Author: "Daniel Abergel" - Searchworks@Jio Institute Digital Library Search Results

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84 results on '"Daniel Abergel"'

1. Dipolar field effects in a solid-state NMR maser pumped by dynamic nuclear polarization

Author: Daniel Abergel and Vineeth Francis Thalakottoor Jose Chacko
Subjects: General Physics and Astronomy, Physical and Theoretical Chemistry
Abstract: We report the observation of pulsed solid state MASER from hyperpolarized proton spin system using Dynamic Nuclear Polarization (DNP) at cryogenic temperature. Induction decays exhibiting multiple asymmetric maser pulses and persistent for tens of second were observed in DNP experiments performed on negatively polarized water samples at cryogenic. These experiments a qualitatively reproduced by simulations of this non-linear spin dynamics by combining the Bloch-Maxwell equations for radiation damping that further incorporate dipolar interactions, on the one hand, and a simplified model of DNP, on the other hand.
Published: 2023

2. Quantitative analysis of cross-talk in partly deuterated samples of nuclear spins hyperpolarized by dynamic nuclear polarization (DNP) in the thermal mixing regime

Author: Bogdan A. Rodin, Vineeth Thalakottoor, Mathieu Baudin, Nicolas Birilirakis, Geoffrey Bodenhausen, Alexandra V. Yurkovskaya, and Daniel Abergel
Subjects: General Physics and Astronomy, Physical and Theoretical Chemistry
Abstract: DNP cross-talk experiments in the thermal mixing regime provide energy transfer rates between the different reservoirs. The dependence of the kinetic parameters on the radical concentration and H/D ratio sheds light onto the nature of “hidden” spins.
Published: 2023

3. Introduction to 'Geoffrey Bodenhausen Festschrift'

Author: Daniel Abergel and Fabien Ferrage
Subjects: Condensed Matter Physics, Atomic and Molecular Physics, and Optics, Analytical Chemistry
Published: 2023

4. Inversion of Hyperpolarized 13C NMR Signals through Cross-Correlated Cross-Relaxation in Dissolution DNP Experiments

Author: Mattia Negroni, David Guarin, Kateryna Che, Ludovica M. Epasto, Ertan Turhan, Albina Selimović, Fanny Kozak, Samuel Cousin, Daniel Abergel, Geoffrey Bodenhausen, and Dennis Kurzbach
Subjects: Materials Chemistry, Physical and Theoretical Chemistry, Surfaces, Coatings and Films
Published: 2022

5. A Toolbox for Glutamine Use in Dissolution Dynamic Nuclear Polarization: from Enzymatic Reaction Monitoring to the Study of Cellular Metabolic Pathways and Imaging

Author: Karen Dos Santos, Gildas Bertho, Cédric Caradeuc, Véronique Baud, Aurélie Montagne, Daniel Abergel, Nicolas Giraud, and Mathieu Baudin
Subjects: Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics
Published: 2023

6. Inversion of Hyperpolarized

Author: Mattia, Negroni, David, Guarin, Kateryna, Che, Ludovica M, Epasto, Ertan, Turhan, Albina, Selimović, Fanny, Kozak, Samuel, Cousin, Daniel, Abergel, Geoffrey, Bodenhausen, and Dennis, Kurzbach
Subjects: Magnetic Resonance Spectroscopy, Solubility, Protons, Magnetic Resonance Imaging
Abstract: Dissolution dynamic nuclear polarization (DDNP) is a versatile tool to boost signal amplitudes in solution-state nuclear magnetic resonance (NMR) spectroscopy. For DDNP, nuclei are spin-hyperpolarized "
Published: 2022

