish sites with P-O-Si linkages from those with P-O-P linkages. The spectra reveal a previously unappreciated diversity of P-sites, including evidence for surface-bound oligomers. In the dry P-zeosil, essentially all P-sites are anchored to the solid phase, including mononuclear sites and dinuclear sites containing the [Si-O-P-O-P-O-Si] motif. The fully-condensed sites evolve rapidly when exposed to humidity, even at room temperature. Partially hydrolyzed species have a wide range of acidities, inferred from their calculated LUMO energies. Initial cleavage of some P-O-Si linkages results in an evolving mixture of surface-bound mono- and oligonuclear P-sites with increased acidity. Subsequent P-O-P cleavage leads to a decrease in acidity as the P-sites are eventually converted to H3PO4. The ability to identify acidic sites in P-zeosils and to describe their structure and stability will play an important role in controlling the activity of microporous catalysts by regulating their water content.
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Affiliation(s)
- Sheetal K Jain
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tarnuma Tabassum
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Li Li
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Limin Ren
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - Wei Fan
- Department of Chemical Engineering, University of Massachusetts Amherst, 686 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Michael Tsapatsis
- Department of Chemical and Biomolecular Engineering and Institute for NanoBiotechnology, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States.,Applied Physics Laboratory, Johns Hopkins University, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Stavros Caratzoulas
- Delaware Energy Institute, 221 Academy Street, Newark, Delaware 19716, United States
| | - Songi Han
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Susannah L Scott
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
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39
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Jeon J, Yau WM, Tycko R. Millisecond Time-Resolved Solid-State NMR Reveals a Two-Stage Molecular Mechanism for Formation of Complexes between Calmodulin and a Target Peptide from Myosin Light Chain Kinase. J Am Chem Soc 2020; 142:21220-21232. [PMID: 33280387 DOI: 10.1021/jacs.0c11156] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Calmodulin (CaM) mediates a wide range of biological responses to changes in intracellular Ca2+ concentrations through its calcium-dependent binding affinities to numerous target proteins. Binding of two Ca2+ ions to each of the two four-helix-bundle domains of CaM results in major conformational changes that create a potential binding site for the CaM binding domain of a target protein, which also undergoes major conformational changes to form the complex with CaM. Details of the molecular mechanism of complex formation are not well established, despite numerous structural, spectroscopic, thermodynamic, and kinetic studies. Here, we report a study of the process by which the 26-residue peptide M13, which represents the CaM binding domain of skeletal muscle myosin light chain kinase, forms a complex with CaM in the presence of excess Ca2+ on the millisecond time scale. Our experiments use a combination of selective 13C labeling of CaM and M13, rapid mixing of CaM solutions with M13/Ca2+ solutions, rapid freeze-quenching of the mixed solutions, and low-temperature solid state nuclear magnetic resonance (ssNMR) enhanced by dynamic nuclear polarization. From measurements of the dependence of 2D 13C-13C ssNMR spectra on the time between mixing and freezing, we find that the N-terminal portion of M13 converts from a conformationally disordered state to an α-helix and develops contacts with the C-terminal domain of CaM in about 2 ms. The C-terminal portion of M13 becomes α-helical and develops contacts with the N-terminal domain of CaM more slowly, in about 8 ms. The level of structural order in the CaM/M13/Ca2+ complexes, indicated by 13C ssNMR line widths, continues to increase beyond 27 ms.
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Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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40
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Ehren HL, Appels FV, Houben K, Renault MA, Wösten HA, Baldus M. Characterization of the cell wall of a mushroom forming fungus at atomic resolution using solid-state NMR spectroscopy. Cell Surf 2020; 6:100046. [PMID: 33204900 PMCID: PMC7649524 DOI: 10.1016/j.tcsw.2020.100046] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/16/2020] [Accepted: 10/21/2020] [Indexed: 01/18/2023] Open
Abstract
Cell walls are essential in the interaction of fungi with the (a)biotic environment and are also key to hyphal morphogenesis and mechanical strength. Here, we used solid-state NMR (ssNMR) spectroscopy combined with HPLC and GC-MS to study the structural organization of the cell wall of a representative of the Basidiomycota, one of the two main phyla of fungi. Based on the data we propose a refined model for the cell wall of a basidiomycete. In this model, the rigid core is built from α- and β-(1,3)-glucan, β-(1,3)-(1,6)-glucan, highly branched and single stranded β-(1,4)-chitin as well as polymeric fucose. The mobile fraction of the cell wall is composed of β-(1,3)-glucan, β-(1,3)-(1,6)-glucan, β-(1,6)-glucan, α-linked reducing and non-reducing ends and polymeric mannose. Together, these findings provide novel insights into the structural organization of the cell wall of the model basidiomycete S. commune that was previously based on destructive chemical and enzymatic analysis.
