1
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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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2
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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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3
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Zhang Y, Gan Y, Zhao W, Zhang X, Zhao Y, Xie H, Yang J. Membrane Protein Structures in Native Cellular Membranes Revealed by Solid-State NMR Spectroscopy. JACS AU 2023; 3:3412-3423. [PMID: 38155644 PMCID: PMC10751765 DOI: 10.1021/jacsau.3c00564] [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: 09/24/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 12/30/2023]
Abstract
The structural characterization of membrane proteins within the cellular membrane environment is critical for understanding the molecular mechanism in their native functional context. However, conducting residue site-specific structural analysis of membrane proteins in native membranes by solid-state NMR faces challenges due to poor spectral sensitivity and serious interference from background protein signals. In this study, we present a new protocol that combines various strategies for cellular membrane sample preparations, enabling us to reveal the secondary structure of the mechanosensitive channel of large conductance from Methanosarcina acetivorans (MaMscL) in Escherichia coli inner membranes. Our findings demonstrate the feasibility of achieving complete resonance assignments and the potential for determining the 3D structures of membrane proteins within cellular membranes. We find that the use of the BL21(DE3) strain in this protocol is crucial for effectively suppressing background protein labeling without compromising the sensitivity of the target protein. Furthermore, our data reveal that the structures of different proteins exhibit varying degrees of sensitivity to the membrane environment. These results underscore the significance of studying membrane proteins within their native cellular membranes when performing structural characterizations. Overall, this study opens up a new avenue for achieving the atomic-resolution structural characterization of membrane proteins within their native cellular membranes, providing valuable insights into the nativeness of membrane proteins.
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Affiliation(s)
- Yan Zhang
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Wuhan National Laboratory for Optoelectronics, Innovation Academy for Precision Measurement Science
and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yuefang Gan
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Wuhan National Laboratory for Optoelectronics, Innovation Academy for Precision Measurement Science
and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Weijing Zhao
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Wuhan National Laboratory for Optoelectronics, Innovation Academy for Precision Measurement Science
and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Xuning Zhang
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Wuhan National Laboratory for Optoelectronics, Innovation Academy for Precision Measurement Science
and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yongxiang Zhao
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Wuhan National Laboratory for Optoelectronics, Innovation Academy for Precision Measurement Science
and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Huayong Xie
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Wuhan National Laboratory for Optoelectronics, Innovation Academy for Precision Measurement Science
and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Jun Yang
- National
Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics
and Mathematics, Wuhan National Laboratory for Optoelectronics, Innovation Academy for Precision Measurement Science
and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Interdisciplinary
Institute of NMR and Molecular Sciences, School of Chemistry and Chemical
Engineering, The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
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4
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Xie H, Zhao Y, Zhao W, Chen Y, Liu M, Yang J. Solid-state NMR structure determination of a membrane protein in E. coli cellular inner membrane. SCIENCE ADVANCES 2023; 9:eadh4168. [PMID: 37910616 PMCID: PMC10619923 DOI: 10.1126/sciadv.adh4168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023]
Abstract
Structure determination of membrane proteins in native cellular membranes is critical to precisely reveal their structures in physiological conditions. However, it remains challenging for solid-state nuclear magnetic resonance (ssNMR) due to the low sensitivity and high complexity of ssNMR spectra of cellular membranes. Here, we present the structure determination of aquaporin Z (AqpZ) by ssNMR in Escherichia coli inner membranes. To enhance the signal sensitivity of AqpZ, we optimized protein overexpression and removed outer membrane components. To suppress the interference of background proteins, we used a "dual-media" expression approach and antibiotic treatment. Using 1017 distance restraints obtained from two-dimensional 13C-13C spectra based on the complete chemical shift assignments, the 1.7-Å ssNMR structure of AqpZ is determined in E. coli inner membranes. This cellular ssNMR structure determination paves the way for analyzing the atomic structural details for membrane proteins in native cellular membranes.
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Affiliation(s)
- Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yongxiang Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Weijing Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Yanke Chen
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Maili Liu
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P.R. China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P.R. China
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5
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Dai D, Denysenkov V, Bagryanskaya EG, Tormyshev VM, Prisner TF, Kuzhelev AA. 13C Hyperpolarization of Viscous Liquids by Transfer of Solid-Effect 1H Dynamic Nuclear Polarization at High Magnetic Field. J Phys Chem Lett 2023; 14:7059-7064. [PMID: 37526333 DOI: 10.1021/acs.jpclett.3c01732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Dynamic nuclear polarization (DNP) is routinely used as a method for increasing the sensitivity to nuclear magnetic resonance (NMR). Recently, high-field solid-effect DNP in viscous liquids on 1H nuclei was demonstrated using narrow-line polarizing agents. Here we expand the applicability of DNP in viscous media to 13C nuclei. To hyperpolarize 13C nuclei, we combined solid-effect 1H DNP with a subsequent transfer of the 1H polarization to 13C via insensitive nuclei enhanced by polarization transfer (INEPT). We demonstrate this approach using a triarylmethyl radical as a polarizing agent and glycerol-13C3 as an analyte. We achieved 13C enhancement factors of up to 45 at a magnetic field of 9.4 T and room temperature.
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Affiliation(s)
- Danhua Dai
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Max von Laue Str. 7, Frankfurt am Main 60438, Germany
| | - Vasyl Denysenkov
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Max von Laue Str. 7, Frankfurt am Main 60438, Germany
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences (SB RAS), Acad. Lavrentiev Avenue 9, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences (SB RAS), Acad. Lavrentiev Avenue 9, Novosibirsk 630090, Russia
| | - Thomas F Prisner
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Max von Laue Str. 7, Frankfurt am Main 60438, Germany
| | - Andrei A Kuzhelev
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Max von Laue Str. 7, Frankfurt am Main 60438, Germany
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6
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Bahri S, Safeer A, Adler A, Smedes H, van Ingen H, Baldus M. 1H-detected characterization of carbon-carbon networks in highly flexible protonated biomolecules using MAS NMR. JOURNAL OF BIOMOLECULAR NMR 2023:10.1007/s10858-023-00415-6. [PMID: 37289305 DOI: 10.1007/s10858-023-00415-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/28/2023] [Indexed: 06/09/2023]
Abstract
In the last three decades, the scope of solid-state NMR has expanded to exploring complex biomolecules, from large protein assemblies to intact cells at atomic-level resolution. This diversity in macromolecules frequently features highly flexible components whose insoluble environment precludes the use of solution NMR to study their structure and interactions. While High-resolution Magic-Angle Spinning (HR-MAS) probes offer the capacity for gradient-based 1H-detected spectroscopy in solids, such probes are not commonly used for routine MAS NMR experiments. As a result, most exploration of the flexible regime entails either 13C-detected experiments, the use of partially perdeuterated systems, or ultra-fast MAS. Here we explore proton-detected pulse schemes probing through-bond 13C-13C networks to study mobile protein sidechains as well as polysaccharides in a broadband manner. We demonstrate the use of such schemes to study a mixture of microtubule-associated protein (MAP) tau and human microtubules (MTs), and the cell wall of the fungus Schizophyllum commune using 2D and 3D spectroscopy, to show its viability for obtaining unambiguous correlations using standard fast-spinning MAS probes at high and ultra-high magnetic fields.
