1
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Costello WN, Xiao Y, Mentink-Vigier F, Kragelj J, Frederick KK. DNP-assisted solid-state NMR enables detection of proteins at nanomolar concentrations in fully protonated cellular milieu. JOURNAL OF BIOMOLECULAR NMR 2024; 78:95-108. [PMID: 38520488 DOI: 10.1007/s10858-024-00436-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/09/2024] [Indexed: 03/25/2024]
Abstract
With the sensitivity enhancements conferred by dynamic nuclear polarization (DNP), magic angle spinning (MAS) solid state NMR spectroscopy experiments can attain the necessary sensitivity to detect very low concentrations of proteins. This potentially enables structural investigations of proteins at their endogenous levels in their biological contexts where their native stoichiometries with potential interactors is maintained. Yet, even with DNP, experiments are still sensitivity limited. Moreover, when an isotopically-enriched target protein is present at physiological levels, which typically range from low micromolar to nanomolar concentrations, the isotope content from the natural abundance isotopes in the cellular milieu can outnumber the isotope content of the target protein. Using isotopically enriched yeast prion protein, Sup35NM, diluted into natural abundance yeast lysates, we optimized sample composition. We found that modest cryoprotectant concentrations and fully protonated environments support efficient DNP. We experimentally validated theoretical calculations of the limit of specificity for an isotopically enriched protein in natural abundance cellular milieu. We establish that, using pulse sequences that are selective for adjacent NMR-active nuclei, proteins can be specifically detected in cellular milieu at concentrations in the hundreds of nanomolar. Finally, we find that maintaining native stoichiometries of the protein of interest to the components of the cellular environment may be important for proteins that make specific interactions with cellular constituents.
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Affiliation(s)
- Whitney N Costello
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
| | | | - Jaka Kragelj
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
- Slovenian NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Kendra K Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA.
- Center for Alzheimer's and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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2
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Chaklashiya RK, Equbal A, Shernyukov A, Li Y, Tsay K, Stern Q, Tormyshev V, Bagryanskaya E, Han S. Dynamic Nuclear Polarization Using Electron Spin Cluster. J Phys Chem Lett 2024; 15:5366-5375. [PMID: 38735065 DOI: 10.1021/acs.jpclett.4c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Dynamic nuclear polarization (DNP) utilizing narrow-line electron spin clusters (ESCs) to achieve nuclear spin resonance matching (ESC-DNP) by microwave irradiation is a promising way to achieve NMR signal enhancements with a wide design scope requiring low microwave power at high magnetic field. Here we present the design for a trityl-based tetra-radical (TetraTrityl) to achieve DNP for 1H NMR at 7 T, supported by experimental data and quantum mechanical simulations. A slow-relaxing (T1e ≈ 1 ms) 4-ESC is found to require at least two electron spin pairs at <8 Å e-e spin distance to yield 1H ESC-DNP enhancement, while squeezing the rest of the e-e spin distances to <12 Å results in optimal 1H ESC-DNP enhancements. Fast-relaxing ESCs (T1e ≈ 10 μs) are found to require a weakly coupled narrow-line radical (sensitizer) to extract polarization from the ESC. These results provide design principles for achieving a power-efficient DNP at high field via ESC-DNP.
