1
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Costello WN, Xiao Y, Mentink-Vigier F, Kragelj J, Frederick KK. DNP-assisted solid-state NMR enables detection of proteins at nanomolar concentrations in fully protonated cellular milieu. JOURNAL OF BIOMOLECULAR NMR 2024; 78:95-108. [PMID: 38520488 DOI: 10.1007/s10858-024-00436-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/09/2024] [Indexed: 03/25/2024]
Abstract
With the sensitivity enhancements conferred by dynamic nuclear polarization (DNP), magic angle spinning (MAS) solid state NMR spectroscopy experiments can attain the necessary sensitivity to detect very low concentrations of proteins. This potentially enables structural investigations of proteins at their endogenous levels in their biological contexts where their native stoichiometries with potential interactors is maintained. Yet, even with DNP, experiments are still sensitivity limited. Moreover, when an isotopically-enriched target protein is present at physiological levels, which typically range from low micromolar to nanomolar concentrations, the isotope content from the natural abundance isotopes in the cellular milieu can outnumber the isotope content of the target protein. Using isotopically enriched yeast prion protein, Sup35NM, diluted into natural abundance yeast lysates, we optimized sample composition. We found that modest cryoprotectant concentrations and fully protonated environments support efficient DNP. We experimentally validated theoretical calculations of the limit of specificity for an isotopically enriched protein in natural abundance cellular milieu. We establish that, using pulse sequences that are selective for adjacent NMR-active nuclei, proteins can be specifically detected in cellular milieu at concentrations in the hundreds of nanomolar. Finally, we find that maintaining native stoichiometries of the protein of interest to the components of the cellular environment may be important for proteins that make specific interactions with cellular constituents.
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Affiliation(s)
- Whitney N Costello
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
| | | | - Jaka Kragelj
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA
- Slovenian NMR centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Kendra K Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, 75390-8816, USA.
- Center for Alzheimer's and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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2
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Yan Z, Zhang R. Measurement of spin-lattice relaxation times in multiphase polymer systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 357:107597. [PMID: 37984029 DOI: 10.1016/j.jmr.2023.107597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
Solid-state Nuclear Magnetic Resonance (NMR) has emerged as a pivotal technique for unraveling the microstructure and dynamics of intricate polymer and biological materials. Within this context, site-specific proton spin-lattice relaxation times in the laboratory frame (T1) and rotating frame (T1ρ) have become indispensable tools for investigating phase separation structures and molecular dynamics in multiphase polymer systems. Notably, the site-specific measurement of proton T1 and T1ρ is usually achieved via 13C detection in polymers, where 1H polarization is typically transferred to 13C via cross polarization (CP). Nevertheless, CP relies on the 1H-13C heteronuclear dipolar couplings, and thus it does not work well for the mobile components. In this study, via the integration of CP and RINEPT (refocused insensitive nuclei enhanced by polarization transfer), we propose a robust approach for the measurement of site-specific proton T1 and T1ρ in multiphase polymers. It overcomes the limitation of CP on transferring 1H polarization to 13C in mobile components, and thus enables simultaneous determination of site-specific proton T1 and T1ρ in rigid and mobile components in multiphase polymers in a single experiment. Such experiment can also be used for dynamics-based spectral editing due to the dynamic selectivity of CP- and RINEPT-based polarization transfer process. The proposed experiments are well demonstrated on three typical multiphase polymer systems, poly(methyl methacrylate)/polybutadiene (PMMA/PB) polymer blend, polyurethane (PU) and polystyrene-polybutadiene-polystyrene (SBS) elastomers. We envisage the proposed experiments can be a universal avenue for structural and dynamic elucidation of multiphase polymers containing both rigid and mobile components.
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Affiliation(s)
- Zhiwei Yan
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter (SESM), South China University of Technology, Guangzhou, 510640, PR China
| | - Rongchun Zhang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter (SESM), South China University of Technology, Guangzhou, 510640, PR China; Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, 510640, PR China.