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Affiliation(s)
- Salima Bahri
- 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
| | - Agnes Adler
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hanneke Smedes
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hugo van Ingen
- 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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7
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Safeer A, Kleijburg F, Bahri S, Beriashvili D, Veldhuizen EJA, van Neer J, Tegelaar M, de Cock H, Wösten HAB, Baldus M. Probing Cell-Surface Interactions in Fungal Cell Walls by High-Resolution 1 H-Detected Solid-State NMR Spectroscopy. Chemistry 2023; 29:e202202616. [PMID: 36181715 PMCID: PMC10099940 DOI: 10.1002/chem.202202616] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/05/2022]
Abstract
Solid-state NMR (ssNMR) spectroscopy facilitates the non-destructive characterization of structurally heterogeneous biomolecules in their native setting, for example, comprising proteins, lipids and polysaccharides. Here we demonstrate the utility of high and ultra-high field 1 H-detected fast MAS ssNMR spectroscopy, which exhibits increased sensitivity and spectral resolution, to further elucidate the atomic-level composition and structural arrangement of the cell wall of Schizophyllum commune, a mushroom-forming fungus from the Basidiomycota phylum. These advancements allowed us to reveal that Cu(II) ions and the antifungal peptide Cathelicidin-2 mainly bind to cell wall proteins at low concentrations while glucans are targeted at high metal ion concentrations. In addition, our data suggest the presence of polysaccharides containing N-acetyl galactosamine (GalNAc) and proteins, including the hydrophobin proteins SC3, shedding more light on the molecular make-up of cells wall as well as the positioning of the polypeptide layer. Obtaining such information may be of critical relevance for future research into fungi in material science and biomedical contexts.
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Affiliation(s)
- Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Fleur Kleijburg
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Salima Bahri
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Edwin J A Veldhuizen
- Division of Infectious Diseases and Immunology, Department of Biomolecular Health Sciences, Utrecht University, Yalelaan 1, 3584 CL, Utrecht (The, Netherlands
| | - Jacq van Neer
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Martin Tegelaar
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Hans de Cock
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Han A B Wösten
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht (The, Netherlands
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8
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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: 8] [Impact Index Per Article: 4.0] [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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9
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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: 17] [Impact Index Per Article: 8.5] [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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10
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In-cell NMR: From target structure and dynamics to drug screening. Curr Opin Struct Biol 2022; 74:102374. [DOI: 10.1016/j.sbi.2022.102374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 11/18/2022]
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11
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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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12
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Tan H, Zhao Y, Zhao W, Xie H, Chen Y, Tong Q, Yang J. Dynamics properties of membrane proteins in native cell membranes revealed by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2022; 1864:183791. [PMID: 34624277 DOI: 10.1016/j.bbamem.2021.183791] [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: 07/15/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/17/2022]
Abstract
Cell membranes provide an environment that is essential to the functions of membrane proteins. Cell membranes are mainly composed of proteins and highly diverse phospholipids. The influence of diverse lipid compositions of native cell membranes on the dynamics of the embedded membrane proteins has not been examined. Here we employ solid-state NMR to investigate the dynamics of E. coli Aquaporin Z (AqpZ) in its native inner cell membranes, and reveal the influence of diverse lipid compositions on the dynamics of AqpZ by comparing it in native cell membranes to that in POPC/POPG bilayers. We demonstrate that the dynamic rigidity of AqpZ generally conserves in both native cell membranes and POPC/POPG bilayers, due to its tightly packed tetrameric structure. In the gel and the liquid crystal phases of lipids, our experimental results show that AqpZ is more dynamic in native cell membranes than that in POPC/POPG bilayers. In addition, we observe that phase transitions of lipids in native membranes are less sensitive to temperature variations compared with that in POPC/POPG bilayers, which results in that the dynamics of AqpZ is less affected by the phase transitions of lipids in native cell membranes than that in POPC/POPG bilayers. This study provides new insights into the dynamics of membrane proteins in native cell membranes.
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Affiliation(s)
- Huan Tan
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yongxiang Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Weijing Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Yanke Chen
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Qiong Tong
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, PR China.
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, PR China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, PR China.
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13
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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: 40] [Impact Index Per Article: 20.0] [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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14
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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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15
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Höfurthner T, Mateos B, Konrat R. On-Cell NMR Contributions to Membrane Receptor Binding Characterization. Chempluschem 2021; 86:938-945. [PMID: 34160899 DOI: 10.1002/cplu.202100134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/28/2021] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy has matured into a powerful tool to characterize interactions between biological molecules at atomic resolution, most importantly even under near to native (physiological) conditions. The field of in-cell NMR aims to study proteins and nucleic acids inside living cells. However, cells interrogate their environment and are continuously modulated by external stimuli. Cell signaling processes are often initialized by membrane receptors on the cell surface; therefore, characterizing their interactions at atomic resolution by NMR, hereafter referred as on-cell NMR, can provide valuable mechanistic information. This review aims to summarize recent on-cell NMR tools that give information about the binding site and the affinity of membrane receptors to their ligands together with potential applications to in vivo drug screening systems.
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Affiliation(s)
- Theresa Höfurthner
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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16
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Phạm TTT, Rainey JK. On-cell nuclear magnetic resonance spectroscopy to probe cell surface interactions. Biochem Cell Biol 2021; 99:683-692. [PMID: 33945753 DOI: 10.1139/bcb-2021-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy allows determination of atomic-level information about intermolecular interactions, molecular structure, and molecular dynamics in the cellular environment. This may be broadly divided into studies focused on obtaining detailed molecular information in the intracellular context ("in-cell") or those focused on characterizing molecules or events at the cell surface ("on-cell"). In this review, we outline some key NMR techniques applied for on-cell NMR studies through both solution-state and solid-state NMR and survey studies that have used these techniques to uncover key information. We particularly focus on application of on-cell NMR spectroscopy to characterize ligand interactions with cell surface membrane proteins such as G-protein coupled receptors (GPCRs), receptor tyrosine kinases, etc. These techniques allow for quantification of binding affinities, competitive binding assays, delineation of portions of ligands involved in binding, ligand bound-state conformational determination, evaluation of receptor structuring and dynamics, and inference of distance constraints characteristic of the ligand-receptor bound state. Excitingly, it is possible to avoid the barriers of production and purification of membrane proteins while obtaining directly physiologically-relevant information through on-cell NMR. We also provide a briefer survey of the applicability of on-cell NMR approaches to other classes of cell surface molecule.
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Affiliation(s)
- Trần Thanh Tâm Phạm
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Nova Scotia, Canada;
| | - Jan K Rainey
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Canada;
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17
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Narasimhan S, Pinto C, Lucini Paioni A, van der Zwan J, Folkers GE, Baldus M. Characterizing proteins in a native bacterial environment using solid-state NMR spectroscopy. Nat Protoc 2021; 16:893-918. [PMID: 33442051 DOI: 10.1038/s41596-020-00439-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/09/2020] [Indexed: 01/29/2023]
Abstract
For a long time, solid-state nuclear magnetic resonance (ssNMR) has been employed to study complex biomolecular systems at the detailed chemical, structural, or dynamic level. Recent progress in high-resolution and high-sensitivity ssNMR, in combination with innovative sample preparation and labeling schemes, offers novel opportunities to study proteins in their native setting irrespective of the molecular tumbling rate. This protocol describes biochemical preparation schemes to obtain cellular samples of both soluble as well as insoluble or membrane-associated proteins in bacteria. To this end, the protocol is suitable for studying a protein of interest in both whole cells and in cell envelope or isolated membrane preparations. In the first stage of the procedure, an appropriate strain of Escherichia coli (DE3) is transformed with a plasmid of interest harboring the protein of interest under the control of an inducible T7 promoter. Next, the cells are adapted to grow in minimal (M9) medium. Before the growth enters stationary phase, protein expression is induced, and shortly thereafter, the native E. coli RNA polymerase is inhibited using rifampicin for targeted labeling of the protein of interest. The cells are harvested after expression and prepared for ssNMR rotor filling. In addition to conventional 13C/15N-detected ssNMR, we also outline how these preparations can be readily subjected to multidimensional ssNMR experiments using dynamic nuclear polarization (DNP) or proton (1H) detection schemes. We estimate that the entire preparative procedure until NMR experiments can be started takes 3-5 days.