7. Effects of Microwave Gating on Nuclear Spin Echoes in Dynamic Nuclear Polarization

Author: David Guarin, Diego Carnevale, Mathieu Baudin, Philippe Pelupessy, Daniel Abergel, Geoffrey Bodenhausen, Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Gestionnaire, Hal Sorbonne Université
Subjects: Dynamic Nuclear Polarization, [SDV.IB] Life Sciences [q-bio]/Bioengineering, Microwave gating, Quadrupolar echoes, Physics::Medical Physics, Surge of spin echoes, Electron spin relaxation, General Materials Science, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Physical and Theoretical Chemistry, Dipolar echoes, Transverse relaxation, Slump of spin echoes
Abstract: International audience; Dipolar or quadrupolar echoes allow one to observe undistorted powder patterns, in contrast to simple Fourier transformations of free induction decays (FIDs). In this work, the build-up of proton polarization due to dynamic nuclear polarization (DNP) is monitored by observing echoes rather than FIDs. When the microwave irradiation is interrupted during the build-up of DNP, the electrons relax back to their Boltzmann distribution at high fields (B0 = 6.7 T) and low temperatures 1.2 < Tsample < 4.0 K, so that dipolar flip-flop-flip terms involving two electrons and one proton become largely ineffective as a mechanism of proton decoherence. This leads to a prolongation of the nuclear coherence lifetime T2'(1 H). The increase in T2'(1 H) leads to transient surges of the amplitudes of spin echoes. Conversely, transient slumps of spin echoes are observed when the microwave irradiation is switched back on, due to a shortening of nuclear coherence lifetimes.
Published: 2021

8. Reply on RC3

Author: Daniel Abergel
Published: 2021

9. Reply on CC1

Author: Daniel Abergel
Published: 2021

10. Spin relaxation: under the sun, anything new?

Author: Bogdan A. Rodin, Daniel Abergel, nternational Tomography Center (ITC), Novosibirsk State University, Pirogova St. 2, Novosibirsk 630090, Russia, Novosibirsk State University (NSU), Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Abergel, Daniel, Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Physics, [PHYS]Physics [physics], Quantum mechanics, Relaxation (NMR), Master equation, Core (graph theory), [CHIM] Chemical Sciences, Spectral density, [CHIM]Chemical Sciences, Spin relaxation, Quantum, [PHYS] Physics [physics]
Abstract: Spin relaxation has been at the core of many studies since the early days of NMR, and the undelying theory worked out by its founding fathers. However, this theory has been recently questioned (Bengs and Levitt (2020)) in the light of Linblad theory of quantum Markovian master equations. In this article, we review the conventional approach of quantum mechanical theory of NMR relaxation and show that under the usual assumptions, it is equivalent to the Linblad formulation. We also comment on the debate over semi-classical versus quantum versions of spectral density functions involved in relaxation.
Published: 2021

11. Editorial: The Second Intercontinental NMR Conference ICONS2021

Author: Daniel Abergel, Konstantin L. Ivanov, Gerd Buntkowsky, Perunthiruthy K. Madhu, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Technical University Darmstadt (TU), Tata Institute of Fundamental Research, Gestionnaire, Hal Sorbonne Université, Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Technische Universität Darmstadt - Technical University of Darmstadt (TU Darmstadt), and Tata Institute of Fundamental Research [Bangalore]
Subjects: Engineering, business.industry, [SDV]Life Sciences [q-bio], 010402 general chemistry, 01 natural sciences, Data science, Atomic and Molecular Physics, and Optics, 030218 nuclear medicine & medical imaging, 0104 chemical sciences, [SDV] Life Sciences [q-bio], 03 medical and health sciences, 0302 clinical medicine, Editorial, business, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