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Affiliation(s)
- Raj K Chaklashiya
- Materials Department, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Asif Equbal
- Division of Chemistry, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Quantum and Topological Systems, NYUAD Research Institute, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Andrey Shernyukov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Yuanxin Li
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Karen Tsay
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Quentin Stern
- Department of Chemistry, Northwestern University, Wilmette, Illinois 60208, United States
| | - Victor Tormyshev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Elena Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
| | - Songi Han
- Department of Chemistry, Northwestern University, Wilmette, Illinois 60208, United States
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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3
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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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4
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Sani MA, Rajput S, Keizer DW, Separovic F. NMR techniques for investigating antimicrobial peptides in model membranes and bacterial cells. Methods 2024; 224:10-20. [PMID: 38295893 DOI: 10.1016/j.ymeth.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
AMPs are short, mainly cationic membrane-active peptides found in all living organism. They perform diverse roles including signaling and acting as a line of defense against bacterial infections. AMPs have been extensively investigated as templates to facilitate the development of novel antimicrobial therapeutics. Understanding the interplay between these membrane-active peptides and the lipid membranes is considered to be a significant step in elucidating the specific mechanism of action of AMPs against prokaryotic and eukaryotic cells to aid the development of new therapeutics. In this review, we have provided a brief overview of various NMR techniques commonly used for studying AMP structure and AMP-membrane interactions in model membranes and whole cells.
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Affiliation(s)
- Marc-Antoine Sani
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Sunnia Rajput
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - David W Keizer
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Frances Separovic
- Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia; School of Chemistry, University of Melbourne, Melbourne, VIC 3010, Australia
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5
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Zhang Z, Zhao Q, Gong Z, Du R, Liu M, Zhang Y, Zhang L, Li C. Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology. JACS AU 2024; 4:369-383. [PMID: 38425916 PMCID: PMC10900494 DOI: 10.1021/jacsau.3c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
The validity of protein structures and interactions, whether determined under ideal laboratory conditions or predicted by AI tools such as Alphafold2, to precisely reflect those found in living cells remains to be examined. Moreover, understanding the changes in protein structures and interactions in response to stimuli within living cells, under both normal and disease conditions, is key to grasping proteins' functionality and cellular processes. Nevertheless, achieving high-resolution identification of these protein structures and interactions within living cells presents a technical challenge. In this Perspective, we summarize the recent advancements in in-cell nuclear magnetic resonance (NMR) and in vivo cross-linking mass spectrometry (XL-MS) for studying protein structures and interactions within a cellular context. Additionally, we discuss the challenges, opportunities, and potential benefits of integrating in-cell NMR and in vivo XL-MS in future research to offer an exhaustive approach to studying proteins in their natural habitat.
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Affiliation(s)
- Zeting Zhang
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qun Zhao
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhou Gong
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ruichen Du
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- University
of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yukui Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
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6
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Venkatesh A, Casano G, Wei R, Rao Y, Lingua H, Karoui H, Yulikov M, Ouari O, Emsley L. Rational Design of Dinitroxide Polarizing Agents for Dynamic Nuclear Polarization to Enhance Overall NMR Sensitivity. Angew Chem Int Ed Engl 2024; 63:e202317337. [PMID: 38193258 DOI: 10.1002/anie.202317337] [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: 11/14/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/10/2024]
Abstract
We evaluate the overall sensitivity gains provided by a series of eighteen nitroxide biradicals for dynamic nuclear polarization (DNP) solid-state NMR at 9.4 T and 100 K, including eight new biradicals. We find that in the best performing group the factors contributing to the overall sensitivity gains, namely the DNP enhancement, the build-up time, and the contribution factor, often compete with each other leading to very similar overall sensitivity across a range of biradicals. NaphPol and HydroPol are found to provide the best overall sensitivity factors, in organic and aqueous solvents respectively. One of the new biradicals, AMUPolCbm, provides high sensitivity for all three solvent formulations measured here, and can be considered to be a "universal" polarizing agent.