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Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Cecilia Pinto
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
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18
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Conformational Dynamics of Light-Harvesting Complex II in a Native Membrane Environment. Biophys J 2020; 120:270-283. [PMID: 33285116 DOI: 10.1016/j.bpj.2020.11.2265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/17/2020] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Photosynthetic light-harvesting complexes (LHCs) of higher plants, moss, and green algae can undergo dynamic conformational transitions, which have been correlated to their ability to adapt to fluctuations in the light environment. Herein, we demonstrate the application of solid-state NMR spectroscopy on native, heterogeneous thylakoid membranes of Chlamydomonas reinhardtii (Cr) and on Cr light-harvesting complex II (LHCII) in thylakoid lipid bilayers to detect LHCII conformational dynamics in its native membrane environment. We show that membrane-reconstituted LHCII contains selective sites that undergo fast, large-amplitude motions, including the phytol tails of two chlorophylls. Protein plasticity is also observed in the N-terminal stromal loop and in protein fragments facing the lumen, involving sites that stabilize the xanthophyll-cycle carotenoid violaxanthin and the two luteins. The results report on the intrinsic flexibility of LHCII pigment-protein complexes in a membrane environment, revealing putative sites for conformational switching. In thylakoid membranes, fast dynamics of protein and pigment sites is significantly reduced, which suggests that in their native organelle membranes, LHCII complexes are locked in specific conformational states.
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19
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Damman R, Lucini Paioni A, Xenaki KT, Beltrán Hernández I, van Bergen En Henegouwen PMP, Baldus M. Development of in vitro-grown spheroids as a 3D tumor model system for solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2020; 74:401-412. [PMID: 32562030 PMCID: PMC7508937 DOI: 10.1007/s10858-020-00328-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/09/2020] [Indexed: 05/11/2023]
Abstract
Recent advances in the field of in-cell NMR spectroscopy have made it possible to study proteins in the context of bacterial or mammalian cell extracts or even entire cells. As most mammalian cells are part of a multi-cellular complex, there is a need to develop novel NMR approaches enabling the study of proteins within the complexity of a 3D cellular environment. Here we investigate the use of the hanging drop method to grow spheroids which are homogenous in size and shape as a model system to study solid tumors using solid-state NMR (ssNMR) spectroscopy. We find that these spheroids are stable under magic-angle-spinning conditions and show a clear change in metabolic profile as compared to single cell preparations. Finally, we utilize dynamic nuclear polarization (DNP)-supported ssNMR measurements to show that low concentrations of labelled nanobodies targeting EGFR (7D12) can be detected inside the spheroids. These findings suggest that solid-state NMR can be used to directly examine proteins or other biomolecules in a 3D cellular microenvironment with potential applications in pharmacological research.
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Affiliation(s)
- Reinier Damman
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Katerina T Xenaki
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Irati Beltrán Hernández
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
- Pharmaceutics, Department of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Paul M P van Bergen En Henegouwen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands.
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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20
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Solid-state NMR spectroscopy for characterization of RNA and RNP complexes. Biochem Soc Trans 2020; 48:1077-1087. [PMID: 32573690 DOI: 10.1042/bst20191080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022]
Abstract
Ribonucleic acids are driving a multitude of biological processes where they act alone or in complex with proteins (ribonucleoproteins, RNP). To understand these processes both structural and mechanistic information about RNA is necessary. Due to their conformational plasticity RNA pose a challenge for mainstream structural biology methods. Solid-state NMR (ssNMR) spectroscopy is an emerging technique that can be applied to biomolecular complexes of any size in close-to-native conditions. This review outlines recent methodological developments in ssNMR for structural characterization of RNA and protein-RNA complexes and provides relevant examples.
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21
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Gadolinium Complexes as Contrast Agent for Cellular NMR Spectroscopy. Int J Mol Sci 2020; 21:ijms21114042. [PMID: 32516957 PMCID: PMC7312942 DOI: 10.3390/ijms21114042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Aqua Gd3+ and Gd-DOTA (gadolinium-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacete) complexes were studied as a contrast agent in cellular NMR (nuclear magnetic resonance) spectroscopy for distinguishing between intracellular and extracellular spaces. The contrast agents for this purpose should provide strong paramagnetic relaxation enhancement and localize in the extracellular space without disturbing biological functions. Cell membrane permeability to Gd complexes was evaluated from the concentrations of gadolinium complexes in the inside and outside of E. coli cells measured by the 1H-NMR relaxation. The site-specific binding of the complexes to E. coli cells was also analyzed by high-resolution solid-state 13C-NMR. The aqua Gd3+ complex did not enhance T1 relaxation in proportion to the amount of added Gd3+. This Gd3+ concentration dependence and the 13C-NMR indicated that its strong cytotoxicity should be due to the binding of the paramagnetic ions to cellular components especially at the lipid membranes. In contrast, Gd-DOTA stayed in the solution states and enhanced relaxation in proportion to the added amount. This agent exhibited strong T1 contrast between the intra- and extracellular spaces by a factor of ten at high concentrations under which the cells were viable over a long experimental time of days. These properties make Gd-DOTA suitable for selectively contrasting the living cellular space in NMR spectroscopy primarily owing to its weak interaction with cellular components.
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22
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Lim BJ, Ackermann BE, Debelouchina GT. Targetable Tetrazine-Based Dynamic Nuclear Polarization Agents for Biological Systems. Chembiochem 2020; 21:1315-1319. [PMID: 31746101 PMCID: PMC7445144 DOI: 10.1002/cbic.201900609] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Indexed: 12/13/2022]
Abstract
Dynamic nuclear polarization (DNP) has shown great promise as a tool to enhance the nuclear magnetic resonance signals of proteins in the cellular environment. As sensitivity increases, the ability to select and efficiently polarize a specific macromolecule over the cellular background has become desirable. Herein, we address this need and present a tetrazine-based DNP agent that can be targeted selectively to proteins containing the unnatural amino acid (UAA) norbornene-lysine. This UAA can be introduced efficiently into the cellular milieu by genetic means. Our approach is bio-orthogonal and easily adaptable to any protein of interest. We illustrate the scope of our methodology and investigate the DNP transfer mechanisms in several biological systems. Our results shed light on the complex polarization-transfer pathways in targeted DNP and ultimately pave the way to selective DNP-enhanced NMR spectroscopy in both bacterial and mammalian cells.