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Affiliation(s)
- Helena Leona Ehren
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Freek V.W. Appels
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Klaartje Houben
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marie A.M. Renault
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Han A.B. Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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41
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Yeh V, Goode A, Bonev BB. Membrane Protein Structure Determination and Characterisation by Solution and Solid-State NMR. BIOLOGY 2020; 9:E396. [PMID: 33198410 PMCID: PMC7697852 DOI: 10.3390/biology9110396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 12/25/2022]
Abstract
Biological membranes define the interface of life and its basic unit, the cell. Membrane proteins play key roles in membrane functions, yet their structure and mechanisms remain poorly understood. Breakthroughs in crystallography and electron microscopy have invigorated structural analysis while failing to characterise key functional interactions with lipids, small molecules and membrane modulators, as well as their conformational polymorphism and dynamics. NMR is uniquely suited to resolving atomic environments within complex molecular assemblies and reporting on membrane organisation, protein structure, lipid and polysaccharide composition, conformational variations and molecular interactions. The main challenge in membrane protein studies at the atomic level remains the need for a membrane environment to support their fold. NMR studies in membrane mimetics and membranes of increasing complexity offer close to native environments for structural and molecular studies of membrane proteins. Solution NMR inherits high resolution from small molecule analysis, providing insights from detergent solubilised proteins and small molecular assemblies. Solid-state NMR achieves high resolution in membrane samples through fast sample spinning or sample alignment. Recent developments in dynamic nuclear polarisation NMR allow signal enhancement by orders of magnitude opening new opportunities for expanding the applications of NMR to studies of native membranes and whole cells.
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Affiliation(s)
| | | | - Boyan B. Bonev
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (V.Y.); (A.G.)
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42
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de Vlugt JE, Xiao P, Munro R, Charchoglyan A, Brewer D, Al-Abdul-Wahid MS, Brown LS, Ladizhansky V. Identifying lipids tightly bound to an integral membrane protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183345. [DOI: 10.1016/j.bbamem.2020.183345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/11/2020] [Accepted: 05/05/2020] [Indexed: 01/02/2023]
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43
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Damman R, Lucini Paioni A, Xenaki KT, Beltrán Hernández I, van Bergen En Henegouwen PMP, Baldus M. Development of in vitro-grown spheroids as a 3D tumor model system for solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2020; 74:401-412. [PMID: 32562030 PMCID: PMC7508937 DOI: 10.1007/s10858-020-00328-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/09/2020] [Indexed: 05/11/2023]
Abstract
Recent advances in the field of in-cell NMR spectroscopy have made it possible to study proteins in the context of bacterial or mammalian cell extracts or even entire cells. As most mammalian cells are part of a multi-cellular complex, there is a need to develop novel NMR approaches enabling the study of proteins within the complexity of a 3D cellular environment. Here we investigate the use of the hanging drop method to grow spheroids which are homogenous in size and shape as a model system to study solid tumors using solid-state NMR (ssNMR) spectroscopy. We find that these spheroids are stable under magic-angle-spinning conditions and show a clear change in metabolic profile as compared to single cell preparations. Finally, we utilize dynamic nuclear polarization (DNP)-supported ssNMR measurements to show that low concentrations of labelled nanobodies targeting EGFR (7D12) can be detected inside the spheroids. These findings suggest that solid-state NMR can be used to directly examine proteins or other biomolecules in a 3D cellular microenvironment with potential applications in pharmacological research.
