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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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2
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Glöggler S, Yang S, Saul P, Mamone S, Kaltschnee L. Bimodal fluorescence/magnetic resonance molecular probes with extended spin lifetimes. Chemistry 2021; 28:e202104158. [PMID: 34854145 PMCID: PMC9302690 DOI: 10.1002/chem.202104158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Indexed: 11/12/2022]
Abstract
Bimodal molecular probes combining nuclear magnetic resonance (NMR) and fluorescence have been widely studied in basic science, as well as clinical research. The investigation of spin phenomena holds promise to broaden the scope of available probes allowing deeper insights into physiological processes. Herein, a class of molecules with a bimodal character with respect to fluorescence and nuclear spin singlet states is introduced. Singlet states are NMR silent but can be probed indirectly. Symmetric, perdeuterated molecules, in which the singlet states can be populated by vanishingly small electron‐mediated couplings (below 1 Hz) are reported. The lifetimes of these states are an order of magnitude longer than the longitudinal relaxation times and up to four minutes at 7 T. Moreover, these molecules show either aggregation induced emission (AIE) or aggregation caused quenching (ACQ) with respect to their fluorescence. In the latter case, the existence of excited dimers, which are proposed to use in a switchable manner in combination with the quenching of nuclear spin singlet states, is observed
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Affiliation(s)
- Stefan Glöggler
- Max-Planck-Institute for Biophysical Chemistry, NMR Signal Enhancement Group, Am Fassberg 11, 37077, Göttingen, GERMANY
| | - Shengjun Yang
- Max-Planck-Institute for Biophysical Chemistry: Max-Planck-Institut fur biophysikalische Chemie, NMR Signal Enhancement, GERMANY
| | - Philip Saul
- Max-Planck-Institute for Biophysical Chemistry: Max-Planck-Institut fur biophysikalische Chemie, NMR Singal Enhancement, GERMANY
| | - Salvatore Mamone
- Max-Planck-Institute for Biophysical Chemistry: Max-Planck-Institut fur biophysikalische Chemie, NMR Signal Enhancement, GERMANY
| | - Lukas Kaltschnee
- Max-Planck-Institute for Biophysical Chemistry: Max-Planck-Institut fur biophysikalische Chemie, NMR Signal Enhancement, GERMANY
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3
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Levitt MH. Long live the singlet state! JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:69-74. [PMID: 31307892 DOI: 10.1016/j.jmr.2019.07.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 03/30/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
The field of long-lived states in NMR is reviewed. The relationship of long-lived-state phenomena to those associated with spin isomerism is discussed. A brief overview is given of key developments in the field of long-lived states, including chemical symmetry-switching, the role of magnetic equivalence and magnetic inequivalence, long-lived coherences, hyperpolarized NMR involving long-lived states, quantum-rotor-induced polarization, and parahydrogen-induced hyperpolarization. Current application areas of long-lived states are reviewed, and a peer into the crystal ball reveals future developments in the field.
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Affiliation(s)
- Malcolm H Levitt
- School of Chemistry, University of Southampton, University Road, SO17 1BJ Southampton, UK.
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Elliott SJ, Stevanato G. Homonuclear ADAPT: A general preparation route to long-lived nuclear singlet order. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 301:49-55. [PMID: 30851665 DOI: 10.1016/j.jmr.2019.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/27/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
We introduce a simple strategy to access and readout nuclear singlet order based on the alternate repetition of hard pulses and delays. We demonstrate the general applicability of the method by accessing nuclear singlet order in spin systems characterized by diverse coupling regimes. We show that the method is highly efficient in the strong-coupling and chemical equivalence regimes, and can overcome some limitations of other well-established and more elaborated pulse sequences. A simulation package is provided which allows the determination of pulse sequence parameters.
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Affiliation(s)
- Stuart J Elliott
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Gabriele Stevanato
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Batochime, CH-1015 Lausanne, Switzerland.
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6
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Elliott SJ, Bengs C, Brown LJ, Hill-Cousins JT, O'Leary DJ, Pileio G, Levitt MH. Nuclear singlet relaxation by scalar relaxation of the second kind in the slow-fluctuation regime. J Chem Phys 2019; 150:064315. [PMID: 30769970 DOI: 10.1063/1.5074199] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The singlet state of nuclear spin-1/2 pairs is protected against many common relaxation mechanisms. Singlet order, which is defined as the population difference between the nuclear singlet and triplet states, usually decays more slowly than the nuclear magnetization. Nevertheless, some decay mechanisms for nuclear singlet order persist. One such mechanism is called scalar relaxation of the second kind (SR2K) and involves the relaxation of additional nuclei ("third spins") which have scalar couplings to the spin-1/2 pair. This mechanism requires a difference between the couplings of at least one third spin with the two members of the spin-1/2 pair, and depends on the longitudinal relaxation time of the third spin. The SR2K mechanism of nuclear singlet relaxation has previously been examined in the case where the relaxation rate of the additional spins is on the time scale of the nuclear Larmor frequency. In this paper, we consider a different regime, in which the longitudinal relaxation of the third spins is on a similar time scale to the J-coupling between the members of the spin pair. This regime is often encountered when the spin-1/2 pair has scalar couplings to nearby deuterium nuclei. We show that the SR2K mechanism may be suppressed in this regime by applying a radiofrequency field which is resonant either with the members of the spin pair, or with the third spins. These phenomena are analyzed theoretically and by numerical simulations, and demonstrated experimentally on a diester of [13C2, 2H2]-labeled fumarate in solution.