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Affiliation(s)
- Amrit Venkatesh
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- Current address: National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Gilles Casano
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire UMR 7273, 13013, Marseille, France
| | - Ran Wei
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Yu Rao
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Hugo Lingua
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire UMR 7273, 13013, Marseille, France
| | - Hakim Karoui
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire UMR 7273, 13013, Marseille, France
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire UMR 7273, 13013, Marseille, France
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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7
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [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: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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8
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Kragelj J, Ghosh R, Xiao Y, Dumarieh R, Lagasca D, Krishna S, Frederick KK. Spatially resolved DNP-assisted NMR illuminates the conformational ensemble of α-synuclein in intact viable cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563877. [PMID: 37961511 PMCID: PMC10634803 DOI: 10.1101/2023.10.24.563877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The protein α-syn adopts a wide variety of conformations including an intrinsically disordered monomeric form and an α-helical rich membrane-associated form that is thought to play an important role in cellular membrane processes. However, despite the high affinity of α-syn for membranes, evidence that the α-helical form of α-syn is adopted inside cells has thus far been indirect. In cell DNP-assisted solid state NMR on frozen samples has the potential to report directly on the entire conformational ensemble. Moreover, because the DNP polarization agent can be dispersed both homogenously and inhomogenously throughout the cellular biomass, in cell DNP-assisted solid state NMR experiments can report either quantitatively upon the structural ensemble or can preferentially report upon the structural ensemble with a spatial bias. Using DNP-assisted MAS NMR we establish that the spectra of purified α-syn in the membrane-associated and intrinsically disordered forms have distinguishable spectra. When the polarization agent is introduced into cells by electroporation and dispersed homogenously, a minority of the α-syn inside HEK293 cells adopts a highly α-helical rich conformation. Alteration of the spatial distribution of the polarization agent preferentially enhances the signal from molecules nearer to the cellular periphery, thus the α-helical rich population is preferentially adopted toward the cellular periphery. This demonstrates how selectively altering the spatial distribution of the DNP polarization agent can be a powerful tool for preferential reporting on specific structural ensembles, paving the way for more nuanced investigations into the conformations that proteins adopt in different areas of the cell.
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Affiliation(s)
- Jaka Kragelj
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Rania Dumarieh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Dominique Lagasca
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Sakshi Krishna
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Kendra K. Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
- Center for Alzheimer’s and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX 75390
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9
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Beriashvili D, Yao R, D'Amico F, Krafčíková M, Gurinov A, Safeer A, Cai X, Mulder MPC, Liu Y, Folkers GE, Baldus M. A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity. Chem Sci 2023; 14:9892-9899. [PMID: 37736634 PMCID: PMC10510770 DOI: 10.1039/d3sc02117c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Studying the structural aspects of proteins within sub-cellular compartments is of growing interest. Dynamic nuclear polarization supported solid-state NMR (DNP-ssNMR) is uniquely suited to provide such information, but critically lacks the desired sensitivity and resolution. Here we utilize SNAPol-1, a novel biradical, to conduct DNP-ssNMR at high-magnetic fields (800 MHz/527 GHz) inside HeLa cells and isolated cell nuclei electroporated with [13C,15N] labeled ubiquitin. We report that SNAPol-1 passively diffuses and homogenously distributes within whole cells and cell nuclei providing ubiquitin spectra of high sensitivity and remarkably improved spectral resolution. For cell nuclei, physical enrichment facilitates a further 4-fold decrease in measurement time and provides an exclusive structural view of the nuclear ubiquitin pool. Taken together, these advancements enable atomic interrogation of protein conformational plasticity at atomic resolution and with sub-cellular specificity.
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Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ru Yao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Francesca D'Amico
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Michaela Krafčíková
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, 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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10
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Kent JE, Ackermann BE, Debelouchina GT, Marassi FM. Dynamic Nuclear Polarization Illuminates Key Protein-Lipid Interactions in the Native Bacterial Cell Envelope. Biochemistry 2023; 62:2252-2256. [PMID: 37459255 PMCID: PMC11019665 DOI: 10.1021/acs.biochem.3c00262] [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] [Indexed: 07/28/2023]
Abstract
Elucidating the structure and interactions of proteins in native environments is a fundamental goal of structural biology. Nuclear magnetic resonance (NMR) spectroscopy is well suited for this task but often suffers from low sensitivity, especially in complex biological settings. Here, we use a sensitivity-enhancement technique called dynamic nuclear polarization (DNP) to overcome this challenge. We apply DNP to capture the membrane interactions of the outer membrane protein Ail, a key component of the host invasion pathway of Yersinia pestis. We show that the DNP-enhanced NMR spectra of Ail in native bacterial cell envelopes are well resolved and enriched in correlations that are invisible in conventional solid-state NMR experiments. Furthermore, we demonstrate the ability of DNP to capture elusive interactions between the protein and the surrounding lipopolysaccharide layer. Our results support a model where the extracellular loop arginine residues remodel the membrane environment, a process that is crucial for host invasion and pathogenesis.