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Affiliation(s)
- Byung Joon Lim
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bryce E. Ackermann
- 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
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23
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Narasimhan S, Folkers GE, Baldus M. When Small becomes Too Big: Expanding the Use of In‐Cell Solid‐State NMR Spectroscopy. Chempluschem 2020; 85:760-768. [DOI: 10.1002/cplu.202000167] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/31/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
| | - Marc Baldus
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
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24
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Park H, Uluca-Yazgi B, Heumann S, Schlögl R, Granwehr J, Heise H, Schleker PPM. Heteronuclear cross-relaxation effect modulated by the dynamics of N-functional groups in the solid state under 15N DP-MAS DNP. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 312:106688. [PMID: 32004819 DOI: 10.1016/j.jmr.2020.106688] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
In a typical magic-angle spinning (MAS) dynamic nuclear polarization (DNP) nuclear magnetic resonance (NMR) experiment, several mechanisms are simultaneously involved when transferring much larger polarization of electron spins to NMR active nuclei of interest. Recently, specific cross-relaxation enhancement by active motions under DNP (SCREAM-DNP) [Daube et al. JACS 2016] has been reported as one of these mechanisms. Thereby 13C enhancement with inverted sign was observed in a direct polarization (DP) MAS DNP experiment, caused by reorientation dynamics of methyl that was not frozen out at 100 K. Here, we report on the spontaneous polarization transfer from hyperpolarized 1H to both primary amine and ammonium nitrogens, resulting in an additional positive signal enhancement in the 15N NMR spectra during 15N DP-MAS DNP. The cross-relaxation induced signal enhancement (CRE) for 15N is of opposite sign compared to that observed for 13C due to the negative sign of the gyromagnetic ratio of 15N. The influence on CRE efficiency caused by variation of the radical solution composition and by temperature was also investigated.
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Affiliation(s)
- Heeyong Park
- Max Planck Institute for Chemical Energy Conversion, Department of Heterogeneous Reactions, 45470 Mülheim an der Ruhr, Germany; Forschungszentrum Jülich, IEK-9, 52425 Jülich, Germany; RWTH Aachen University, Institute of Technical and Macromolecular Chemistry, 52074 Aachen, Germany
| | - Boran Uluca-Yazgi
- Forschungszentrum Jülich, IBI-7 and JuStruct, 52425 Jülich, Germany; Heinrich Heine Universität Düsseldorf, Institute of Physical Biology, 40225 Düsseldorf, Germany
| | - Saskia Heumann
- Max Planck Institute for Chemical Energy Conversion, Department of Heterogeneous Reactions, 45470 Mülheim an der Ruhr, Germany
| | - Robert Schlögl
- Max Planck Institute for Chemical Energy Conversion, Department of Heterogeneous Reactions, 45470 Mülheim an der Ruhr, Germany; Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Josef Granwehr
- Forschungszentrum Jülich, IEK-9, 52425 Jülich, Germany; RWTH Aachen University, Institute of Technical and Macromolecular Chemistry, 52074 Aachen, Germany
| | - Henrike Heise
- Forschungszentrum Jülich, IBI-7 and JuStruct, 52425 Jülich, Germany; Heinrich Heine Universität Düsseldorf, Institute of Physical Biology, 40225 Düsseldorf, Germany
| | - P Philipp M Schleker
- Max Planck Institute for Chemical Energy Conversion, Department of Heterogeneous Reactions, 45470 Mülheim an der Ruhr, Germany; Forschungszentrum Jülich, IEK-9, 52425 Jülich, Germany.
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Chen PH, Gao C, Barnes AB. Perspectives on microwave coupling into cylindrical and spherical rotors with dielectric lenses for magic angle spinning dynamic nuclear polarization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106518. [PMID: 31345770 DOI: 10.1016/j.jmr.2019.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 06/10/2023]
Abstract
Continuous wave dynamic nuclear polarization (DNP) increases the sensitivity of NMR, yet intense microwave fields are required to transition magic angle spinning (MAS) DNP to the time domain. Here we describe and analyze Teflon lenses for cylindrical and spherical MAS rotors that focus microwave power and increase the electron Rabi frequency, ν1s. Using a commercial simulation package, we solve the Maxwell equations and determine the propagation and focusing of millimeter waves (198 GHz). We then calculate the microwave intensity in a time-independent fashion to compute the ν1s. With a nominal microwave power input of 5 W, the average ν1s is 0.38 MHz within a 22 μL sample volume in a 3.2 mm outer diameter (OD) cylindrical rotor without a Teflon lens. Decreasing the sample volume to 3 μL and focusing the microwave beam with a Teflon lens increases the ν1s to 1.5 MHz. Microwave polarization and intensity perturbations associated with diffraction through the radiofrequency coil, losses from penetration through the rotor wall, and mechanical limitations of the separation between the lens and sample are significant challenges to improving microwave coupling in MAS DNP instrumentation. To overcome these issues, we introduce a novel focusing strategy using dielectric microwave lenses installed within spinning rotors. One such 9.5 mm OD cylindrical rotor assembly implements a Teflon focusing lens to increase the ν1s to 2.7 MHz within a 2 μL sample. Further, to access high spinning frequencies while also increasing ν1s, we analyze microwave coupling into MAS spheres. For 9.5 mm OD spherical rotors, we compute a ν1s of 0.36 MHz within a sample volume of 161 μL, and 2.5 MHz within a 3 μL sample placed at the focal point of a novel double lens insert. We conclude with an analysis and discussion of sub-millimeter diamond spherical rotors for time domain DNP at spinning frequencies >100 kHz. Sub-millimeter spherical rotors better overlap a tightly focused microwave beam, resulting in a ν1s of 2.2 MHz. Lastly, we propose that sub-millimeter dielectric spherical microwave resonators will provide a means to substantially improve electron spin control in the future.
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Affiliation(s)
- Pin-Hui Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Chukun Gao
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexander B Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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26
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Schlagnitweit J, Friebe Sandoz S, Jaworski A, Guzzetti I, Aussenac F, Carbajo RJ, Chiarparin E, Pell AJ, Petzold K. Observing an Antisense Drug Complex in Intact Human Cells by in-Cell NMR Spectroscopy. Chembiochem 2019; 20:2474-2478. [PMID: 31206961 DOI: 10.1002/cbic.201900297] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Gaining insight into the uptake, trafficking and target engagement of drugs in cells can enhance understanding of a drug's function and efficiency. However, there are currently no reliable methods for studying untagged biomolecules in macromolecular complexes in intact human cells. Here we have studied an antisense oligonucleotide (ASO) drug in HEK 293T and HeLa cells by NMR spectroscopy. Using a combination of transfection, cryoprotection and dynamic nuclear polarization (DNP), we were able to detect the drug directly in intact frozen cells. Activity of the drug was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). By applying DNP NMR to frozen cells, we overcame limitations both of solution-state in-cell NMR spectroscopy (e.g., size, stability and sensitivity) and of visualization techniques, in which (e.g., fluorescent) tagging of the ASO decreases its activity. The capability to detect an untagged, active drug, interacting in its natural environment, represents a first step towards studying molecular mechanisms in intact cells.