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3
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Kragelj J, Ghosh R, Xiao Y, Dumarieh R, Lagasca D, Krishna S, Frederick KK. Spatially resolved DNP-assisted NMR illuminates the conformational ensemble of α-synuclein in intact viable cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563877. [PMID: 37961511 PMCID: PMC10634803 DOI: 10.1101/2023.10.24.563877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The protein α-syn adopts a wide variety of conformations including an intrinsically disordered monomeric form and an α-helical rich membrane-associated form that is thought to play an important role in cellular membrane processes. However, despite the high affinity of α-syn for membranes, evidence that the α-helical form of α-syn is adopted inside cells has thus far been indirect. In cell DNP-assisted solid state NMR on frozen samples has the potential to report directly on the entire conformational ensemble. Moreover, because the DNP polarization agent can be dispersed both homogenously and inhomogenously throughout the cellular biomass, in cell DNP-assisted solid state NMR experiments can report either quantitatively upon the structural ensemble or can preferentially report upon the structural ensemble with a spatial bias. Using DNP-assisted MAS NMR we establish that the spectra of purified α-syn in the membrane-associated and intrinsically disordered forms have distinguishable spectra. When the polarization agent is introduced into cells by electroporation and dispersed homogenously, a minority of the α-syn inside HEK293 cells adopts a highly α-helical rich conformation. Alteration of the spatial distribution of the polarization agent preferentially enhances the signal from molecules nearer to the cellular periphery, thus the α-helical rich population is preferentially adopted toward the cellular periphery. This demonstrates how selectively altering the spatial distribution of the DNP polarization agent can be a powerful tool for preferential reporting on specific structural ensembles, paving the way for more nuanced investigations into the conformations that proteins adopt in different areas of the cell.
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Affiliation(s)
- Jaka Kragelj
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Rania Dumarieh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Dominique Lagasca
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Sakshi Krishna
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Kendra K. Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
- Center for Alzheimer’s and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX 75390
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4
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Ackermann BE, Lim BJ, Elathram N, Narayanan S, Debelouchina GT. A Comparative Study of Nitroxide-Based Biradicals for Dynamic Nuclear Polarization in Cellular Environments. Chembiochem 2022; 23:e202200577. [PMID: 36250276 PMCID: PMC9856215 DOI: 10.1002/cbic.202200577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/15/2022] [Indexed: 01/25/2023]
Abstract
Dynamic nuclear polarization (DNP) is a powerful tool to enhance the NMR signals of molecules by transferring polarization from unpaired electron spins to nuclei through microwave irradiation. The resulting signal enhancements can enable the analysis of samples that have previously been intractable by NMR spectroscopy, including proteins, nucleic acids, and metabolites in cells. To carry out DNP, the sample is doped with a polarization agent, a biradical containing two nitroxide moieties. DNP applications in cells, however, present significant challenges as nitroxides are often susceptible to the reducing cellular environment. Here, we introduce a novel polarization agent, POPAPOL, that exhibits increased lifetimes under reducing conditions. We also compare its bioresistance and DNP performance with three popular, commercially available polarization agents. Our work indicates that pyrrolidine-based nitroxides can outperform piperidine-based nitroxides in cellular environments, and that future polarization agent designs must carefully balance DNP performance and stability for cellular applications.
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Affiliation(s)
- Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Byung Joon Lim
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nesreen Elathram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sirish Narayanan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA,Corresponding author: , http://debelouchinalab.ucsd.edu/
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5
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Zhu W, Guseman AJ, Bhinderwala F, Lu M, Su XC, Gronenborn AM. Visualizing Proteins in Mammalian Cells by 19 F NMR Spectroscopy. Angew Chem Int Ed Engl 2022; 61:e202201097. [PMID: 35278268 PMCID: PMC9156538 DOI: 10.1002/anie.202201097] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Indexed: 12/20/2022]
Abstract
In-cell NMR spectroscopy is a powerful tool to investigate protein behavior in physiologically relevant environments. Although proven valuable for disordered proteins, we show that in commonly used 1 H-15 N HSQC spectra of globular proteins, interactions with cellular components often broaden resonances beyond detection. This contrasts 19 F spectra in mammalian cells, in which signals are readily observed. Using several proteins, we demonstrate that surface charges and interaction with cellular binding partners modulate linewidths and resonance frequencies. Importantly, we establish that 19 F paramagnetic relaxation enhancements using stable, rigid Ln(III) chelate pendants, attached via non-reducible thioether bonds, provide an effective means to obtain accurate distances for assessing protein conformations in the cellular milieu.
