1
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Price LE, Alaniva N, Millen M, Epprecht T, Urban M, Däpp A, Barnes AB. Cryogenic-compatible spherical rotors and stators for magic angle spinning dynamic nuclear polarization. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2023; 4:231-241. [PMID: 37904856 PMCID: PMC10539783 DOI: 10.5194/mr-4-231-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/21/2023] [Indexed: 11/01/2023]
Abstract
Cryogenic magic angle spinning (MAS) is a standard technique utilized for dynamic nuclear polarization (DNP) in solid-state nuclear magnetic resonance (NMR). Here we describe the optimization and implementation of a stator for cryogenic MAS with 9.5 mm diameter spherical rotors, allowing for DNP experiments on large sample volumes. Designs of the stator and rotor for cryogenic MAS build on recent advancements of MAS spheres and take a step further to incorporate sample insert and eject and a temperature-independent spinning stability of ± 1 Hz. At a field of 7 T and spinning at 2.0 kHz with a sample temperature of 105-107 K, DNP enhancements of 256 and 200 were observed for 124 and 223 µ L sample volumes, respectively, each consisting of 4 M 13 C, 15 N-labeled urea and 20 mM AMUPol in a glycerol-water glassy matrix.
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Affiliation(s)
- Lauren E. Price
- Department of Chemistry and Applied Biochemistry, ETH Zürich,
Zurich 8093, Switzerland
| | - Nicholas Alaniva
- Department of Chemistry and Applied Biochemistry, ETH Zürich,
Zurich 8093, Switzerland
| | - Marthe Millen
- Department of Chemistry and Applied Biochemistry, ETH Zürich,
Zurich 8093, Switzerland
| | - Till Epprecht
- Department of Chemistry and Applied Biochemistry, ETH Zürich,
Zurich 8093, Switzerland
| | - Michael Urban
- Department of Chemistry and Applied Biochemistry, ETH Zürich,
Zurich 8093, Switzerland
| | - Alexander Däpp
- Department of Chemistry and Applied Biochemistry, ETH Zürich,
Zurich 8093, Switzerland
| | - Alexander B. Barnes
- Department of Chemistry and Applied Biochemistry, ETH Zürich,
Zurich 8093, Switzerland
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2
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Sani MA, Le Brun AP, Rajput S, Attard T, Separovic F. The membrane activity of the antimicrobial peptide caerin 1.1 is pH dependent. Biophys J 2023; 122:1058-1067. [PMID: 36680343 PMCID: PMC10111263 DOI: 10.1016/j.bpj.2023.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/09/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Antimicrobial peptides are an important class of membrane-active peptides that can provide alternatives or complements to classic antibiotics. Among the many classes of AMPs, the histidine-rich family is of particular interest since they may induce pH-sensitive interactions with cell membranes. The AMP caerin 1.1 (Cae-1), from Australian tree frogs, has three histidine residues, and thus we studied the pH dependence of its interactions with model cell membranes. Using NMR spectroscopy and molecular dynamics simulations, we showed that Cae-1 induced greater perturbation of the lipid dynamics and water penetrations within the membrane interior in an acidic environment compared with physiological conditions. Using 31P solid-state NMR, the packing, chemical environment, and dynamics of the lipid headgroup were monitored. 2H solid-state NMR showed that Cae-1 ordered the acyl chains of the hydrophobic core of the bilayer. These results supported the molecular dynamics data, which showed that Cae-1 was mainly inserted within the lipid bilayer for both neutral and negatively charged membranes, with the charged residues pulling the water and phosphate groups inward. This could be an early step in the mechanism of membrane disruption by histidine-rich antimicrobial peptides and indicated that Cae-1 acts via a transmembrane mechanism in bilayers of neutral and anionic phospholipid membranes, especially in acidic conditions.
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Affiliation(s)
- Marc-Antoine Sani
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
| | - Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Kirrawee, New South Wales, Australia
| | - Sunnia Rajput
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Troy Attard
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Frances Separovic
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia.