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Affiliation(s)
- Reinier Damman
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Katerina T Xenaki
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Irati Beltrán Hernández
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Pharmaceutics, Department of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Paul M P van Bergen En Henegouwen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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44
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Li J, Sae Her A, Traaseth NJ. Site-specific resolution of anionic residues in proteins using solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2020; 74:355-363. [PMID: 32514875 PMCID: PMC7472563 DOI: 10.1007/s10858-020-00323-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
NMR spectroscopy is commonly used to infer site-specific acid dissociation constants (pKa) since the chemical shift is sensitive to the protonation state. Methods that probe atoms nearest to the functional groups involved in acid/base chemistry are the most sensitive for determining the protonation state. In this work, we describe a magic-angle-spinning (MAS) solid-state NMR approach to measure chemical shifts on the side chain of the anionic residues aspartate and glutamate. This method involves a combination of double quantum spectroscopy in the indirect dimension and REDOR dephasing to provide a sensitive and resolved view of these amino acid residues that are commonly involved in enzyme catalysis and membrane protein transport. To demonstrate the applicability of the approach, we carried out measurements using a microcrystalline soluble protein (ubiquitin) and a membrane protein embedded in lipid bilayers (EmrE). Overall, the resolution available from the double quantum dimension and confidence in identification of aspartate and glutamate residues from the REDOR filter make this method the most convenient for characterizing protonation states and deriving pKa values using MAS solid-state NMR.
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Affiliation(s)
- Jianping Li
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Ampon Sae Her
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Nathaniel J Traaseth
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA.
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45
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein–RNA Complex by Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
- Group of NMR-based Structural ChemistryHelmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
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46
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2020; 59:6866-6873. [PMID: 32023357 PMCID: PMC7187219 DOI: 10.1002/anie.201915465] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Indexed: 12/17/2022]
Abstract
Solid‐state NMR (ssNMR) is applicable to high molecular‐weight (MW) protein assemblies in a non‐amorphous precipitate. The technique yields atomic resolution structural information on both soluble and insoluble particles without limitations of MW or requirement of crystals. Herein, we propose and demonstrate an approach that yields the structure of protein–RNA complexes (RNP) solely from ssNMR data. Instead of using low‐sensitivity magnetization transfer steps between heteronuclei of the protein and the RNA, we measure paramagnetic relaxation enhancement effects elicited on the RNA by a paramagnetic tag coupled to the protein. We demonstrate that this data, together with chemical‐shift‐perturbation data, yields an accurate structure of an RNP complex, starting from the bound structures of its components. The possibility of characterizing protein–RNA interactions by ssNMR may enable applications to large RNP complexes, whose structures are not accessible by other methods.
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Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany.,Group of NMR-based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
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47
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Mayen L, Jensen ND, Laurencin D, Marsan O, Bonhomme C, Gervais C, Smith ME, Coelho C, Laurent G, Trebosc J, Gan Z, Chen K, Rey C, Combes C, Soulié J. A soft-chemistry approach to the synthesis of amorphous calcium ortho/pyrophosphate biomaterials of tunable composition. Acta Biomater 2020; 103:333-345. [PMID: 31881314 DOI: 10.1016/j.actbio.2019.12.027] [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: 09/26/2019] [Revised: 12/15/2019] [Accepted: 12/19/2019] [Indexed: 12/27/2022]
Abstract
The development of amorphous phosphate-based materials is of major interest in the field of biomaterials science, and especially for bone substitution applications. In this context, we herein report the synthesis of gel-derived hydrated amorphous calcium/sodium ortho/pyrophosphate materials at ambient temperature and in water. For the first time, such materials have been obtained in a large range of tunable orthophosphate/pyrophosphate molar ratios. Multi-scale characterization was carried out thanks to various techniques, including advanced multinuclear solid state NMR. It allowed the quantification of each ionic/molecular species leading to a general formula for these materials: [(Ca2+y Na+z H+3+x-2y-z)(PO43-)1-x(P2O74-)x](H2O)u. Beyond this formula, the analyses suggest that these amorphous solids are formed by the aggregation of colloids and that surface water and sodium could play a role in the cohesion of the whole material. Although the full comprehension of mechanisms of formation and structure is still to be investigated in detail, the straightforward synthesis of these new amorphous materials opens up many perspectives in the field of materials for bone substitution and regeneration. STATEMENT OF SIGNIFICANCE: The metastability of amorphous phosphate-based materials with various chain length often improves their (bio)chemical reactivity. However, the control of the ratio of the different phosphate entities has not been yet described especially for small ions (pyrophosphate/orthophosphate) and using soft chemistry, whereas it opens the way for the tuning of enzyme- and/or pH-driven degradation and biological properties. Our study focuses on elaboration of amorphous gel-derived hydrated calcium/sodium ortho/pyrophosphate solids at 70 °C with a large range of orthophosphate/pyrophosphate ratios. Multi-scale characterization was carried out using various techniques such as advanced multinuclear SSNMR (31P, 23Na, 1H, 43Ca). Analyses suggest that these solids are formed by colloids aggregation and that the location of mobile water and sodium could play a role in the material cohesion.