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Affiliation(s)
- James E Kent
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Bryce E Ackermann
- Department Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Galia T Debelouchina
- Department Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesca M Marassi
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226-3548, United States
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11
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Menzildjian G, Schlagnitweit J, Casano G, Ouari O, Gajan D, Lesage A. Polarizing agents for efficient high field DNP solid-state NMR spectroscopy under magic-angle spinning: from design principles to formulation strategies. Chem Sci 2023; 14:6120-6148. [PMID: 37325158 PMCID: PMC10266460 DOI: 10.1039/d3sc01079a] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Dynamic Nuclear Polarization (DNP) has recently emerged as a cornerstone approach to enhance the sensitivity of solid-state NMR spectroscopy under Magic Angle Spinning (MAS), opening unprecedented analytical opportunities in chemistry and biology. DNP relies on a polarization transfer from unpaired electrons (present in endogenous or exogenous polarizing agents) to nearby nuclei. Developing and designing new polarizing sources for DNP solid-state NMR spectroscopy is currently an extremely active research field per se, that has recently led to significant breakthroughs and key achievements, in particular at high magnetic fields. This review describes recent developments in this area, highlighting key design principles that have been established over time and led to the introduction of increasingly more efficient polarizing sources. After a short introduction, Section 2 presents a brief history of solid-state DNP, highlighting the main polarization transfer schemes. The third section is devoted to the development of dinitroxide radicals, discussing the guidelines that were progressively established to design the fine-tuned molecular structures in use today. In Section 4, we describe recent efforts in developing hybrid radicals composed of a narrow EPR line radical covalently linked to a nitroxide, highlighting the parameters that modulate the DNP efficiency of these mixed structures. Section 5 reviews recent advances in the design of metal complexes suitable for DNP MAS NMR as exogenous electron sources. In parallel, current strategies that exploit metal ions as endogenous polarization sources are discussed. Section 6 briefly describes the recent introduction of mixed-valence radicals. In the last part, experimental aspects regarding sample formulation are reviewed to make best use of these polarizing agents in a broad panel of application fields.
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Affiliation(s)
- Georges Menzildjian
- Centre de RMN à, Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1) 5 Rue de la doua 69100 Villeurbanne France
| | - Judith Schlagnitweit
- Centre de RMN à, Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1) 5 Rue de la doua 69100 Villeurbanne France
| | - Gilles Casano
- Aix Marseille Univ., CNRS, Institut de Chimie Radicalaire, UMR 7273 Marseille France
| | - Olivier Ouari
- Aix Marseille Univ., CNRS, Institut de Chimie Radicalaire, UMR 7273 Marseille France
| | - David Gajan
- Centre de RMN à, Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1) 5 Rue de la doua 69100 Villeurbanne France
| | - Anne Lesage
- Centre de RMN à, Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1) 5 Rue de la doua 69100 Villeurbanne France
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12
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Kenyaga JM, Oteino SA, Sun Y, Qiang W. In-cell 31P solid-state NMR measurements of the lipid dynamics and influence of exogeneous β-amyloid peptides on live neuroblastoma neuro-2a cells. Biophys Chem 2023; 297:107008. [PMID: 36989875 DOI: 10.1016/j.bpc.2023.107008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/18/2023] [Accepted: 03/19/2023] [Indexed: 03/29/2023]
Abstract