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Affiliation(s)
- Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 17165, Solna, Sweden
| | - Sarah Friebe Sandoz
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 17165, Solna, Sweden
| | - Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, 106 91, Stockholm, Sweden
| | - Ileana Guzzetti
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 17165, Solna, Sweden
| | - Fabien Aussenac
- Bruker BioSpin, 34 Rue de l'Industrie, 67160, Wissembourg, France
| | - Rodrigo J Carbajo
- Analytical and Structural Chemistry Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Elisabetta Chiarparin
- Analytical and Structural Chemistry Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Andrew J Pell
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, 106 91, Stockholm, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solnavägen 9, 17165, Solna, Sweden
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27
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Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. DNP-Supported Solid-State NMR Spectroscopy of Proteins Inside Mammalian Cells. Angew Chem Int Ed Engl 2019; 58:12969-12973. [PMID: 31233270 PMCID: PMC6772113 DOI: 10.1002/anie.201903246] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Indexed: 11/25/2022]
Abstract
Elucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier in structural biology. We have developed a tailored solid‐state NMR spectroscopic approach that allows studying protein structure inside human cells at atomic level under high‐sensitivity dynamic nuclear polarization (DNP) conditions. We demonstrate the method using ubiquitin (Ub), which is critically involved in cellular functioning. Our results pave the way for structural studies of larger proteins or protein complexes inside human cells, which have remained elusive to in‐cell solution‐state NMR spectroscopy due to molecular size limitations.
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Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
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28
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Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903246] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
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29
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Tripathi A, Rane V. Toward Achieving the Theoretical Limit of Electron Spin Polarization in Covalently Linked Radical-Chromophore Dyads. J Phys Chem B 2019; 123:6830-6841. [DOI: 10.1021/acs.jpcb.9b04726] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alok Tripathi
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - Vinayak Rane
- Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
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30
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Gao C, Judge PT, Sesti EL, Price LE, Alaniva N, Saliba EP, Albert BJ, Soper NJ, Chen PH, Barnes AB. Four millimeter spherical rotors spinning at 28 kHz with double-saddle coils for cross polarization NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 303:1-6. [PMID: 30978570 DOI: 10.1016/j.jmr.2019.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/07/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Spherical rotors in magic angle spinning (MAS) experiments have significant advantages over traditional cylindrical rotors including simplified spinning implementation, easy sample exchange, more efficient microwave coupling for dynamic nuclear polarization (DNP), and feasibility of downscaling to access higher spinning frequencies. Here, we implement spherical rotors with 4 mm outside diameter (o.d.) and demonstrate spinning >28 kHz using a single aperture for spinning gas. We show a modified stator geometry to improve fiber optic detection, increase NMR filling factor, and improve alignment for sample exchange and microwave irradiation. Higher NMR Rabi frequencies were obtained using smaller radiofrequency (RF) coils on small-diameter spherical rotors, compared to our previous implementation of MAS spheres with an o.d. of 9.5 mm. We report nutation fields of 110 kHz on 13C with 820 W of input power and 100 kHz on 1H with 800 W of input power. Proton decoupling fields of 78 kHz were applied over 20 ms of signal acquisition without any sign of arcing. Compared to our initial demonstration of a split coil for 9.5 mm spheres, this current implementation of a double-saddle coil inductor for 4 mm spheres not only intensifies the RF fields, but also improves RF homogeneity. We achieve an 810°/90° nutation intensity ratio of 0.84 at 300.197 MHz (1H). We also show electromagnetic simulations predicting a nearly 3-fold improvement in electron Rabi frequency of 0.99 MHz (with 4 mm spheres) compared to 0.38 MHz (with 3.2 mm cylinders), with 5 W of incident microwave power. Further improvements in magnetic resonance spin control are expected as RF inductors and microwave coupling are optimized for spherical rotors and scaled down to the micron scale.
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Affiliation(s)
- Chukun Gao
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Patrick T Judge
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biochemistry, Biophysics & Structural Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Erika L Sesti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lauren E Price
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas Alaniva
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Edward P Saliba
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brice J Albert
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nathan J Soper
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Pin-Hui Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexander B Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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31
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König A, Schölzel D, Uluca B, Viennet T, Akbey Ü, Heise H. Hyperpolarized MAS NMR of unfolded and misfolded proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 98:1-11. [PMID: 30641444 DOI: 10.1016/j.ssnmr.2018.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/28/2018] [Accepted: 12/30/2018] [Indexed: 05/09/2023]
Abstract
In this article we give an overview over the use of DNP-enhanced solid-state NMR spectroscopy for the investigation of unfolded, disordered and misfolded proteins. We first provide an overview over studies in which DNP spectroscopy has successfully been applied for the structural investigation of well-folded amyloid fibrils formed by short peptides as well as full-length proteins. Sample cooling to cryogenic temperatures often leads to severe line broadening of resonance signals and thus a loss in resolution. However, inhomogeneous line broadening at low temperatures provides valuable information about residual dynamics and flexibility in proteins, and, in combination with appropriate selective isotope labeling techniques, inhomogeneous linewidths in disordered proteins or protein regions may be exploited for evaluation of conformational ensembles. In the last paragraph we highlight some recent studies where DNP-enhanced MAS-NMR-spectroscopy was applied to the study of disordered proteins/protein regions and inhomogeneous sample preparations.
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Affiliation(s)
- Anna König
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Daniel Schölzel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Boran Uluca
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Thibault Viennet
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ümit Akbey
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Henrike Heise
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Center Jülich, 52425, Jülich, Germany; Institute of Physical Biology, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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32
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Pinto C, Mance D, Julien M, Daniels M, Weingarth M, Baldus M. Studying assembly of the BAM complex in native membranes by cellular solid-state NMR spectroscopy. J Struct Biol 2019; 206:1-11. [DOI: 10.1016/j.jsb.2017.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 12/31/2022]
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33
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Scott FJ, Alaniva N, Golota NC, Sesti EL, Saliba EP, Price LE, Albert BJ, Chen P, O'Connor RD, Barnes AB. A versatile custom cryostat for dynamic nuclear polarization supports multiple cryogenic magic angle spinning transmission line probes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 297:23-32. [PMID: 30342370 DOI: 10.1016/j.jmr.2018.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/29/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
Dynamic nuclear polarization (DNP) with cryogenic magic angle spinning (MAS) provides significant improvements in NMR sensitivity, yet presents unique technical challenges. Here we describe a custom cryostat and suite of NMR probes capable of manipulating nuclear spins with multi-resonant radiofrequency circuits, cryogenic spinning below 6 K, sample exchange, and microwave coupling for DNP. The corrugated waveguide and six transfer lines needed for DNP and cryogenic spinning functionality are coupled to the probe from the top of the magnet. Transfer lines are vacuum-jacketed and provide bearing and drive gas, variable temperature fluid, two exhaust pathways, and a sample ejection port. The cryostat thermally isolates the magnet bore, thereby protecting the magnet and increasing cryogen efficiency. This novel design supports cryogenic MAS-DNP performance over an array of probes without altering DNP functionality. We present three MAS probes (two supporting 3.2 mm rotors and one supporting 9.5 mm rotors) interfacing with the single cryostat. Mechanical details, transmission line radio frequency design, and performance of the cryostat and three probes are described.