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Affiliation(s)
- Wenkai Zhu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Alex J Guseman
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Fatema Bhinderwala
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Manman Lu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, 300071, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, 300071, Tianjin, China
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, USA.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, USA
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6
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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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
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7
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Nami F, Ferraz MJ, Bakkum T, Aerts JMFG, Pandit A. Real‐Time NMR Recording of Fermentation and Lipid Metabolism Processes in Live Microalgae Cells. Angew Chem Int Ed Engl 2022; 61:e202117521. [PMID: 35103372 PMCID: PMC9305762 DOI: 10.1002/anie.202117521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 11/10/2022]
Abstract
Non‐invasive and real‐time recording of processes in living cells has been limited to detection of small cellular components such as soluble proteins and metabolites. Here we report a multiphase NMR approach using magic‐angle spinning NMR to synchronously follow microbial processes of fermentation, lipid metabolism and structural dynamic changes in live microalgae cells. Chlamydomonas reinhardtii green algae were highly concentrated, introducing dark fermentation and anoxia conditions. Single‐pulse NMR experiments were applied to obtain temperature‐dependent kinetic profiles of the formed fermentation products. Through dynamics‐based spectral editing NMR, simultaneous conversion of galactolipids into TAG and free fatty acids was observed and rapid loss of rigid lipid structures. This suggests that lipolysis under dark and anoxia conditions finally results in the breakdown of cell and organelle membranes, which could be beneficial for recovery of intracellular microbial useful products.
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Affiliation(s)
- Faezeh Nami
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Maria Joao Ferraz
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Dept. of Bio Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anjali Pandit
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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8
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Gronenborn AM, Zhu W, Guseman AJ, Bhinderwala F, Lu M, Su XC. Visualizing Proteins in Mammalian Cells by 19F NMR spectroscopy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Angela M Gronenborn
- University of Pittsburgh, School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Wenkai Zhu
- University of Pittsburgh School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Alex J Guseman
- University of Pittsburgh School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Fatema Bhinderwala
- University of Pittsburgh School of Medicine Department of Structural Biology UNITED STATES
| | - Manman Lu
- University of Pittsburgh School of Medicine Department of Structural Biology 3501 Fifth AvenueBiomedical Science Tower 3 15260 Pittsburgh UNITED STATES
| | - Xun-Cheng Su
- Nankai University College of Chemistry State Key Laboratory of Elemento-Organic Chemistry 300071 Tianjin CHINA
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9
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Nami F, Ferraz MJ, Bakkum T, Aerts JMFG, Pandit A. Real‐Time NMR Recording of Fermentation and Lipid Metabolism Processes in Live Microalgae Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Faezeh Nami
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Maria Joao Ferraz
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Dept. of Bio Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anjali Pandit
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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10
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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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11
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Xiao Y, Ghosh R, Frederick KK. In-Cell NMR of Intact Mammalian Cells Preserved with the Cryoprotectants DMSO and Glycerol Have Similar DNP Performance. Front Mol Biosci 2022; 8:789478. [PMID: 35145995 PMCID: PMC8824258 DOI: 10.3389/fmolb.2021.789478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/31/2021] [Indexed: 11/26/2022] Open
Abstract
NMR has the resolution and specificity to determine atomic-level protein structures of isotopically-labeled proteins in complex environments and, with the sensitivity gains conferred by dynamic nuclear polarization (DNP), NMR has the sensitivity to detect proteins at their endogenous concentrations. Prior work established that DNP MAS NMR is compatible with cellular viability. However, in that work, 15% glycerol, rather than the more commonly used 10% DMSO, was used as the cellular cryoprotectant. Moreover, incubation of cells cryoprotected 15% glycerol with the polarization agent, AMUPol, resulted in an inhomogeneous distribution of AMUPol through the cellular biomass, which resulted in a spatial bias of the NMR peak intensities. Because 10% DMSO is not only the most used cryoprotectant for mammalian cells, but also because DMSO is often used to improve delivery of molecules to cells, we sought to characterize the DNP performance of cells that were incubated with AMUPol and cryoprotected with 10% DMSO. We found that, like cells preserved with 15% glycerol, cells preserved with 10% DMSO retain high viability during DNP MAS NMR experiments if they are frozen at a controlled rate. However, DMSO did not improve the dispersion of AMUPol throughout the cellular biomass. Cells preserved with 15% glycerol and with 10% DMSO had similar DNP performance for both the maximal DNP enhancements as well as the inhomogeneous dispersion of AMUPol throughout the cellular biomass. Therefore, 10% DMSO and 15% glycerol are both appropriate cryoprotectant systems for DNP-assisted MAS NMR of intact viable mammalian cells.