Non-specific disruption of cellular membranes induced by aggregation of exogeneous β-amyloid (Aβ) peptides is considered a viable pathological mechanism in Alzheimer's disease (AD). The solid-state nuclear magnetic resonance (ssNMR) spectroscopy has been widely applied in model liposomes to provide important insights on the molecular interactions between membranes and Aβ aggregates. Yet, the feasibility of in-cell ssNMR spectroscopy to probe Aβ-membrane interactions in native cellular environments has rarely been tested. Here we report the application of in-cell31P ssNMR spectroscopy on live mouse neuroblastoma Neuro-2a (N2a) cells under moderate magic angle spinning (MAS) conditions. Both cell viability and cytoplasmic membrane integrity are retained for up to six hours under 5 kHz MAS frequency at 277 K, which allow applications of direct-polarization 31P spectroscopy and 31P spin-spin (T2) relaxation measurements. The 31P T2 relaxation time constant of N2a cells is significantly increased compared with the model liposome prepared with comparable major phospholipid compositions. With the addition of 5 μM 40-residue Aβ (Aβ1-40) peptides, the 31P T2 relaxation is instantly accelerated. This work demonstrates the feasibility of using in-cell31P ssNMR to investigate the Aβ-membrane interactions in the biologically relevant cellular system.
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13
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Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins. Mol Cell 2023; 83:1936-1952.e7. [PMID: 37267908 PMCID: PMC10281453 DOI: 10.1016/j.molcel.2023.05.006] [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: 04/12/2022] [Revised: 01/29/2023] [Accepted: 05/03/2023] [Indexed: 06/04/2023]
Abstract
Non-native conformations drive protein-misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well suited for elucidating them and their phenotypic effects. Especially intractable are the transient conformations populated by intrinsically disordered proteins. We describe an approach to systematically discover, stabilize, and purify native and non-native conformations, generated in vitro or in vivo, and directly link conformations to molecular, organismal, or evolutionary phenotypes. This approach involves high-throughput disulfide scanning (HTDS) of the entire protein. To reveal which disulfides trap which chromatographically resolvable conformers, we devised a deep-sequencing method for double-Cys variant libraries of proteins that precisely and simultaneously locates both Cys residues within each polypeptide. HTDS of the abundant E. coli periplasmic chaperone HdeA revealed distinct classes of disordered hydrophobic conformers with variable cytotoxicity depending on where the backbone was cross-linked. HTDS can bridge conformational and phenotypic landscapes for many proteins that function in disulfide-permissive environments.
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Affiliation(s)
- Eugene Serebryany
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Victor Y Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kibum Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amir Bitran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sunia A Trauger
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Bogdan Budnik
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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14
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Kent JE, Ackermann BE, Debelouchina GT, Marassi FM. Dynamic nuclear polarization illuminates key protein-lipid interactions in the native bacterial cell envelope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541325. [PMID: 37292594 PMCID: PMC10245764 DOI: 10.1101/2023.05.18.541325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Elucidating the structure and interactions of proteins in native environments has become a fundamental goal of structural biology. Nuclear magnetic resonance (NMR) spectroscopy is well suited for this task but often suffers from low sensitivity, especially in complex biological settings. Here, we use a sensitivity-enhancement technique called dynamic nuclear polarization (DNP) to overcome this challenge. We apply DNP to capture the membrane interactions of the outer membrane protein Ail, a key component of the host invasion pathway of Yersinia pestis . We show that the DNP-enhanced NMR spectra of Ail in native bacterial cell envelopes are well resolved and enriched in correlations that are invisible in conventional solid-state NMR experiments. Furthermore, we demonstrate the ability of DNP to capture elusive interactions between the protein and the surrounding lipopolysaccharide layer. Our results support a model where the extracellular loop arginine residues remodel the membrane environment, a process that is crucial for host invasion and pathogenesis.