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Affiliation(s)
- Faith J Scott
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas Alaniva
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Natalie C Golota
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Erika L Sesti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Edward P Saliba
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lauren E Price
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brice J Albert
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Pinhui Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert D O'Connor
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Alexander B Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Leavesley A, Jain S, Kamniker I, Zhang H, Rajca S, Rajca A, Han S. Maximizing NMR signal per unit time by facilitating the e-e-n cross effect DNP rate. Phys Chem Chem Phys 2018; 20:27646-27657. [PMID: 30375593 DOI: 10.1039/c8cp04909b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamic nuclear polarization (DNP) efficiency is critically dependent on the properties of the radical, solvent, and solute constituting the sample system. In this study, we focused on the three spin e-e-n cross effect (CE)'s influence on the nuclear longitudinal relaxation time constant T1n, the build-up time constants of nuclear magnetic resonance (NMR) signal, TDNP and DNP-enhancement of NMR signal. The dipolar interaction strength between the electron spins driving the e-e-n process was systematically modulated using mono-, di-, tri-, and dendritic-nitroxide radicals, while maintaining a constant global electron spin concentration of 10 mM. Experimental results showed that an increase in electron spin clustering led to an increased electron spin depolarization, as mapped by electron double resonance (ELDOR), and a dramatically shortened T1n and TDNP time constants under static and magic angle spinning (MAS) conditions. A theoretical analysis reveals that strong e-e interactions, caused by electron spin clustering, increase the CE rate. The three spin e-e-n CE is a hitherto little recognized mechanism for shortening T1n and TDNP in solid-state NMR experiments at cryogenic temperatures, and offers a design principle to enhance the effective CE DNP enhancement per unit time. Fast CE rates will benefit DNP at liquid helium temperatures, or at higher magnetic fields and pulsed DNP, where slow e-e-n polarization transfer rate is a key bottleneck to achieving maximal DNP performance.
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Affiliation(s)
- Alisa Leavesley
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
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35
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Jaudzems K, Polenova T, Pintacuda G, Oschkinat H, Lesage A. DNP NMR of biomolecular assemblies. J Struct Biol 2018; 206:90-98. [PMID: 30273657 DOI: 10.1016/j.jsb.2018.09.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/13/2018] [Accepted: 09/27/2018] [Indexed: 11/30/2022]
Abstract
Dynamic Nuclear Polarization (DNP) is an effective approach to alleviate the inherently low sensitivity of solid-state NMR (ssNMR) under magic angle spinning (MAS) towards large-sized multi-domain complexes and assemblies. DNP relies on a polarization transfer at cryogenic temperatures from unpaired electrons to adjacent nuclei upon continuous microwave irradiation. This is usually made possible via the addition in the sample of a polarizing agent. The first pioneering experiments on biomolecular assemblies were reported in the early 2000s on bacteriophages and membrane proteins. Since then, DNP has experienced tremendous advances, with the development of extremely efficient polarizing agents or with the introduction of new microwaves sources, suitable for NMR experiments at very high magnetic fields (currently up to 900 MHz). After a brief introduction, several experimental aspects of DNP enhanced NMR spectroscopy applied to biomolecular assemblies are discussed. Recent demonstration experiments of the method on viral capsids, the type III and IV bacterial secretion systems, ribosome and membrane proteins are then described.
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Affiliation(s)
- Kristaps Jaudzems
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 163 The Green, DE 19716, USA
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Hartmut Oschkinat
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP), Campus Berlin-Buch Robert-Roessle-Str. 10 13125 Berlin, Germany
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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36
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Saliba E, Sesti EL, Alaniva N, Barnes AB. Pulsed Electron Decoupling and Strategies for Time Domain Dynamic Nuclear Polarization with Magic Angle Spinning. J Phys Chem Lett 2018; 9:5539-5547. [PMID: 30180584 PMCID: PMC6151657 DOI: 10.1021/acs.jpclett.8b01695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/04/2018] [Indexed: 05/05/2023]
Abstract
Magic angle spinning (MAS) dynamic nuclear polarization (DNP) is widely used to increase nuclear magnetic resonance (NMR) signal intensity. Frequency-chirped microwaves yield superior control of electron spins and are expected to play a central role in the development of DNP MAS experiments. Time domain electron control with MAS has considerable promise to improve DNP performance at higher fields and temperatures. We have recently demonstrated that pulsed electron decoupling using frequency-chirped microwaves improves MAS DNP experiments by partially attenuating detrimental hyperfine interactions. The continued development of pulsed electron decoupling will enable a new suite of MAS DNP experiments that transfer polarization directly to observed spins. Time domain DNP transfers to nuclear spins in conjunction with pulsed electron decoupling is described as a viable avenue toward DNP-enhanced, high-resolution NMR spectroscopy over a range of temperatures from <6 to 320 K.
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Affiliation(s)
- Edward
P. Saliba
- Department of Chemistry, Washington
University in St. Louis, St. Louis, Missouri 63130, United States
| | - Erika L. Sesti
- Department of Chemistry, Washington
University in St. Louis, St. Louis, Missouri 63130, United States
| | - Nicholas Alaniva
- Department of Chemistry, Washington
University in St. Louis, St. Louis, Missouri 63130, United States
| | - Alexander B. Barnes
- Department of Chemistry, Washington
University in St. Louis, St. Louis, Missouri 63130, United States
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37
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Chen P, Albert BJ, Gao C, Alaniva N, Price LE, Scott FJ, Saliba EP, Sesti EL, Judge PT, Fisher EW, Barnes AB. Magic angle spinning spheres. SCIENCE ADVANCES 2018; 4:eaau1540. [PMID: 30255153 PMCID: PMC6155130 DOI: 10.1126/sciadv.aau1540] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/10/2018] [Indexed: 05/18/2023]
Abstract
Magic angle spinning (MAS) is commonly used in nuclear magnetic resonance of solids to improve spectral resolution. Rather than using cylindrical rotors for MAS, we demonstrate that spherical rotors can be spun stably at the magic angle. Spherical rotors conserve valuable space in the probe head and simplify sample exchange and microwave coupling for dynamic nuclear polarization. In this current implementation of spherical rotors, a single gas stream provides bearing gas to reduce friction, drive propulsion to generate and maintain angular momentum, and variable temperature control for thermostating. Grooves are machined directly into zirconia spheres, thereby converting the rotor body into a robust turbine with high torque. We demonstrate that 9.5-mm-outside diameter spherical rotors can be spun at frequencies up to 4.6 kHz with N2(g) and 10.6 kHz with He(g). Angular stability of the spinning axis is demonstrated by observation of 79Br rotational echoes out to 10 ms from KBr packed within spherical rotors. Spinning frequency stability of ±1 Hz is achieved with resistive heating feedback control. A sample size of 36 μl can be accommodated in 9.5-mm-diameter spheres with a cylindrical hole machined along the spinning axis. We further show that spheres can be more extensively hollowed out to accommodate 161 μl of the sample, which provides superior signal-to-noise ratio compared to traditional 3.2-mm-diameter cylindrical rotors.
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Affiliation(s)
- Pinhui Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brice J. Albert
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Chukun Gao
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas Alaniva
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lauren E. Price
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Faith J. Scott
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Edward P. Saliba
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Erika L. Sesti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Patrick T. Judge
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Biochemistry, Biophysics and Structural Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Edward W. Fisher
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Biochemistry, Biophysics and Structural Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Alexander B. Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Corresponding author.
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38
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Ward ME, Daniëls MA, van Kappel EC, Maurice MM, Baldus M. Investigations of dynamic amyloid-like structures of the Wnt signalling pathway by solid-state NMR. Chem Commun (Camb) 2018; 54:3959-3962. [PMID: 29561051 DOI: 10.1039/c8cc01346b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report solid-state Nuclear Magnetic Resonance (ssNMR) studies on amyloid-like protein complexes formed by DIX domains that mediate key protein interactions in the Wnt signalling pathway. Our results provide insight into the 3D fold of the self-associated Axin-DIX domain and identify a potential lipid cofactor.