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Affiliation(s)
- Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, United States
| | - Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, United States
| | - Kendra K. Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, United States
- Center for Alzheimer’s and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX, United States
- *Correspondence: Kendra K. Frederick,
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12
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Ghosh R, Xiao Y, Kragelj J, Frederick KK. In-Cell Sensitivity-Enhanced NMR of Intact Viable Mammalian Cells. J Am Chem Soc 2021; 143:18454-18466. [PMID: 34724614 DOI: 10.1021/jacs.1c06680] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NMR has the resolution and specificity to determine atomic-level protein structures of isotopically labeled proteins in complex environments, and with the sensitivity gains conferred by dynamic nuclear polarization (DNP), NMR has the sensitivity to detect proteins at their endogenous concentrations. However, DNP sensitivity enhancements are critically dependent on experimental conditions and sample composition. While some of these conditions are theoretically compatible with cellular viability, the effects of others on cellular sample integrity are unknown. Uncertainty about the integrity of cellular samples limits the utility of experimental outputs of in-cell experiments. Using several measures, we establish conditions that support DNP enhancements that can enable detection of micromolar concentrations of proteins in experimentally tractable times that are compatible with cellular viability. Taken together, we establish DNP-assisted MAS NMR as a technique for structural investigations of biomolecules in intact viable cells that can be phenotyped both before and after NMR experiments.
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Affiliation(s)
- Rupam Ghosh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390-8816, United States
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390-8816, United States
| | - Jaka Kragelj
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390-8816, United States
| | - Kendra K Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390-8816, United States.,Center for Alzheimer's and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, Texas 75390, United States
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13
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Cai X, Lucini Paioni A, Adler A, Yao R, Zhang W, Beriashvili D, Safeer A, Gurinov A, Rockenbauer A, Song Y, Baldus M, Liu Y. Highly Efficient Trityl-Nitroxide Biradicals for Biomolecular High-Field Dynamic Nuclear Polarization. Chemistry 2021; 27:12758-12762. [PMID: 34181286 DOI: 10.1002/chem.202102253] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Indexed: 12/22/2022]
Abstract
Dynamic nuclear polarization (DNP) is a powerful method to enhance the sensitivity of solid-state magnetic nuclear resonance (ssNMR) spectroscopy. However, its biomolecular applications at high magnetic fields (preferably>14 T) have so far been limited by the intrinsically low efficiency of polarizing agents and sample preparation aspects. Herein, we report a new class of trityl-nitroxide biradicals, dubbed SNAPols that combine high DNP efficiency with greatly enhanced hydrophilicity. SNAPol-1, the best compound in the series, shows DNP enhancement factors at 18.8 T of more than 100 in small molecules and globular proteins and also exhibits strong DNP enhancements in membrane proteins and cellular preparations. By integrating optimal sensitivity and high resolution, we expect widespread applications of this new polarizing agent in high-field DNP/ssNMR spectroscopy, especially for complex biomolecules.