12. Natural abundance oxygen-17 solid-state NMR of metal organic frameworks enhanced by dynamic nuclear polarization

Author: Diego Carnevale, Geoffrey Bodenhausen, Sujing Wang, Daniel Abergel, Christian Serre, Georges Mouchaham, Mathieu Baudin, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Matériaux Poreux de Paris (IMAP ), Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Mouchaham, Georges
Subjects: Materials science, Diego, General Physics and Astronomy, Protonation, 010402 general chemistry, 01 natural sciences, Magic Angle Spinning, chemistry.chemical_compound, Carnevale, Wang, Baudin, [CHIM]Chemical Sciences, Carboxylate, Physical and Theoretical Chemistry, Polarization (electrochemistry), Bodenhausen, Metal-Organic Frameworks, Sujing, Oxygen-17, Dynamic Nuclear Polarization, [CHIM.MATE] Chemical Sciences/Material chemistry, Mathieu, 010405 organic chemistry, Christian, Chemical shift, Serre, Nuclear magnetic resonance spectroscopy, [CHIM.MATE]Chemical Sciences/Material chemistry, Zirconium-Oxo Clusters, 0104 chemical sciences, Geoffrey, chemistry, Solid-state nuclear magnetic resonance, Chemical physics, Physical chemistry, Oxygen-17 NMR, Metal-organic framework, Density functional theory, Mouchaham, Georges, Solid-State NMR
Abstract: International audience; The 17 O resonances of Zirconium-oxo clusters that can be found in porous Zr carboxylate metal-organic frameworks (MOFs) have been investigated by magic-angle spinning (MAS) NMR spectroscopy enhanced by dynamic nuclear polarization (DNP). High-resolution 17 O spectra at 0.037 % natural abundance could be obtained in 48 hours, thanks to DNP enhancement of the 1 H polarization by factors   = S with /S without = 28, followed by 1 H 17 O cross-polarization, allowing a saving in experimental time by a factor of ca. 800. The distinct 17 O sites from the oxo-clusters can be resolved at 18.8 T. Their assignment is supported by density functional theory (DFT) calculations of chemical shifts and quadrupolar parameters. Protonation of 17 O sites seems to be leading to large characteristic shifts. Markedly, natural abundance 17 O NMR spectra of diamagnetic MOFs can thus be used to probe and characterize the local environment of different 17 O sites on an atomic scale.
Published: 2021

13. Assessing the onset of calcium phosphate nucleation by hyperpolarized real-time NMR

Author: Daniel Abergel, Dennis Kurzbach, Emmanuelle M M Weber, Thierry Azaïs, Thomas Kress, Steffi Sewsurn, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Vienna [Vienna], Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Spectroscopie, Modélisation, Interfaces pour L'Environnement et la Santé (LCMCP-SMiLES), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Abergel, Daniel, Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Calcium Phosphates, Magnetic Resonance Spectroscopy, Time Factors, Chemistry, Precipitation (chemistry), 010401 analytical chemistry, Nucleation, Ionic bonding, 010402 general chemistry, 01 natural sciences, Article, 0104 chemical sciences, Analytical Chemistry, law.invention, Crystal, law, Chemical physics, Phase (matter), [CHIM] Chemical Sciences, [CHIM]Chemical Sciences, Crystallization, Polarization (electrochemistry), Dissolution
Abstract: International audience; We report an experimental approach for highresolution real-time monitoring of transiently formed species occurring during the onset of precipitation of ionic solids from solution. This is made possible by real-time nuclear magnetic resonance (NMR) monitoring using dissolution dynamic nuclear polarization (D-DNP) to amplify signals of functional intermediates and is supported by turbidimetry, cryo-electron microscopy and solid-state NMR measurements. D-DNP can provide drastic signal improvements in NMR signal amplitudes, permitting dramatic reductions in acquisition times and thereby enabling to probe fast interaction kinetics such as those underlying the formation of pre-nucleation species (PNS) that precede solid-liquid phase separation. This experimental strategy allows, at unprecedented detail, for investigation of the formation of calcium phosphate (CaP)-based minerals by 31 P NMR-a process of substantial industrial, geological, and biological interest. So far, many aspects of the mechanisms of CaP nucleation remain unclear due to the absence of experimental methods capable of accessing such processes on sufficiently short time scales. The approach reported here aims to address this by an improved characterization of the initial steps of CaP precipitation, permitting the detection of PNS by NMR and determination of their formation rates, exchange dynamics and sizes. Using D-DNP monitoring, we find that under our conditions i) in the first 2 seconds after preparation of oversaturated calcium phosphate solutions, PNS with a hydrodynamic radius of Rh ≈ 1 nm are formed; and ii) following this rapid initial formation, the entire crystallization processes proceed on considerably longer timescales, requiring > 20 s to form the final crystal phase.
Published: 2020