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Affiliation(s)
- M E Ward
- NMR spectroscopy, Bijvoet Center for Biomolecular Research, Universiteit Utrecht, Padualaan 8, Utrecht, The Netherlands.
| | - M A Daniëls
- NMR spectroscopy, Bijvoet Center for Biomolecular Research, Universiteit Utrecht, Padualaan 8, Utrecht, The Netherlands.
| | - E C van Kappel
- Oncode Institute, Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
| | - M M Maurice
- Oncode Institute, Center for Molecular Medicine, Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, The Netherlands
| | - M Baldus
- NMR spectroscopy, Bijvoet Center for Biomolecular Research, Universiteit Utrecht, Padualaan 8, Utrecht, The Netherlands.
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39
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iNEXT: a European facility network to stimulate translational structural biology. FEBS Lett 2018; 592:1909-1917. [DOI: 10.1002/1873-3468.13062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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40
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Giassa IC, Rynes J, Fessl T, Foldynova-Trantirkova S, Trantirek L. Advances in the cellular structural biology of nucleic acids. FEBS Lett 2018; 592:1997-2011. [PMID: 29679394 DOI: 10.1002/1873-3468.13054] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/31/2018] [Accepted: 04/09/2018] [Indexed: 01/01/2023]
Abstract
Conventional biophysical and chemical biology approaches for delineating relationships between the structure and biological function of nucleic acids (NAs) abstract NAs from their native biological context. However, cumulative experimental observations have revealed that the structure, dynamics and interactions of NAs might be strongly influenced by a broad spectrum of specific and nonspecific physical-chemical environmental factors. This consideration has recently sparked interest in the development of novel tools for structural characterization of NAs in the native cellular context. Here, we review the individual methods currently being employed for structural characterization of NA structure in a native cellular environment with a focus on recent advances and developments in the emerging fields of in-cell NMR and electron paramagnetic resonance spectroscopy and in-cell single-molecule FRET of NAs.
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Affiliation(s)
- Ilektra-Chara Giassa
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Rynes
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Silvie Foldynova-Trantirkova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Institute of Biophysics, Academy of Science of the Czech Republic, Brno, Czech Republic
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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41
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Jaudzems K, Bertarello A, Chaudhari SR, Pica A, Cala-De Paepe D, Barbet-Massin E, Pell AJ, Akopjana I, Kotelovica S, Gajan D, Ouari O, Tars K, Pintacuda G, Lesage A. Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kristaps Jaudzems
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Bertarello
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Sachin R. Chaudhari
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia I-80126 Naples Italy
| | - Diane Cala-De Paepe
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Emeline Barbet-Massin
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrew J. Pell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
- Present address: Department of Materials and Environmental Chemistry; Arrhenius Laboratory; Stockholm University; Svante Arrhenius Väg 16 C SE-106 91 Stockholm Sweden
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | | | - David Gajan
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273; 13397 Marseille cedex 20 France
| | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | - Guido Pintacuda
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Anne Lesage
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
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42
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Jaudzems K, Bertarello A, Chaudhari SR, Pica A, Cala-De Paepe D, Barbet-Massin E, Pell AJ, Akopjana I, Kotelovica S, Gajan D, Ouari O, Tars K, Pintacuda G, Lesage A. Dynamic Nuclear Polarization-Enhanced Biomolecular NMR Spectroscopy at High Magnetic Field with Fast Magic-Angle Spinning. Angew Chem Int Ed Engl 2018; 57:7458-7462. [DOI: 10.1002/anie.201801016] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/06/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Kristaps Jaudzems
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Bertarello
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Sachin R. Chaudhari
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrea Pica
- Department of Chemical Sciences; University of Naples Federico II; Via Cintia I-80126 Naples Italy
| | - Diane Cala-De Paepe
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Emeline Barbet-Massin
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Andrew J. Pell
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
- Present address: Department of Materials and Environmental Chemistry; Arrhenius Laboratory; Stockholm University; Svante Arrhenius Väg 16 C SE-106 91 Stockholm Sweden
| | - Inara Akopjana
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | | | - David Gajan
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Olivier Ouari
- Aix-Marseille Université, CNRS, ICR UMR 7273; 13397 Marseille cedex 20 France
| | - Kaspars Tars
- Biomedical Research and Study Centre; Rātsupītes 1 LV1067 Riga Latvia
| | - Guido Pintacuda
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
| | - Anne Lesage
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1; Ens Lyon; Institut des Sciences Analytiques, UMR 5280; 5 rue de la Doua F-69100 VILLEURBANNE France
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43
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New structural and functional insights from in-cell NMR. Emerg Top Life Sci 2018; 2:29-38. [PMID: 33525780 DOI: 10.1042/etls20170136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 11/17/2022]
Abstract
In recent years, it has become evident that structural characterization would gain significantly in terms of biological relevance if framed within a cellular context, while still maintaining the atomic resolution. Therefore, major efforts have been devoted to developing Cellular Structural Biology approaches. In this respect, in-cell NMR can provide and has provided relevant contributions to the field, not only to investigate the structural and dynamical properties of macromolecules in solution but, even more relevant, to understand functional processes directly in living cells and the factors that modulate them, such as exogenous molecules, partner proteins, and oxidative stress. In this commentary, we review and discuss some of the main contributions to the understanding of protein structural and functional properties achieved by in-cell NMR.
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Narasimhan S, Mance D, Pinto C, Weingarth M, Bonvin AMJJ, Baldus M. Rapid Prediction of Multi-dimensional NMR Data Sets Using FANDAS. Methods Mol Biol 2018; 1688:111-132. [PMID: 29151207 DOI: 10.1007/978-1-4939-7386-6_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Solid-state NMR (ssNMR) can provide structural information at the most detailed level and, at the same time, is applicable in highly heterogeneous and complex molecular environments. In the last few years, ssNMR has made significant progress in uncovering structure and dynamics of proteins in their native cellular environments [1-4]. Additionally, ssNMR has proven to be useful in studying large biomolecular complexes as well as membrane proteins at the atomic level [5]. In such studies, innovative labeling schemes have become a powerful approach to tackle spectral crowding. In fact, selecting the appropriate isotope-labeling schemes and a careful choice of the ssNMR experiments to be conducted are critical for applications of ssNMR in complex biomolecular systems. Previously, we have introduced a software tool called FANDAS (Fast Analysis of multidimensional NMR DAta Sets) that supports such investigations from the early stages of sample preparation to the final data analysis [6]. Here, we present a new version of FANDAS, called FANDAS 2.0, with improved user interface and extended labeling scheme options allowing the user to rapidly predict and analyze ssNMR data sets for a given protein-based application. It provides flexible options for advanced users to customize the program for tailored applications. In addition, the list of ssNMR experiments that can be predicted now includes proton (1H) detected pulse sequences. FANDAS 2.0, written in Python, is freely available through a user-friendly web interface at http://milou.science.uu.nl/services/FANDAS .
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Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Cecilia Pinto
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Computational Structural Biology, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands.