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15
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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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16
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Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. Systematic conformation-to-phenotype mapping via limited deep-sequencing of proteins. ARXIV 2023:2204.06159. [PMID: 36776823 PMCID: PMC9915745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Non-native conformations drive protein misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well-suited for elucidating them and their phenotypic effects. Especially intractable are the transient conformations populated by intrinsically disordered proteins. We describe an approach to systematically discover, stabilize, and purify native and non-native conformations, generated in vitro or in vivo, and directly link conformations to molecular, organismal, or evolutionary phenotypes. This approach involves high-throughput disulfide scanning (HTDS) of the entire protein. To reveal which disulfides trap which chromatographically resolvable conformers, we devised a deep-sequencing method for double-Cys variant libraries of proteins that precisely and simultaneously locates both Cys residues within each polypeptide. HTDS of the abundant E. coli periplasmic chaperone HdeA revealed distinct classes of disordered hydrophobic conformers with variable cytotoxicity depending on where the backbone was cross-linked. HTDS can bridge conformational and phenotypic landscapes for many proteins that function in disulfide-permissive environments.
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Affiliation(s)
- Eugene Serebryany
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | - Victor Y. Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | - Kibum Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | - Amir Bitran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | | | - Bogdan Budnik
- Center for Mass Spectrometry, Harvard University, Cambridge, MA
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17
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Ketter S, Joseph B. Gd 3+-Trityl-Nitroxide Triple Labeling and Distance Measurements in the Heterooligomeric Cobalamin Transport Complex in the Native Lipid Bilayers. J Am Chem Soc 2023; 145:960-966. [PMID: 36599418 PMCID: PMC9853854 DOI: 10.1021/jacs.2c10080] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Increased efforts are being made for observing proteins in their native environments. Pulsed electron-electron double resonance spectroscopy (PELDOR, also known as DEER) is a powerful tool for this purpose. Conventionally, PELDOR employs an identical spin pair, which limits the output to a single distance for monomeric samples. Here, we show that the Gd3+-trityl-nitroxide (NO) three-spin system is a versatile tool to study heterooligomeric membrane protein complexes, even within their native membrane. This allowed for an independent determination of four different distances (Gd3+-trityl, Gd3+-NO, trityl-NO, and Gd3+-Gd3+) within the same sample. We demonstrate the feasibility of this approach by observing sequential ligand binding and the dynamics of complex formation in the cobalamin transport system involving four components (cobalamin, BtuB, TonB, and BtuF). Our results reveal that TonB binding alone is sufficient to release cobalamin from BtuB in the native asymmetric bilayers. This approach provides a potential tool for the structural and quantitative analysis of dynamic protein-protein interactions in oligomeric complexes, even within their native surroundings.
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18
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Ackermann BE, Lim BJ, Elathram N, Narayanan S, Debelouchina GT. A Comparative Study of Nitroxide-Based Biradicals for Dynamic Nuclear Polarization in Cellular Environments. Chembiochem 2022; 23:e202200577. [PMID: 36250276 PMCID: PMC9856215 DOI: 10.1002/cbic.202200577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/15/2022] [Indexed: 01/25/2023]
Abstract
Dynamic nuclear polarization (DNP) is a powerful tool to enhance the NMR signals of molecules by transferring polarization from unpaired electron spins to nuclei through microwave irradiation. The resulting signal enhancements can enable the analysis of samples that have previously been intractable by NMR spectroscopy, including proteins, nucleic acids, and metabolites in cells. To carry out DNP, the sample is doped with a polarization agent, a biradical containing two nitroxide moieties. DNP applications in cells, however, present significant challenges as nitroxides are often susceptible to the reducing cellular environment. Here, we introduce a novel polarization agent, POPAPOL, that exhibits increased lifetimes under reducing conditions. We also compare its bioresistance and DNP performance with three popular, commercially available polarization agents. Our work indicates that pyrrolidine-based nitroxides can outperform piperidine-based nitroxides in cellular environments, and that future polarization agent designs must carefully balance DNP performance and stability for cellular applications.