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Affiliation(s)
- Xinyi Cai
- 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
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Agnes Adler
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - 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
| | - 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
| | - David Beriashvili
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - 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
| | - 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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14
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Gurinov A, Sieland B, Kuzhelev A, Elgabarty H, Kühne TD, Prisner T, Paradies J, Baldus M, Ivanov KL, Pylaeva S. Gemischtvalente Verbindungen als polarisierende Mittel für die dynamische Kern‐Overhauser‐Polarisation in Festkörpern**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrei Gurinov
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584CH Utrecht Niederlande
| | - Benedikt Sieland
- Department of Chemistry Paderborn University Warburger Straße 100 Paderborn 33098 Deutschland
| | - Andrey Kuzhelev
- Goethe University Frankfurt am Main Institute of Physical and Theoretical Chemistry Center for Biomolecular Magnetic Resonance Max von Laue Straße 7 60438 Frankfurt am Main Deutschland
| | - Hossam Elgabarty
- Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry University of Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Thomas D. Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry University of Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Thomas Prisner
- Goethe University Frankfurt am Main Institute of Physical and Theoretical Chemistry Center for Biomolecular Magnetic Resonance Max von Laue Straße 7 60438 Frankfurt am Main Deutschland
| | - Jan Paradies
- Department of Chemistry Paderborn University Warburger Straße 100 Paderborn 33098 Deutschland
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584CH Utrecht Niederlande
| | - Konstantin L. Ivanov
- International Tomography Center Siberian Branch of the Russian Academy of Sciences Novosibirsk 630090 Russland
- Novosibirsk State University Novosibirsk 630090 Russland
| | - Svetlana Pylaeva
- Dynamics of Condensed Matter and Center for Sustainable Systems Design Chair of Theoretical Chemistry University of Paderborn Warburger Straße 100 33098 Paderborn Deutschland
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15
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Gurinov A, Sieland B, Kuzhelev A, Elgabarty H, Kühne TD, Prisner T, Paradies J, Baldus M, Ivanov KL, Pylaeva S. Mixed-Valence Compounds as Polarizing Agents for Overhauser Dynamic Nuclear Polarization in Solids*. Angew Chem Int Ed Engl 2021; 60:15371-15375. [PMID: 33908694 PMCID: PMC8361920 DOI: 10.1002/anie.202103215] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 11/25/2022]
Abstract
Herein, we investigate a novel set of polarizing agents—mixed‐valence compounds—by theoretical and experimental methods and demonstrate their performance in high‐field dynamic nuclear polarization (DNP) NMR experiments in the solid state. Mixed‐valence compounds constitute a group of molecules in which molecular mobility persists even in solids. Consequently, such polarizing agents can be used to perform Overhauser‐DNP experiments in the solid state, with favorable conditions for dynamic nuclear polarization formation at ultra‐high magnetic fields.
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Affiliation(s)
- Andrei Gurinov
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Benedikt Sieland
- Department of Chemistry, Paderborn University, Warburger Strasse 100, Paderborn, 33098, Germany
| | - Andrey Kuzhelev
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Max von Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Hossam Elgabarty
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
| | - Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
| | - Thomas Prisner
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Max von Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jan Paradies
- Department of Chemistry, Paderborn University, Warburger Strasse 100, Paderborn, 33098, Germany
| | - Marc Baldus
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands
| | - Konstantin L Ivanov
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Svetlana Pylaeva
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, University of Paderborn, Warburger Strasse 100, 33098, Paderborn, Germany
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16
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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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17
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Chordia S, Narasimhan S, Lucini Paioni A, Baldus M, Roelfes G. In Vivo Assembly of Artificial Metalloenzymes and Application in Whole-Cell Biocatalysis*. Angew Chem Int Ed Engl 2021; 60:5913-5920. [PMID: 33428816 PMCID: PMC7986609 DOI: 10.1002/anie.202014771] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Indexed: 12/14/2022]
Abstract
We report the supramolecular assembly of artificial metalloenzymes (ArMs), based on the Lactococcal multidrug resistance regulator (LmrR) and an exogeneous copper(II)-phenanthroline complex, in the cytoplasm of E. coli cells. A combination of catalysis, cell-fractionation, and inhibitor experiments, supplemented with in-cell solid-state NMR spectroscopy, confirmed the in-cell assembly. The ArM-containing whole cells were active in the catalysis of the enantioselective Friedel-Crafts alkylation of indoles and the Diels-Alder reaction of azachalcone with cyclopentadiene. Directed evolution resulted in two different improved mutants for both reactions, LmrR_A92E_M8D and LmrR_A92E_V15A, respectively. The whole-cell ArM system required no engineering of the microbial host, the protein scaffold, or the cofactor to achieve ArM assembly and catalysis. We consider this a key step towards integrating abiological catalysis with biosynthesis to generate a hybrid metabolism.