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45
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Baker LA, Sinnige T, Schellenberger P, de Keyzer J, Siebert CA, Driessen AJM, Baldus M, Grünewald K. Combined 1H-Detected Solid-State NMR Spectroscopy and Electron Cryotomography to Study Membrane Proteins across Resolutions in Native Environments. Structure 2017; 26:161-170.e3. [PMID: 29249608 PMCID: PMC5758107 DOI: 10.1016/j.str.2017.11.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/02/2017] [Accepted: 11/15/2017] [Indexed: 11/15/2022]
Abstract
Membrane proteins remain challenging targets for structural biology, despite much effort, as their native environment is heterogeneous and complex. Most methods rely on detergents to extract membrane proteins from their native environment, but this removal can significantly alter the structure and function of these proteins. Here, we overcome these challenges with a hybrid method to study membrane proteins in their native membranes, combining high-resolution solid-state nuclear magnetic resonance spectroscopy and electron cryotomography using the same sample. Our method allows the structure and function of membrane proteins to be studied in their native environments, across different spatial and temporal resolutions, and the combination is more powerful than each technique individually. We use the method to demonstrate that the bacterial membrane protein YidC adopts a different conformation in native membranes and that substrate binding to YidC in these native membranes differs from purified and reconstituted systems. CryoET and ssNMR give complementary information about proteins in native membranes One sample can be prepared for both methods without the use of detergents Hybrid method shows differences between purified and native preparations of YidC Sample preparation reduces costs and time and suggests new strategy for assignment
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Affiliation(s)
- Lindsay A Baker
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Tessa Sinnige
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Pascale Schellenberger
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jeanine de Keyzer
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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46
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Mentink-Vigier F, Mathies G, Liu Y, Barra AL, Caporini MA, Lee D, Hediger S, G Griffin R, De Paëpe G. Efficient cross-effect dynamic nuclear polarization without depolarization in high-resolution MAS NMR. Chem Sci 2017; 8:8150-8163. [PMID: 29619170 PMCID: PMC5861987 DOI: 10.1039/c7sc02199b] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/01/2017] [Indexed: 11/21/2022] Open
Abstract
Dynamic nuclear polarization (DNP) has the potential to enhance the sensitivity of magic-angle spinning (MAS) NMR by many orders of magnitude and therefore to revolutionize atomic resolution structural analysis. Currently, the most widely used approach to DNP for studies of chemical, material, and biological systems involves the cross-effect (CE) mechanism, which relies on biradicals as polarizing agents. However, at high magnetic fields (≥5 T), the best biradicals used for CE MAS-DNP are still far from optimal, primarily because of the nuclear depolarization effects they induce. In the presence of bisnitroxide biradicals, magic-angle rotation results in a reverse CE that can deplete the initial proton Boltzmann polarization by more than a factor of 2. In this paper we show that these depolarization losses can be avoided by using a polarizing agent composed of a narrow-line trityl radical tethered to a broad-line TEMPO. Consequently, we show that a biocompatible trityl-nitroxide biradical, TEMTriPol-1, provides the highest MAS NMR sensitivity at ≥10 T, and its relative efficiency increases with the magnetic field strength. We use numerical simulations to explain the absence of depolarization for TEMTriPol-1 and its high efficiency, paving the way for the next generation of polarizing agents for DNP. We demonstrate the superior sensitivity enhancement using TEMTriPol-1 by recording the first solid-state 2D 13C-13C correlation spectrum at natural isotopic abundance at a magnetic field of 18.8 T.
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Affiliation(s)
| | - Guinevere Mathies
- Francis Bitter Magnet Laboratory , Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics , School of Pharmacy , Tianjin Medical University , Tianjin 300070 , China
| | - Anne-Laure Barra
- Laboratoire National des Champs Magnétiques Intenses - CNRS , Univ. Grenoble Alpes , F-38042 Grenoble , France
| | - Marc A Caporini
- Bruker BioSpin Corporation , 15 Fortune Drive , Billerica , MA 01821 , USA
| | - Daniel Lee
- Univ. Grenoble Alpes , CEA , CNRS , INAC-MEM , F-38000 Grenoble , France .
| | - Sabine Hediger
- Univ. Grenoble Alpes , CEA , CNRS , INAC-MEM , F-38000 Grenoble , France .
| | - Robert G Griffin
- Francis Bitter Magnet Laboratory , Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA
| | - Gaël De Paëpe
- Univ. Grenoble Alpes , CEA , CNRS , INAC-MEM , F-38000 Grenoble , France .
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47
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Lilly Thankamony AS, Wittmann JJ, Kaushik M, Corzilius B. Dynamic nuclear polarization for sensitivity enhancement in modern solid-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:120-195. [PMID: 29157490 DOI: 10.1016/j.pnmrs.2017.06.002] [Citation(s) in RCA: 263] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/03/2017] [Accepted: 06/08/2017] [Indexed: 05/03/2023]
Abstract
The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.
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Affiliation(s)
- Aany Sofia Lilly Thankamony
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Johannes J Wittmann
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Monu Kaushik
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany.
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48
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Jain SK, Mathies G, Griffin RG. Off-resonance NOVEL. J Chem Phys 2017; 147:164201. [PMID: 29096491 PMCID: PMC5659863 DOI: 10.1063/1.5000528] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/10/2017] [Indexed: 11/14/2022] Open
Abstract
Dynamic nuclear polarization (DNP) is theoretically able to enhance the signal in nuclear magnetic resonance (NMR) experiments by a factor γe/γn, where γ's are the gyromagnetic ratios of an electron and a nuclear spin. However, DNP enhancements currently achieved in high-field, high-resolution biomolecular magic-angle spinning NMR are well below this limit because the continuous-wave DNP mechanisms employed in these experiments scale as ω0-n where n ∼ 1-2. In pulsed DNP methods, such as nuclear orientation via electron spin-locking (NOVEL), the DNP efficiency is independent of the strength of the main magnetic field. Hence, these methods represent a viable alternative approach for enhancing nuclear signals. At 0.35 T, the NOVEL scheme was demonstrated to be efficient in samples doped with stable radicals, generating 1H NMR enhancements of ∼430. However, an impediment in the implementation of NOVEL at high fields is the requirement of sufficient microwave power to fulfill the on-resonance matching condition, ω0I = ω1S, where ω0I and ω1S are the nuclear Larmor and electron Rabi frequencies, respectively. Here, we exploit a generalized matching condition, which states that the effective Rabi frequency, ω1Seff, matches ω0I. By using this generalized off-resonance matching condition, we generate 1H NMR signal enhancement factors of 266 (∼70% of the on-resonance NOVEL enhancement) with ω1S/2π = 5 MHz. We investigate experimentally the conditions for optimal transfer of polarization from electrons to 1H both for the NOVEL mechanism and the solid-effect mechanism and provide a unified theoretical description for these two historically distinct forms of DNP.
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Affiliation(s)
- Sheetal K Jain
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Guinevere Mathies
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Robert G Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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49
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Rogawski R, McDermott AE. New NMR tools for protein structure and function: Spin tags for dynamic nuclear polarization solid state NMR. Arch Biochem Biophys 2017; 628:102-113. [PMID: 28623034 PMCID: PMC5815514 DOI: 10.1016/j.abb.2017.06.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/05/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022]
Abstract
Magic angle spinning solid state NMR studies of biological macromolecules [1-3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University, NY, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, NY, NY 10027, United States.
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Applications of solid-state NMR to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1577-1586. [PMID: 28709996 DOI: 10.1016/j.bbapap.2017.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022]
Abstract
Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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