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Affiliation(s)
- Laëtitia Mayen
- CIRIMAT, Université de Toulouse, CNRS, INPT-ENSIACET, Toulouse, France
| | - Nicholai D Jensen
- ICGM, CNRS-UM-ENSCM, Université de Montpellier, Montpellier, France; Sorbonne Université, CNRS, LCMCP, Paris, France
| | | | - Olivier Marsan
- CIRIMAT, Université de Toulouse, CNRS, INPT-ENSIACET, Toulouse, France
| | | | | | - Mark E Smith
- Department of Chemistry, Lancaster University, Lancaster, UK
| | | | | | - Julien Trebosc
- Université de Lille, UMR 8181, UCCS: Unit of Catalysis and Chemistry of Solids, Lille, France
| | - Zhehong Gan
- National High Magnetic Field Laboratory, Tallahassee, FL, USA
| | - Kuizhi Chen
- National High Magnetic Field Laboratory, Tallahassee, FL, USA
| | - Christian Rey
- CIRIMAT, Université de Toulouse, CNRS, INPT-ENSIACET, Toulouse, France
| | - Christèle Combes
- CIRIMAT, Université de Toulouse, CNRS, INPT-ENSIACET, Toulouse, France
| | - Jérémy Soulié
- CIRIMAT, Université de Toulouse, CNRS, INPT-ENSIACET, Toulouse, France.
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48
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Struppe J, Quinn CM, Sarkar S, Gronenborn AM, Polenova T. Ultrafast 1H MAS NMR Crystallography for Natural Abundance Pharmaceutical Compounds. Mol Pharm 2020; 17:674-682. [PMID: 31891271 DOI: 10.1021/acs.molpharmaceut.9b01157] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Magic angle spinning (MAS) NMR is a powerful method for the study of pharmaceutical compounds, and probes with spinning frequencies above 100 kHz enable an atomic-resolution analysis of sub-micromole quantities of fully protonated solids. Here, we present an ultrafast NMR crystallography approach for structural characterization of organic solids at MAS frequencies of 100-111 kHz. We assess the efficiency of 1H-detected experiments in the solid state and demonstrate the utility of 2D and 3D homo- and heteronuclear correlation spectra for resonance assignments. These experiments are demonstrated for an amino acid, U-13C,15N-histidine, and also for the significantly larger, natural product Posaconazole, an antifungal compound investigated at natural abundance. Our results illustrate the power for characterizing organic molecules, enabled by exploiting the increased 1H resolution and sensitivity at MAS frequencies above 100 kHz.