14. Rates of Chemical Reactions Embedded in a Metabolic Network by Dissolution Dynamic Nuclear Polarisation NMR

Author: Aditya Jhajharia, Aude Sadet, Daniel Abergel, Dennis Kurzbach, Emeric Miclet, Geoffrey Bodenhausen, Emmanuelle M. M. Weber, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Structure et Dynamique des Biomolécules (LBM-E3), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0301 basic medicine, Magnetic Resonance Spectroscopy, Metabolic network, 010402 general chemistry, Gluconates, 01 natural sciences, Chemical reaction, Catalysis, Pentose Phosphate Pathway, Reaction rate, 03 medical and health sciences, Hydrolysis, Computational chemistry, [CHIM]Chemical Sciences, Dissolution, Chemistry, Organic Chemistry, Dynamic nuclear polarisation, General Chemistry, 0104 chemical sciences, Kinetics, 030104 developmental biology, Solubility, Scientific method, Isomerization, Metabolic Networks and Pathways
Abstract: International audience; The isomerisation of 6-phosphogluconolactones and their hydrolyses into 6-phosphogluconic acid form a non enzymatic side cycle of the pentose-phosphate pathway (PPP) in cells. We show that dissolution dynamic nuclear polarization can be used for determining the kinetic rates of the involved transformations in real time. It is found that the hydrolysis of both lactones is significantly slower than the isomeration process, thereby shedding new light onto this subtle chemical process.
Published: 2018

15. Characterizing Thermal Mixing Dynamic Nuclear Polarization via Cross-Talk between Spin Reservoirs

Author: Geoffrey Bodenhausen, Dennis Kurzbach, David Guarin, Konstantin L. Ivanov, Alberto Rosso, Daniel Abergel, Sina Marhabaie, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Novosibirsk State University (NSU), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Chemistry, Radical, Physics::Medical Physics, Time evolution, Analytical chemistry, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, Polarization (waves), 01 natural sciences, Nitroxide radical, 0104 chemical sciences, Magnetic field, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Chemical physics, Thermal, General Materials Science, Hyperpolarization (physics), Physical and Theoretical Chemistry, 0210 nano-technology, Spectroscopy
Abstract: International audience; Dynamic nuclear polarization (DNP) embraces a family of methods to increase signal intensities in nuclear magnetic resonance (NMR) spectroscopy. Despite extensive theoretical work that allows one to distinguish at least five distinct mechanisms, it remains challenging to determine the relative weights of the processes that are responsible for DNP in state-of-the-art experiments operating with stable organic radicals like nitroxides at high magnetic fields and low temperatures. Specifically, determining experimental conditions where DNP involves thermal mixing, which denotes a spontaneous heat exchange between different spin reservoirs, remains challenging. We propose an experimental approach to ascertain the prevalence of the thermal mixing regime by monitoring characteristic signature properties of the time evolution of the hyperpolarization. We find that thermal mixing is the dominant DNP mechanism at high nitroxide radical concentrations, while a mixture of different mechanisms prevails at lower concentrations.
Published: 2017

16. Single-Scan 13 C Diffusion-Ordered NMR Spectroscopy of DNP-Hyperpolarised Substrates

Author: Dennis Kurzbach, Daniel Abergel, Ludmilla Guduff, Carine van Heijenoort, Jean-Nicolas Dumez, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)
Subjects: 010405 organic chemistry, Chemistry, Orders of magnitude (temperature), Organic Chemistry, Dynamic nuclear polarisation, Analytical chemistry, General Chemistry, Fluorine-19 NMR, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, 01 natural sciences, Signal, Catalysis, Spectral line, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Nuclear magnetic resonance, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Transverse relaxation-optimized spectroscopy, Diffusion (business)
Abstract: International audience; Diffusion-ordered NMR spectroscopy (DOSY) is a powerful approach for the analysis of molecular mixtures, yet its application range is limited by the relatively low sensitivity of NMR. We show here that spectrally resolved 13 C DOSY data can be collected, in a single scan, for substrates hyperpolarised by dissolution dynamic nuclear polarisation (D-DNP), which provides signal enhancements of several orders of magnitude. For this we use a convection-compensation pulse scheme, which we also analyse by numerical simulation. The proposed method further allows the acquisition of several consecutive DOSY spectra in a single D-DNP experiment.
Published: 2017

17. Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions

Author: Marco Gerolin, Paolo Calligari, Daniel Abergel, Antonino Polimeno, Dipartimento di Scienze Chimiche [Padova], Università degli Studi di Padova = University of Padua (Unipd), Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Universita degli Studi di Padova, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: 0301 basic medicine, Quantitative Biology::Biomolecules, Theoretical computer science, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 010304 chemical physics, Basis (linear algebra), Cross-correlation, Chemistry, Structure (category theory), Proteins, Domain decomposition methods, Molecular Dynamics Simulation, 01 natural sciences, Computer Science Applications, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Quantitative Biology::Subcellular Processes, Distance correlation, 03 medical and health sciences, 030104 developmental biology, Protein structure, 0103 physical sciences, Decomposition (computer science), Physical and Theoretical Chemistry, Biological system, Cluster analysis
Abstract: International audience; In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pairwise correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure, illustrate the approach proposed.
Published: 2016

18. A DNP-hyperpolarized solid-state water NMR MASER: observation and qualitative analysis

Author: Emmanuelle M. M. Weber, Dennis Kurzbach, Daniel Abergel, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Physics, Magnetization dynamics, Spins, Time evolution, General Physics and Astronomy, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, 0104 chemical sciences, law.invention, Magnetic field, Magnetization, Radiation damping, law, Stimulated emission, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Physical and Theoretical Chemistry, Atomic physics, Maser, 0210 nano-technology
Abstract: International audience; We present observations of an NMR MASER (microwave amplification by stimulated emission of radiation) of hyperpolarized 1H nuclei by dynamic nuclear polarization (DNP) at 1.2 K and in a magnetic field of 6.7 T. The sustained maser pulses originate from the interplay between radiation damping (RD) due to the large 1H magnetization, and the remagnetization to a negative value by the DNP process. NMR signals lasting for several tens of seconds are thus observed on an ensemble of dipolar-coupled nuclear spins. Magnetization dynamics are analyzed in terms of the combined Bloch–Maxwell and Provotorov (BMP) equations for RD and DNP. Insight into the long time evolution of the magnetization is provided by a theoretical analysis of this nonlinear dynamical system, and by fitting the NMR signal to a simplified version of the BMP equations.
Published: 2019

19. Stochastic modeling of macromolecules in solution. II. Spectral densities

Author: Daniel Abergel, Mirco Zerbetto, Antonino Polimeno, Dipartimento di Scienze Chimiche [Padova], and Universita degli Studi di Padova
Subjects: Physics, Coupling, 010304 chemical physics, Stochastic process, Degrees of freedom (physics and chemistry), General Physics and Astronomy, Dissipation, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Simple (abstract algebra), Orientation (geometry), 0103 physical sciences, Relaxation (approximation), Statistical physics, Physical and Theoretical Chemistry, Brownian motion
Abstract: In Paper I [Polimeno et al., J. Chem. Phys. 150, 184107 (2019)], we proposed a general approach for interpreting relaxation properties of a macromolecule in solution, derived from an atomistic description. A simple scheme (the semiflexible Brownian, SFB, model) has been defined for the case of limited internal flexibility, but retaining full coupling with external degrees of freedom, inclusion of all of the momenta, and dissipation. Here we discuss the application of the SFB model to the practical evaluation of orientation spectral densities, based on two complementary computational treatments.
Published: 2019