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3
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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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4
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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5
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Carnahan SL, Chen Y, Wishart JF, Lubach JW, Rossini AJ. Magic angle spinning dynamic nuclear polarization solid-state NMR spectroscopy of γ-irradiated molecular organic solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 119:101785. [PMID: 35405629 DOI: 10.1016/j.ssnmr.2022.101785] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/22/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
In the past 15 years, magic angle spinning (MAS) dynamic nuclear polarization (DNP) has emerged as a method to increase the sensitivity of high-resolution solid-state NMR spectroscopy experiments. Recently, γ-irradiation has been used to generate significant concentrations of homogeneously distributed free radicals in a variety of solids, including quartz, glucose, and cellulose. Both γ-irradiated quartz and glucose previously showed significant MAS DNP enhancements. Here, γ-irradiation is applied to twelve small organic molecules to test the applicability of γ-irradiation as a general method of creating stable free radicals for MAS DNP experiments on organic solids and pharmaceuticals. Radical concentrations in the range of 0.25 mM-10 mM were observed in irradiated glucose, histidine, malic acid, and malonic acid, and significant 1H DNP enhancements of 32, 130, 19, and 11 were obtained, respectively, as measured by 1H→13C CPMAS experiments. However, concentrations of free radicals below 0.05 mM were generally observed in organic molecules containing aromatic rings, preventing sizeable DNP enhancements. DNP sensitivity gains for several of the irradiated compounds exceed that which can be obtained with the relayed DNP approach that uses exogeneous polarizing agent solutions and impregnation procedures. In several cases, significant 1H DNP enhancements were realized at room temperature. This study demonstrates that in many cases γ-irradiation is a viable alternative to addition of stable exogenous radicals for DNP experiments on organic solids.
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Affiliation(s)
- Scott L Carnahan
- US DOE Ames Laboratory, Ames, IA, 50011, USA; Iowa State University, Department of Chemistry, Ames, IA, 50011, USA
| | - Yunhua Chen
- US DOE Ames Laboratory, Ames, IA, 50011, USA; Iowa State University, Department of Chemistry, Ames, IA, 50011, USA
| | - James F Wishart
- Brookhaven National Laboratory, Chemistry Division, Upton, NY, 11973, United States
| | - Joseph W Lubach
- Genentech Inc., South San Francisco, CA, 94080, United States
| | - Aaron J Rossini
- US DOE Ames Laboratory, Ames, IA, 50011, USA; Iowa State University, Department of Chemistry, Ames, IA, 50011, USA.
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6
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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7
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Bertarello A, Berruyer P, Artelsmair M, Elmore CS, Heydarkhan-Hagvall S, Schade M, Chiarparin E, Schantz S, Emsley L. In-Cell Quantification of Drugs by Magic-Angle Spinning Dynamic Nuclear Polarization NMR. J Am Chem Soc 2022; 144:6734-6741. [PMID: 35385274 PMCID: PMC9026252 DOI: 10.1021/jacs.1c12442] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The determination of intracellular drug concentrations can provide a better understanding of the drug function and efficacy. Ideally, this should be performed nondestructively, with no modification of either the drug or the target, and with the capability to detect low amounts of the molecule of interest, in many cases in the μM to nM range (pmol to fmol per million cells). Unfortunately, it is currently challenging to have an experimental technique that provides direct quantitative measurements of intracellular drug concentrations that simultaneously satisfies these requirements. Here, we show that magic-angle spinning dynamic nuclear polarization (MAS DNP) can be used to fulfill these requirements. We apply a quantitative 15N MAS DNP approach in combination with 15N labeling to quantify the intracellular amount of the drug [15N]CHIR-98014, an activator of the Wingless and Int-1 signaling pathway, determining intracellular drug amounts in the range of tens to hundreds of picomoles per million cells. This is, to our knowledge, the first time that MAS DNP has been used to successfully estimate intracellular drug amounts.