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Affiliation(s)
- Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sucharita Sarkar
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Angela M Gronenborn
- Department of Structural Biology , University of Pittsburgh School of Medicine , Pittsburgh , Pennsylvania 15260 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , Pittsburgh , Pennsylvania 15260 , United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , Pittsburgh , Pennsylvania 15260 , United States
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49
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Melánová K, Brus J, Zima V, Beneš L, Svoboda J, Kobera L, Kutálek P. Formation of Layered Proton-Conducting Zirconium and Titanium Organophosphonates by Topotactic Reaction: Physicochemical Properties, Proton Dynamics, and Atomic-Resolution Structure. Inorg Chem 2020; 59:505-513. [PMID: 31808683 DOI: 10.1021/acs.inorgchem.9b02755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of new zirconium and titanium phosphates-organophosphonates, in which the organophosphonate moiety is functionalized with a sulfo group, was prepared by a topotactic reaction involving the gamma modification of zirconium or titanium hydrogen phosphate with 2-bis(phosphonomethyl)amino-ethan-1-sulfonic acid (H4TDP). H4TDP represents a new type of functionalizing agent, which can be easily prepared by a Moedritzer-Irani reaction from taurine (2-aminoethanesulfonic acid). The gamma modification of zirconium hydrogen phosphate (γ-ZrP) with H4TDP provides mixed phosphate-organophosphonate compounds with the formula Zr(PO4)(H2PO4)1-2x(H2TDP)x·yH2O, where x = 0.15, 0.34, 0.45, and is controlled by the γ-ZrP/H4TDP ratio in the starting mixture. On the contrary, by the topotactic gamma modification of titanium hydrogen phosphate (γ-TiP) with H4TDP, only one product with the formula Ti(PO4)(H2PO4)1-2z(H2TDP)z·yH2O, where z = 0.41 ± 0.01, was obtained regardless of the composition of the starting mixture. The synthesized compounds were characterized by elemental analysis, thermogravimetric analysis, energy-dispersive X-ray analysis, and infrared spectroscopy. The way the topotactic reaction proceeds and how the grafted organophosphonate groups are bonded to the layers of the host structure were suggested on the basis of the solid-state NMR data. It was found that the grafted moieties are spread evenly in the host layers among the hydrogen phosphate groups. The obtained solids are able to intercalate basic molecules, as was proved by the intercalation reactions of the zirconium series with butylamine. The amount of intercalated butylamine increases with increasing x. It is known that both host compounds, γ-ZrP and γ-TiP, are protonic conductors. It was found that the incorporation of H2TDP increases conductivity of the zirconium compound when x = 0.15, but further incorporation of H2TDP into the γ-ZrP host structure leads to a decrease of conductivity. This behavior is explained on the basis of the 1H MAS and the 1H-1H EXSY NMR data.
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Affiliation(s)
- K Melánová
- Institute of Macromolecular Chemistry , Czech Academy of Sciences , Heyrovsky sq. 2 , 162 06 Prague 6 , Czech Republic.,Joint Laboratory of Solid State Chemistry, Faculty of Chemical Technology , University of Pardubice , 532 10 Pardubice , Czech Republic
| | - J Brus
- Institute of Macromolecular Chemistry , Czech Academy of Sciences , Heyrovsky sq. 2 , 162 06 Prague 6 , Czech Republic
| | - V Zima
- Institute of Macromolecular Chemistry , Czech Academy of Sciences , Heyrovsky sq. 2 , 162 06 Prague 6 , Czech Republic
| | - L Beneš
- Joint Laboratory of Solid State Chemistry, Faculty of Chemical Technology , University of Pardubice , 532 10 Pardubice , Czech Republic
| | - J Svoboda
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology , University of Pardubice , 532 10 Pardubice , Czech Republic
| | - L Kobera
- Institute of Macromolecular Chemistry , Czech Academy of Sciences , Heyrovsky sq. 2 , 162 06 Prague 6 , Czech Republic
| | - P Kutálek
- Joint Laboratory of Solid State Chemistry, Faculty of Chemical Technology , University of Pardubice , 532 10 Pardubice , Czech Republic
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50
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Smith AN, Märker K, Hediger S, De Paëpe G. Natural Isotopic Abundance 13C and 15N Multidimensional Solid-State NMR Enabled by Dynamic Nuclear Polarization. J Phys Chem Lett 2019; 10:4652-4662. [PMID: 31361489 DOI: 10.1021/acs.jpclett.8b03874] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Dynamic nuclear polarization (DNP) has made feasible solid-state NMR experiments that were previously thought impractical due to sensitivity limitations. One such class of experiments is the structural characterization of organic and biological samples at natural isotopic abundance (NA). Herein, we describe the many advantages of DNP-enabled ssNMR at NA, including the extraction of long-range distance constraints using dipolar recoupling pulse sequences without the deleterious effects of dipolar truncation. In addition to the theoretical underpinnings in the analysis of these types of experiments, numerous applications of DNP-enabled ssNMR at NA are discussed.
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Affiliation(s)
- Adam N Smith
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM , F-38000 Grenoble , France
| | - Katharina Märker
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM , F-38000 Grenoble , France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM , F-38000 Grenoble , France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, MEM , F-38000 Grenoble , France
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