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Affiliation(s)
- S J Elliott
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - C Bengs
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - L J Brown
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - J T Hill-Cousins
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - D J O'Leary
- Department of Chemistry, Pomona College, Claremont, California 91711, USA
| | - G Pileio
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - M H Levitt
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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Yang S, McCormick J, Mamone S, Bouchard L, Glöggler S. Nuclear Spin Singlet States in Photoactive Molecules: From Fluorescence/NMR Bimodality to a Bimolecular Switch for Spin Singlet States. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shengjun Yang
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Str. 3A 37075 Göttingen Germany
| | - Jeffrey McCormick
- Department of Chemistry and Biochemistry University of California at Los Angeles Los Angeles CA 90095-1569 USA
| | - Salvatore Mamone
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Str. 3A 37075 Göttingen Germany
| | - Louis‐S. Bouchard
- Department of Chemistry and Biochemistry University of California at Los Angeles Los Angeles CA 90095-1569 USA
| | - Stefan Glöggler
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Str. 3A 37075 Göttingen Germany
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Yang S, McCormick J, Mamone S, Bouchard L, Glöggler S. Nuclear Spin Singlet States in Photoactive Molecules: From Fluorescence/NMR Bimodality to a Bimolecular Switch for Spin Singlet States. Angew Chem Int Ed Engl 2019; 58:2879-2883. [DOI: 10.1002/anie.201814198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/27/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Shengjun Yang
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Str. 3A 37075 Göttingen Germany
| | - Jeffrey McCormick
- Department of Chemistry and Biochemistry University of California at Los Angeles Los Angeles CA 90095-1569 USA
| | - Salvatore Mamone
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Str. 3A 37075 Göttingen Germany
| | - Louis‐S. Bouchard
- Department of Chemistry and Biochemistry University of California at Los Angeles Los Angeles CA 90095-1569 USA
| | - Stefan Glöggler
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Str. 3A 37075 Göttingen Germany
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Kiryutin AS, Panov MS, Yurkovskaya AV, Ivanov KL, Bodenhausen G. Proton Relaxometry of Long-Lived Spin Order. Chemphyschem 2019; 20:766-772. [PMID: 30600920 DOI: 10.1002/cphc.201800960] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/28/2018] [Indexed: 11/06/2022]
Abstract
A study of long-lived spin order in chlorothiophene carboxylates at both high and low magnetic fields is presented. Careful sample preparation (removal of dissolved oxygen in solution, chelating of paramagnetic impurities, reduction of convection) allows one to obtain very long-lived singlet order of the two coupled protons in chlorothiophene derivatives, having lifetimes of about 130 s in D2 O and 240 s in deuterated methanol, which are much longer than the T1 -relaxation times (18 and 30 s, respectively, at a field B 0 =9.4 T). In protonated solvents the relaxation times become shorter, but the lifetime is still substantially longer than T 1 . In addition, long-lived coherences are shown to have lifetimes as long as 30 s. Thiophene derivatives can be used as molecular tags to study slow transport, slow dynamics and slow chemical processes, as has been shown in recent years.