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Affiliation(s)
- Andrea Bertarello
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Pierrick Berruyer
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Markus Artelsmair
- Early Chemical Development, Pharmaceutical Science, R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Charles S Elmore
- Early Chemical Development, Pharmaceutical Science, R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Sepideh Heydarkhan-Hagvall
- Bioscience, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceutical R&D AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Markus Schade
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Staffan Schantz
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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8
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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9
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Xiao Y, Ghosh R, Frederick KK. In-Cell NMR of Intact Mammalian Cells Preserved with the Cryoprotectants DMSO and Glycerol Have Similar DNP Performance. Front Mol Biosci 2022; 8:789478. [PMID: 35145995 PMCID: PMC8824258 DOI: 10.3389/fmolb.2021.789478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022] Open
Abstract
NMR has the resolution and specificity to determine atomic-level protein structures of isotopically-labeled proteins in complex environments and, with the sensitivity gains conferred by dynamic nuclear polarization (DNP), NMR has the sensitivity to detect proteins at their endogenous concentrations. Prior work established that DNP MAS NMR is compatible with cellular viability. However, in that work, 15% glycerol, rather than the more commonly used 10% DMSO, was used as the cellular cryoprotectant. Moreover, incubation of cells cryoprotected 15% glycerol with the polarization agent, AMUPol, resulted in an inhomogeneous distribution of AMUPol through the cellular biomass, which resulted in a spatial bias of the NMR peak intensities. Because 10% DMSO is not only the most used cryoprotectant for mammalian cells, but also because DMSO is often used to improve delivery of molecules to cells, we sought to characterize the DNP performance of cells that were incubated with AMUPol and cryoprotected with 10% DMSO. We found that, like cells preserved with 15% glycerol, cells preserved with 10% DMSO retain high viability during DNP MAS NMR experiments if they are frozen at a controlled rate. However, DMSO did not improve the dispersion of AMUPol throughout the cellular biomass. Cells preserved with 15% glycerol and with 10% DMSO had similar DNP performance for both the maximal DNP enhancements as well as the inhomogeneous dispersion of AMUPol throughout the cellular biomass. Therefore, 10% DMSO and 15% glycerol are both appropriate cryoprotectant systems for DNP-assisted MAS NMR of intact viable mammalian cells.
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Affiliation(s)
- Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, United States
| | - Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, United States
| | - Kendra K. Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, United States
- Center for Alzheimer’s and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX, United States
- *Correspondence: Kendra K. Frederick,
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10
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Mikhailov OV. The Physical Chemistry and Chemical Physics (PCCP) Section of the International Journal of Molecular Sciences in Its Publications: The First 300 Thematic Articles in the First 3 Years. Int J Mol Sci 2021; 23:241. [PMID: 35008667 PMCID: PMC8745423 DOI: 10.3390/ijms23010241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The Physical Chemistry and Chemical Physics Section (PCCP Section) is one of the youngest among the sections of the International Journal of Molecular Sciences (IJMS)-the year 2021 will only mark three years since its inception [...].
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Affiliation(s)
- Oleg V Mikhailov
- Department of Analytical Chemistry, Certification and Quality Management, Kazan National Research Technological University, K. Marx Street 68, 420015 Kazan, Russia
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11
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Poulhazan A, Dickwella Widanage MC, Muszyński A, Arnold AA, Warschawski DE, Azadi P, Marcotte I, Wang T. Identification and Quantification of Glycans in Whole Cells: Architecture of Microalgal Polysaccharides Described by Solid-State Nuclear Magnetic Resonance. J Am Chem Soc 2021; 143:19374-19388. [PMID: 34735142 PMCID: PMC8630702 DOI: 10.1021/jacs.1c07429] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Indexed: 12/15/2022]
Abstract
Microalgae are photosynthetic organisms widely distributed in nature and serve as a sustainable source of bioproducts. Their carbohydrate components are also promising candidates for bioenergy production and bioremediation, but the structural characterization of these heterogeneous polymers in cells remains a formidable problem. Here we present a widely applicable protocol for identifying and quantifying the glycan content using magic-angle-spinning (MAS) solid-state NMR (ssNMR) spectroscopy, with validation from glycosyl linkage and composition analysis deduced from mass-spectrometry (MS). Two-dimensional 13C-13C correlation ssNMR spectra of a uniformly 13C-labeled green microalga Parachlorella beijerinckii reveal that starch is the most abundant polysaccharide in a naturally cellulose-deficient strain, and this polymer adopts a well-organized and highly rigid structure in the cell. Some xyloses are present in both the mobile and rigid domains of the cell wall, with their chemical shifts partially aligned with the flat-ribbon 2-fold xylan identified in plants. Surprisingly, most other carbohydrates are largely mobile, regardless of their distribution in glycolipids or cell walls. These structural insights correlate with the high digestibility of this cellulose-deficient strain, and the in-cell ssNMR methods will facilitate the investigations of other economically important algae species.