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Affiliation(s)
- Shreyans Chordia
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.,Current address: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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18
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Chordia S, Narasimhan S, Lucini Paioni A, Baldus M, Roelfes G. In Vivo Assembly of Artificial Metalloenzymes and Application in Whole‐Cell Biocatalysis**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014771] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shreyans Chordia
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
- Current address: Structural and Computational Biology Unit European Molecular Biology Laboratory Meyerhofstraße 1 69117 Heidelberg Germany
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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19
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Zhu S, Sani MA, Separovic F. In-Cell Solid-State NMR Analysis of Membrane Proteins. Aust J Chem 2021. [DOI: 10.1071/ch20330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Korchak S, Jagtap AP, Glöggler S. Signal-enhanced real-time magnetic resonance of enzymatic reactions at millitesla fields. Chem Sci 2020; 12:314-319. [PMID: 34163599 PMCID: PMC8178804 DOI: 10.1039/d0sc04884d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The phenomenon of nuclear magnetic resonance (NMR) is widely applied in biomedical and biological science to study structures and dynamics of proteins and their reactions. Despite its impact, NMR is an inherently insensitive phenomenon and has driven the field to construct spectrometers with increasingly higher magnetic fields leading to more detection sensitivity. Here, we are demonstrating that enzymatic reactions can be followed in real-time at millitesla fields, three orders of magnitude lower than the field of state-of-the-art NMR spectrometers. This requires signal-enhancing samples via hyperpolarization. Within seconds, we have enhanced the signals of 2-13C-pyruvate, an important metabolite to probe cancer metabolism, in 22 mM concentrations (up to 10.1% ± 0.1% polarization) and show that such a large signal allows for the real-time detection of enzymatic conversion of pyruvate to lactate at 24 mT. This development paves the pathways for biological studies in portable and affordable NMR systems with a potential for medical diagnostics. We demonstrate that metabolism can be monitored in real-time with magnetic resonance at milli-tesla fields that are 1000 fold lower than state-of-the-art high field spectrometers.![]()
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Affiliation(s)
- Sergey Korchak
- NMR Signal Enhancement Group, Max-Planck-Insitute for Biophysical Chemistry Am Faßberg 11 37077 Göttingen Germany .,Center for Biostructural Imaging of Neurodegeneration of UMG Von-Siebold-Str. 3A 37075 Göttingen Germany
| | - Anil P Jagtap
- NMR Signal Enhancement Group, Max-Planck-Insitute for Biophysical Chemistry Am Faßberg 11 37077 Göttingen Germany .,Center for Biostructural Imaging of Neurodegeneration of UMG Von-Siebold-Str. 3A 37075 Göttingen Germany
| | - Stefan Glöggler
- NMR Signal Enhancement Group, Max-Planck-Insitute for Biophysical Chemistry Am Faßberg 11 37077 Göttingen Germany .,Center for Biostructural Imaging of Neurodegeneration of UMG Von-Siebold-Str. 3A 37075 Göttingen Germany
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21
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Tran NT, Mentink-Vigier F, Long JR. Dynamic Nuclear Polarization of Biomembrane Assemblies. Biomolecules 2020; 10:E1246. [PMID: 32867275 PMCID: PMC7565305 DOI: 10.3390/biom10091246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 01/02/2023] Open
Abstract
While atomic scale structural and dynamic information are hallmarks of nuclear magnetic resonance (NMR) methodologies, sensitivity is a fundamental limitation in NMR studies. Fully exploiting NMR capabilities to study membrane proteins is further hampered by their dilution within biological membranes. Recent developments in dynamic nuclear polarization (DNP), which can transfer the relatively high polarization of unpaired electrons to nuclear spins, show promise for overcoming the sensitivity bottleneck and enabling NMR characterization of membrane proteins under native-like conditions. Here we discuss fundamental aspects of DNP-enhanced solid-state NMR spectroscopy, experimental details relevant to the study of lipid assemblies and incorporated proteins, and sensitivity gains which can be realized in biomembrane-based samples. We also present unique insights which can be gained from DNP measurements and prospects for further development of the technique for elucidating structures and orientations of membrane proteins in native lipid environments.