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Affiliation(s)
- Alexey S. Kiryutin
- International Tomography Center SB RAS; Institutskaya 3 A Novosibirsk 630090 Russia
- Novosibirsk State University; Pirogova 2 Novosibirsk 630090 Russia
| | - Mikhail S. Panov
- International Tomography Center SB RAS; Institutskaya 3 A Novosibirsk 630090 Russia
- Novosibirsk State University; Pirogova 2 Novosibirsk 630090 Russia
| | - Alexandra V. Yurkovskaya
- International Tomography Center SB RAS; Institutskaya 3 A Novosibirsk 630090 Russia
- Novosibirsk State University; Pirogova 2 Novosibirsk 630090 Russia
| | - Konstantin L. Ivanov
- International Tomography Center SB RAS; Institutskaya 3 A Novosibirsk 630090 Russia
- Novosibirsk State University; Pirogova 2 Novosibirsk 630090 Russia
| | - Geoffrey Bodenhausen
- Laboratoire des biomolécules; LBM; Département de chimie; École Normale Supérieure; PSL University; Sorbonne Université; CNRS; 24 rue Lhomond 75231 Paris cedex 05 France
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Saul P, Mamone S, Glöggler S. Nuclear singlet multimers (NUSIMERs) with long-lived singlet states. Chem Sci 2019; 10:413-417. [PMID: 30746089 PMCID: PMC6334717 DOI: 10.1039/c8sc02831a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/24/2018] [Indexed: 01/13/2023] Open
Abstract
Magnetic resonance (NMR) is a powerful tool in chemical analysis, structure determination and in medical diagnostics. Developing novel biological sensors for this field holds promise to better investigate protein structures or target diseases more efficiently. Herein, we explore nuclear spin singlet states in dendritic macromolecules as a platform molecule to develop stimuli responsive probes. We have developed a nuclear singlet multimer (NUSIMER) based on a generation 5 poly(amidoamine) dendrimer (PAMAM) which contains on average about 90 accessible nuclear spin singlet states with lifetimes up to 10-fold longer than the T 1 relaxation times (up to 10 seconds T s vs. T 1 < 0.5 seconds) in a single molecule. We demonstrate little influence on the singlet lifetime in phosphate buffer (H2O) and a high viscosity gel environment in the presence of paramagnetic oxygen. Additionally, we demonstrate an increase in singlet lifetime upon the release of a protective chemical moiety from the NUSIMER following a stimulus, whereby no change in longitudinal relaxation time is observed. The robustness and change in singlet lifetime of the NUSIMER holds promise for the development of a novel type of biosensors.
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Affiliation(s)
- Philip Saul
- NMR Signal Enhancement Group , Max-Planck-Institutefor Biophysical Chemistry , Am Faßberg 11 , 37077 Göttingen , Germany .
- Center for Biostructural Imaging of Neurodegeneration of UMG , Von-Siebold-Straße 3A , 37075 Göttingen , Germany
| | - Salvatore Mamone
- NMR Signal Enhancement Group , Max-Planck-Institutefor Biophysical Chemistry , Am Faßberg 11 , 37077 Göttingen , Germany .
- Center for Biostructural Imaging of Neurodegeneration of UMG , Von-Siebold-Straße 3A , 37075 Göttingen , Germany
| | - Stefan Glöggler
- NMR Signal Enhancement Group , Max-Planck-Institutefor Biophysical Chemistry , Am Faßberg 11 , 37077 Göttingen , Germany .
- Center for Biostructural Imaging of Neurodegeneration of UMG , Von-Siebold-Straße 3A , 37075 Göttingen , Germany
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Erriah B, Elliott SJ. Experimental evidence for the role of paramagnetic oxygen concentration on the decay of long-lived nuclear spin order. RSC Adv 2019; 9:23418-23424. [PMID: 35514498 PMCID: PMC9067289 DOI: 10.1039/c9ra03748a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/09/2019] [Indexed: 11/21/2022] Open
Abstract
The sensitivity of longitudinal magnetization and singlet order to relaxation from dissolved paramagnetic oxygen sources in solution is investigated experimentally.
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Affiliation(s)
- Bryan Erriah
- School of Chemistry
- University of Southampton
- Southampton SO17 1BJ
- UK
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12
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Elliott SJ, Kadeřávek P, Brown LJ, Sabba M, Glöggler S, O'Leary DJ, Brown RCD, Ferrage F, Levitt MH. Field-cycling long-lived-state NMR of 15N2 spin pairs. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1543906] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Stuart J. Elliott
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Pavel Kadeřávek
- Laboratoire des Biomolécules, Département de Chimie, Ecole Normale Supérieure, Paris, France
| | - Lynda J. Brown
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Mohamed Sabba
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Stefan Glöggler
- Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration of UMG, Göttingen, Germany
| | - Daniel J. O'Leary
- Department of Chemistry, Pomona College, Claremont, California, United States of America
| | | | - Fabien Ferrage
- Laboratoire des Biomolécules, Département de Chimie, Ecole Normale Supérieure, Paris, France
| | - Malcolm H. Levitt
- School of Chemistry, University of Southampton, Southampton, United Kingdom
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Mamone S, Glöggler S. Nuclear spin singlet states as magnetic on/off probes in self-assembling systems. Phys Chem Chem Phys 2018; 20:22463-22467. [DOI: 10.1039/c8cp04448a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear singlet states in thermo-responsive peptides are introduced as magnetic on/off switches.
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Affiliation(s)
- Salvatore Mamone
- Max Planck Institute for Biophysical Chemistry
- 37077 Göttingen
- Germany
- Center for Biostructural Imaging of Neurodegeneration of UMG
- 37075 Göttingen
| | - Stefan Glöggler
- Max Planck Institute for Biophysical Chemistry
- 37077 Göttingen
- Germany
- Center for Biostructural Imaging of Neurodegeneration of UMG
- 37075 Göttingen
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