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Affiliation(s)
- Alexandre Poulhazan
- Department
of Chemistry, University of Quebec at Montreal, Montreal H2X 2J6, Canada
| | | | - Artur Muszyński
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Alexandre A. Arnold
- Department
of Chemistry, University of Quebec at Montreal, Montreal H2X 2J6, Canada
| | - Dror E. Warschawski
- Laboratoire
des Biomolécules, LBM, CNRS UMR 7203,
Sorbonne Université, École Normale Supérieure,
PSL University, 75005 Paris, France
| | - Parastoo Azadi
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Isabelle Marcotte
- Department
of Chemistry, University of Quebec at Montreal, Montreal H2X 2J6, Canada
| | - Tuo Wang
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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12
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Overall SA, Barnes AB. Biomolecular Perturbations in In-Cell Dynamic Nuclear Polarization Experiments. Front Mol Biosci 2021; 8:743829. [PMID: 34751246 PMCID: PMC8572051 DOI: 10.3389/fmolb.2021.743829] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022] Open
Abstract
In-cell DNP is a growing application of NMR to the study of biomolecular structure and function within intact cells. An important unresolved question for in-cell DNP spectroscopy is the integrity of cellular samples under the cryogenic conditions of DNP. Despite the rich literature around cryopreservation of cells in the fields of stem cell/embryonic cell therapeutics, cell line preservation and in cryo-EM applications, the effect of cryopreservation procedures on DNP parameters is unclear. In this report we investigate cell survival and apoptosis in the presence of cryopreserving agents and DNP radicals. We also assess the effects of these reagents on cellular enhancements. We show that the DNP radical AMUPol has no effect on membrane permeability and does not induce apoptosis. Furthermore, the standard aqueous glass forming reagent, comprised of 60/30/10 d8-glycerol/D2O/H2O (DNP juice), rapidly dehydrates cells and induces apoptosis prior to freezing, reducing structural integrity of the sample prior to DNP analysis. Preservation with d6-DMSO at 10% v/v provided similar DNP enhancements per √unit time compared to glycerol preservation with superior maintenance of cell size and membrane integrity prior to freezing. DMSO preservation also greatly enhanced post-thaw survival of cells slow-frozen at 1°C/min. We therefore demonstrate that in-cell DNP-NMR studies should be done with d6-DMSO as cryoprotectant and raise important considerations for the progression of in-cell DNP-NMR towards the goal of high quality structural studies.
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Affiliation(s)
- Sarah A Overall
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
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Zhu S, Kachooei E, Harmer JR, Brown LJ, Separovic F, Sani MA. TOAC spin-labeled peptides tailored for DNP-NMR studies in lipid membrane environments. Biophys J 2021; 120:4501-4511. [PMID: 34480924 DOI: 10.1016/j.bpj.2021.08.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/08/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
The benefit of combining in-cell solid-state dynamic nuclear polarization (DNP) NMR and cryogenic temperatures is providing sufficient signal/noise and preservation of bacterial integrity via cryoprotection to enable in situ biophysical studies of antimicrobial peptides. The radical source required for DNP was delivered into cells by adding a nitroxide-tagged peptide based on the antimicrobial peptide maculatin 1.1 (Mac1). In this study, the structure, localization, and signal enhancement properties of a single (T-MacW) and double (T-T-MacW) TOAC (2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxylic acid) spin-labeled Mac1 analogs were determined within micelles or lipid vesicles. The solution NMR and circular dichroism results showed that the spin-labeled peptides adopted helical structures in contact with micelles. The peptides behaved as an isolated radical source in the presence of multilamellar vesicles, and the electron paramagnetic resonance (EPR) electron-electron distance for the doubly spin-labeled peptide was ∼1 nm. The strongest paramagnetic relaxation enhancement (PRE) was observed for the lipid NMR signals near the glycerol-carbonyl backbone and was stronger for the doubly spin-labeled peptide. Molecular dynamics simulation of the T-T-MacW radical source in phospholipid bilayers supported the EPR and PRE observations while providing further structural insights. Overall, the T-T-MacW peptide achieved better 13C and 15N signal NMR enhancements and 1H spin-lattice T1 relaxation than T-MacW.
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Affiliation(s)
- Shiying Zhu
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Ehsan Kachooei
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - Louise J Brown
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
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