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Affiliation(s)
- Nhi T. Tran
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA;
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA;
| | - Joanna R. Long
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA;
- Department of Biochemistry & Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
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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: 20] [Impact Index Per Article: 5.0] [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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Common Functions of Disordered Proteins across Evolutionary Distant Organisms. Int J Mol Sci 2020; 21:ijms21062105. [PMID: 32204351 PMCID: PMC7139818 DOI: 10.3390/ijms21062105] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022] Open
Abstract
Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence–structure–function relationship. Hence, classic sequence- or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism.
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24
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Jekhmane S, Prachar M, Pugliese R, Fontana F, Medeiros‐Silva J, Gelain F, Weingarth M. Design Parameters of Tissue‐Engineering Scaffolds at the Atomic Scale. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shehrazade Jekhmane
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Marek Prachar
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Raffaele Pugliese
- Fondazione IRCCS Casa Sollievo della SofferenzaUnita' di Ingegneria Tissutale Viale Cappuccini 1 71013 San Giovanni Rotondo Italy
| | - Federico Fontana
- Fondazione IRCCS Casa Sollievo della SofferenzaUnita' di Ingegneria Tissutale Viale Cappuccini 1 71013 San Giovanni Rotondo Italy
- ASST Grande Ospedale Metropolitano NiguardaCenter for Nanomedicine and Tissue Engineering Piazza dell'Ospedale Maggiore 3 20162 Milan Italy
| | - João Medeiros‐Silva
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Fabrizio Gelain
- Fondazione IRCCS Casa Sollievo della SofferenzaUnita' di Ingegneria Tissutale Viale Cappuccini 1 71013 San Giovanni Rotondo Italy
- ASST Grande Ospedale Metropolitano NiguardaCenter for Nanomedicine and Tissue Engineering Piazza dell'Ospedale Maggiore 3 20162 Milan Italy
| | - Markus Weingarth
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
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25
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Jekhmane S, Prachar M, Pugliese R, Fontana F, Medeiros-Silva J, Gelain F, Weingarth M. Design Parameters of Tissue-Engineering Scaffolds at the Atomic Scale. Angew Chem Int Ed Engl 2019; 58:16943-16951. [PMID: 31573131 PMCID: PMC6899630 DOI: 10.1002/anie.201907880] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/03/2019] [Indexed: 01/08/2023]
Abstract
Stem-cell behavior is regulated by the material properties of the surrounding extracellular matrix, which has important implications for the design of tissue-engineering scaffolds. However, our understanding of the material properties of stem-cell scaffolds is limited to nanoscopic-to-macroscopic length scales. Herein, a solid-state NMR approach is presented that provides atomic-scale information on complex stem-cell substrates at near physiological conditions and at natural isotope abundance. Using self-assembled peptidic scaffolds designed for nervous-tissue regeneration, we show at atomic scale how scaffold-assembly degree, mechanics, and homogeneity correlate with favorable stem cell behavior. Integration of solid-state NMR data with molecular dynamics simulations reveals a highly ordered fibrillar structure as the most favorable stem-cell scaffold. This could improve the design of tissue-engineering scaffolds and other self-assembled biomaterials.
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Affiliation(s)
- Shehrazade Jekhmane
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Marek Prachar
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Raffaele Pugliese
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unita' di Ingegneria Tissutale, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Italy
| | - Federico Fontana
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unita' di Ingegneria Tissutale, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Italy.,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Fabrizio Gelain
- Fondazione IRCCS Casa Sollievo della Sofferenza, Unita' di Ingegneria Tissutale, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Italy.,ASST Grande Ospedale Metropolitano Niguarda, Center for Nanomedicine and Tissue Engineering, Piazza dell'Ospedale Maggiore 3, 20162, Milan, Italy
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
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26
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Günther Laukien Prize 2019: C. Griesinger and G. Bodenhausen / Bessel Research Award: H. Ovaa. Angew Chem Int Ed Engl 2019; 58:14023. [PMID: 31529665 DOI: 10.1002/anie.201910381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Günther‐Laukien‐Preis 2019: C. Griesinger und G. Bodenhausen / Bessel‐Forschungspreis: H. Ovaa. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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