20. Transport of hyperpolarized samples in dissolution-DNP experiments

Author: Dennis Kurzbach, Alexandra V. Yurkovskaya, Konstantin L. Ivanov, Geoffrey Bodenhausen, Bogdan A. Rodin, Alexey S. Kiryutin, Sami Jannin, David Guarin, Daniel Abergel, Novosibirsk State University (NSU), University of Vienna [Vienna], Centre de RMN à très hauts champs de Lyon (CRMN), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des biomolécules (LBM UMR 7203), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Physics, Field cycling, General Physics and Astronomy, Spin hamiltonian, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, Polarization (waves), 01 natural sciences, Molecular physics, 0104 chemical sciences, Magnet, Singlet state, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Physical and Theoretical Chemistry, 0210 nano-technology, Adiabatic process, Multiplet, Dissolution
Abstract: International audience; Dissolution dynamic nuclear polarization (D-DNP) experiments rely on the transfer of a sample between two high-field magnets. During this transfer, samples might experience passage through regions where the stray fields of the magnets are very weak, can approach zero, and even change their sign. This can lead to unexpected spectral features in spin systems that undergo transitions from weak-to strong-coupling regimes and vice versa, much like in field cycling nuclear magnetic resonance experiments. We herein demonstrate that the spectral features observed in D-DNP experiments can be rationalized, provided the time-dependence of the spin Hamiltonian upon field cycling is sufficiently adiabatic. Under such conditions, a passage through a weak static field can lead to the emergence of a long-lived state (LLS) based on an imbalance between the populations of singlet and triplet states in pairs of nuclei that are strongly coupled during the passage through low field. The LLS entails the appearance of anti-phase multiplet components upon transfer to a high-field magnet for observation of NMR signals.
Published: 2019
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21. Reifung von Proben beeinflusst die Effizienz der Kernpolarisation

Author: Dennis Kurzbach, Geoffrey Bodenhausen, Hervé Vezin, Daniel Abergel, Giuseppe Sicoli, Ghislaine Frébourg, Emmanuelle M. M. Weber, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), Microscopie Electronique [IBPS] (IBPS-ME), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), European Project: 339754,EC:FP7:ERC,ERC-2013-ADG,DILUTEPARAWATER(2014), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Phasentrennung, Kernspinresonanz, Nanophasen, 02 engineering and technology, General Medicine, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], 010402 general chemistry, 021001 nanoscience & nanotechnology, 0210 nano-technology, 01 natural sciences, Dynamische Kernpolarisation, 0104 chemical sciences
Abstract: International audience; Mischungen von Wasser und Glycerin sind populäre Matrizen für die Tieftemperaturspektroskopie verglaster Proben. Allerdings besitzen solche Mischungen konterintuitive Eigenschaften, wie spontane Nanophasenseparation in Lösungen, die makroskopisch homogen scheinen. Wir zeigen hier, dass solche Phänomene die Effizienz der dynamischen Kernpolarisation stark beeinflussen können, durch Fluktuation der lokalen Konzentration der Polarisationsmittel (Radikale) um bis zu 20 %. Spontane Nanophasenseparationen, die auf Zeitskalen von 30–60 min stattfinden, resultieren in lokalen wasserreichen Einschlüssen mit erhöhter Radikalkonzentration. Solche Phänomene wurden für die drei häufigen Polarisationsmittel TEMPOL, AMUPol und Trityl beobachtet.
Published: 2018