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Affiliation(s)
- Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Byung Joon Lim
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sirish Narayanan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA,Corresponding author: , http://debelouchinalab.ucsd.edu/
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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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Pierro A, Bonucci A, Normanno D, Ansaldi M, Pilet E, Ouari O, Guigliarelli B, Etienne E, Gerbaud G, Magalon A, Belle V, Mileo E. Probing the Structural Dynamics of a Bacterial Chaperone in Its Native Environment by Nitroxide‐Based EPR Spectroscopy. Chemistry 2022; 28:e202202249. [DOI: 10.1002/chem.202202249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
- Department of Chemistry University of Konstanz, and Konstanz Research School Chemical Biology 78457 Konstanz Germany
| | - Alessio Bonucci
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Davide Normanno
- Aix Marseille Univ CNRS, Inserm Institut Paoli-Calmettes, CRCM Centre de Recherche en Cancérologie de Marseille 13273 Marseille France
- Univ Montpellier CNRS, IGH Institut de Génétique Humaine 34396 Montpellier France
| | - Mireille Ansaldi
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Eric Pilet
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Olivier Ouari
- Aix Marseille Univ CNRS, ICR Institut de Chimie Radicalaire 13397 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Emilien Etienne
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Axel Magalon
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
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21
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Rao Y, Palumbo CT, Venkatesh A, Keener M, Stevanato G, Chauvin AS, Menzildjian G, Kuzin S, Yulikov M, Jeschke G, Lesage A, Mazzanti M, Emsley L. Design Principles for the Development of Gd(III) Polarizing Agents for Magic Angle Spinning Dynamic Nuclear Polarization. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2022; 126:11310-11317. [PMID: 35865791 PMCID: PMC9289950 DOI: 10.1021/acs.jpcc.2c01721] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nuclear magnetic resonance suffers from an intrinsically low sensitivity, which can be overcome by dynamic nuclear polarization (DNP). Gd(III) complexes are attractive exogenous polarizing agents for magic angle spinning (MAS) DNP due to their high chemical stability in contrast to nitroxide-based radicals. However, even the state-of-the-art Gd(III) complexes have so far provided relatively low DNP signal enhancements of ca. 36 in comparison to standard DNP biradicals, which show enhancements of over 200. Here, we report a series of new Gd(III) complexes for DNP and show that the observed DNP enhancements of the new and existing Gd(III) complexes are inversely proportional to the square of the zero-field splitting (ZFS) parameter D, which is in turn determined by the ligand-type and the local coordination environment. The experimental DNP enhancements at 9.4 T and the ZFS parameters measured with pulsed electron paramagnetic resonance (EPR) spectroscopy agree with the above model, paving the way for the development of more efficient Gd(III) polarizing agents.
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Affiliation(s)
- Yu Rao
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Chad T. Palumbo
- Group
of Coordination Chemistry, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL, CH-1015 Lausanne, Switzerland
| | - Amrit Venkatesh
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Megan Keener
- Group
of Coordination Chemistry, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL, CH-1015 Lausanne, Switzerland
| | - Gabriele Stevanato
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Anne-Sophie Chauvin
- Group
of Coordination Chemistry, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL, CH-1015 Lausanne, Switzerland
| | - Georges Menzildjian
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sergei Kuzin
- Laboratory
of Physical Chemistry, Department of Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Maxim Yulikov
- Laboratory
of Physical Chemistry, Department of Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Gunnar Jeschke
- Laboratory
of Physical Chemistry, Department of Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Anne Lesage
- Centre
de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
| | - Marinella Mazzanti
- Group
of Coordination Chemistry, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL, CH-1015 Lausanne, Switzerland
| | - Lyndon Emsley
- Laboratory
of Magnetic Resonance, Institut des Sciences et Ingénierie
Chimiques, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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22
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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: 25] [Impact Index Per Article: 12.5] [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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23
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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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24
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Shekar SC, Zhao W, Fernando LD, Hung I, Wang T. A 13C three-dimensional DQ-SQ-SQ correlation experiment for high-resolution analysis of complex carbohydrates using solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 336:107148. [PMID: 35121490 DOI: 10.1016/j.jmr.2022.107148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Complex carbohydrates are the key components of the protective cell walls of microbial pathogens and the bioenergy reservoir in plants and algae. Structural characterization of these polymorphic molecules requires assistance from multidimensional 13C correlation approaches. To facilitate the analysis of carbohydrate structure using solid-state NMR, we present a three-dimensional (3D) 13C-13C-13C experiment that includes a double-quantum (DQ) dimension and is thus free of the cube's body diagonal. The enhanced resolution supports the unambiguous resonance assignment of many polysaccharides in plant and fungal cell walls using uniformly 13C-labeled cells of spruce and Aspergillus fumigatus. Long-range structural restraints were effectively obtained to revisit our understanding of the spatial organization of plant cellulose microfibrils. The method is widely applicable to the investigations of cellular carbohydrates and carbon-based biomaterials.
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Affiliation(s)
- S Chandra Shekar
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Wancheng Zhao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Liyanage D Fernando
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Ivan Hung
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA.
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25
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Ghosh R, Dumarieh R, Xiao Y, Frederick KK. Stability of the nitroxide biradical AMUPol in intact and lysed mammalian cells. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 336:107150. [PMID: 35151975 PMCID: PMC8961433 DOI: 10.1016/j.jmr.2022.107150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Dynamic Nuclear Polarization (DNP) enhanced solid state NMR increases experimental sensitivity, potentially enabling detection of biomolecules at their physiological concentrations. The sensitivity of DNP experiments is due to the transfer of polarization from electron spins of free radicals to the nuclear spins of interest. Here, we investigate the reduction of AMUPol in both lysed and intact HEK293 cells. We find that nitroxide radicals are reduced with first order reduction kinetics by cell lysates at a rate of ∼ 12% of the added nitroxide radical concentration per hour. We also found that electroporation delivered a consistent amount of AMUPol to intact cells and that nitroxide radicals are reduced just slightly more rapidly (∼15% per hour) by intact cells than by cell lysates. The two nitroxide radicals of AMUPol are reduced independently and this leads to considerable accumulation of the DNP-silent monoradical form of AMUPol, particularly in preparations of intact cells where nearly half of the AMUPol is already reduced to the DNP silent monoradical form at the earliest experimental time points. This confirms that the loss of the DNP-active biradical form of AMUPol is faster than the nitroxide reduction rate. Finally, we investigate the effect of adding N-ethyl maleimide, a well-known inhibitor of thiol (-SH) group-based reduction of nitroxide biradicals in cells, on AMUPol reduction, cellular viability, and DNP performance. Although pre-treatment of cells with NEM effectively inhibited the reduction of AMUPol, exposure to NEM compromised cellular viability and, surprisingly, did not improve DNP performance. Collectively, these results indicate that, currently, the most effective strategy to obtain high DNP enhancements for DNP-assisted in-cell NMR is to minimize room temperature contact times with cellular constituents and suggest that the development of bio-resistant polarization agents for DNP could considerably increase the sensitivity of DNP-assisted in-cell NMR experiments.
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Affiliation(s)
- Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States
| | - Rania Dumarieh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States
| | - Kendra K Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, 75390-8816, United States; Center for Neurodegenerative and Alzheimer's Disease, UT Southwestern Medical Center, Dallas 75390, United States.
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26
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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: 42] [Impact Index Per Article: 21.0] [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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27
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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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28
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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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29
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Ghassemi N, Poulhazan A, Deligey F, Mentink-Vigier F, Marcotte I, Wang T. Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants. Chem Rev 2021; 122:10036-10086. [PMID: 34878762 DOI: 10.1021/acs.chemrev.1c00669] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.
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Affiliation(s)
- Nader Ghassemi
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Alexandre Poulhazan
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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