22. Targeting the Pentose Phosphate Pathway: Characterization of a New 6PGL Inhibitor

Author: Jamal Ouazzani, Philippe Lopes, Daniel Abergel, Paolo Calligari, Anh Tuan Tran, Matthieu Sollogoub, Emeric Miclet, Aude Sadet, Gestionnaire, HAL Sorbonne Université 5, Institut Parisien de Chimie Moléculaire (IPCM), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des biomolécules (LBM UMR 7203), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma Tor Vergata [Roma], Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Université Pierre et Marie Curie - Paris 6 (UPMC)-ESPCI ParisTech-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-ESPCI ParisTech-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), PSL Research University (PSL), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Neurobiologie des Réseaux Sensorimoteurs (LNRS), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5), Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Biomolécules : synthèse, structure et mode d'action (UMR 8642) (BIOSYMA), and École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Models, Molecular, 0301 basic medicine, Drug, Lactams, media_common.quotation_subject, [CHIM.THER] Chemical Sciences/Medicinal Chemistry, Trypanosoma brucei brucei, Biophysics, Dehydrogenase, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Trypanosoma brucei, Pentose phosphate pathway, Gluconates, 01 natural sciences, Substrate Specificity, Pentose Phosphate Pathway, 03 medical and health sciences, 0103 physical sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Glycolysis, Enzyme Inhibitors, ComputingMilieux_MISCELLANEOUS, media_common, chemistry.chemical_classification, 010304 chemical physics, biology, Chemistry, Phosphogluconate Dehydrogenase, Proteins, biology.organism_classification, 3. Good health, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, Enzyme, Biochemistry, Drug development, Docking (molecular), Carboxylic Ester Hydrolases
Abstract: International audience; Human African trypanosomiasis, or sleeping sickness, is a lethal disease caused by the protozoan parasite Trypanosoma brucei. However, although many efforts have been made to understand the biochemistry of this parasite, drug development has led to treatments that are of limited efficiency and of great toxicity. To develop new drugs, new targets must be identified, and among the several metabolic processes of trypanosomes that have been proposed as drug targets, carbohydrate metabolism (glycolysis and the pentose phosphate pathway (PPP)) appears as a promising one. As far as the PPP is concerned, a limited number of studies are related to the glucose-6-phosphate dehydrogenase. In this work, we have focused on the activity of the second PPP enzyme (6-phospho-gluconolactonase (6PGL)) that transforms 6-phosphogluconolactone into 6-phosphogluconic acid. A lactam analog of the natural substrate has been synthesized, and binding of the ligand to 6PGL has been investigated by NMR titration. The ability of this ligand to inhibit 6PGL has also been demonstrated using ultraviolet experiments, and protein-inhibitor interactions have been investigated through docking calculations and molecular dynamics simulations. In addition, a marginal inhibition of the third enzyme of the PPP (6-phosphogluconate dehydrogenase) was also demonstrated. Our results thus open new prospects for targeting T. brucei.
Published: 2018

23. Relaxation of long-lived modes in NMR of deuterated methyl groups

Author: Daniel Abergel, Thomas Kress, Geoffrey Bodenhausen, Dennis Kurzbach, Mathieu Baudin, David Guarin, Konstantin L. Ivanov, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk State University (NSU), Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), and Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Physics, 010304 chemical physics, Spin states, Dynamic nuclear polarisation, General Physics and Astronomy, Symmetry group, 010402 general chemistry, Polarization (waves), 01 natural sciences, Molecular physics, 0104 chemical sciences, Deuterium, Irreducible representation, 0103 physical sciences, Molecule, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Physical and Theoretical Chemistry, Order of magnitude
Abstract: International audience; Long-lived imbalances of spin state populations can circumvent fast quadrupolar relaxation by reducing effective longitudinal relaxation rates by about an order of magnitude. This opens new avenues for the study of dynamic processes in deuterated molecules. Here we present an analysis of the relaxation properties of deuterated methyl groups CD3. The number of coupled equations that describe cross-relaxation between the 27 symmetry-adapted spin states of a D3 system can be reduced to only 2 non-trivial “lumped modes” by (i) taking the sums of the populations of all states that equilibrate rapidly within each irreducible representation of the symmetry group, and (ii) by combining populations that have similar relaxation rates although they belong to different irreducible representations. The quadrupolar relaxation rates of the spin state imbalances in CD3 groups are determined not by the correlation time of overall tumbling of the molecule, but by the frequency of jumps of methyl groups about their three-fold symmetry axis. We access these states via dissolution dynamic nuclear polarization (D-DNP), a method that allows one to populate the desired long-lived states at cryogenic temperatures and their subsequent detection at ambient temperatures after rapid dissolution. Experimental examples of DMSO-d6 and ethanol-d6 demonstrate that long-lived deuterium spin states are indeed accessible and that their lifetimes can be determined. Our analysis of the system via “lumped” modes allows us to visualize different possible spin-state populations of symmetry A, B, or E. Thus, we identify a long-lived spin state involving all three deuterons in a CD3 group as an A/E imbalance that can be populated through DNP at low temperatures.
Published: 2018

24. Sample Ripening through Nanophase Separation Influences the Performance of Dynamic Nuclear Polarization

Author: Ghislaine Frébourg, Emmanuelle M. M. Weber, Geoffrey Bodenhausen, Daniel Abergel, Dennis Kurzbach, Giuseppe Sicoli, Hervé Vezin, Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Chimie Moléculaire de Paris Centre (FR 2769), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Lille, CNRS, Laboratoire des biomolécules [LBM UMR 7203], Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement (LASIRE) - UMR 8516, and Université Pierre et Marie Curie - Paris 6 [UPMC]
Subjects: Materials science, Radical, Vesicle, 02 engineering and technology, General Chemistry, 010402 general chemistry, 021001 nanoscience & nanotechnology, 01 natural sciences, Catalysis, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Dynamic nuclear polarization, nanophases, nuclear magnetic resonance, phase separation, chemistry.chemical_compound, chemistry, Homogeneous, Chemical physics, Phase (matter), Glycerol, 0210 nano-technology, Polarization (electrochemistry), Spectroscopy, Nanoscopic scale
Abstract: International audience; Mixtures of water and glycerol provide popular matrices for low‐temperature spectroscopy of vitrified samples. However, they involve counterintuitive physicochemical properties, such as spontaneous nanoscopic phase separations (NPS) in solutions that appear macroscopically homogeneous. We demonstrate that such phenomena can substantially influence the efficiency of dynamic nuclear polarization (DNP) by factors up to 20 % by causing fluctuations in local concentrations of polarization agents (radicals). Thus, a spontaneous NPS of water/glycerol mixtures that takes place on time scales on the order of 30–60 min results in a confinement of polarization agents in nanoscopic water‐rich vesicles, which in return affects the DNP. Such effects were found for three common polarization agents, TEMPOL, AMUPol and Trityl.
Published: 2018

25. Frontispiece: Single-Scan 13 C Diffusion-Ordered NMR Spectroscopy of DNP-Hyperpolarised Substrates

Author: Ludmilla Guduff, Carine van Heijenoort, Daniel Abergel, Jean-Nicolas Dumez, and Dennis Kurzbach
Subjects: Nuclear magnetic resonance, Chemistry, Organic Chemistry, Dynamic nuclear polarisation, General Chemistry, Nuclear magnetic resonance spectroscopy, Single scan, Diffusion (business), Catalysis
Published: 2017

26. Single-Scan

Author: Ludmilla, Guduff, Dennis, Kurzbach, Carine, van Heijenoort, Daniel, Abergel, and Jean-Nicolas, Dumez
Abstract: Diffusion-ordered NMR spectroscopy (DOSY) is a powerful approach for the analysis of molecular mixtures, yet its application range is limited by the relatively low sensitivity of NMR. We show here that spectrally resolved
Published: 2017

27. Anisotropic longitudinal electronic relaxation affects DNP at cryogenic temperatures

Author: Dennis Kurzbach, Daniel Abergel, Hervé Vezin, Geoffrey Bodenhausen, Emmanuelle M. M. Weber, James G. Kempf, Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL)-Institut de Chimie du CNRS (INC)-Université de Lille, Bruker BioSpin, GmbH, Université de Lille, CNRS, Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 [LASIRE], Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL)
Subjects: [PHYS]Physics [physics], Nitroxide mediated radical polymerization, Condensed matter physics, Chemistry, Radical, Relaxation (NMR), General Physics and Astronomy, 02 engineering and technology, 010402 general chemistry, 021001 nanoscience & nanotechnology, Polarization (waves), 01 natural sciences, 0104 chemical sciences, law.invention, Magnetic field, law, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry, Diffusion (business), 0210 nano-technology, Electron paramagnetic resonance, Anisotropy
Abstract: International audience; We report the observation of anisotropic longitudinal electronic relaxation in nitroxide radicals under typical dynamic nuclear polarization conditions. This anisotropy affects the efficiency of dynamic nuclear polarization at cryogenic temperatures of 4 K and high magnetic fields of 6.7 T. Under our experimental conditions, the electron paramagnetic resonance spectrum of nitroxides such as TEMPOL (4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl) is only partly averaged by electronic spectral diffusion, so that the relaxation times T 1e (o) vary across the spectrum. We demonstrate how the anisotropy of T 1e (o) can be taken into account in simple DNP models.
Published: 2017

28. Multiple Scale Dynamics in Proteins Probed at Multiple Time Scales through Fluctuations of NMR Chemical Shifts

Author: Daniel Abergel, Paolo Calligari, and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Materials Chemistry2506 Metals and Alloys, Diffusion, Models, Theoretical, Molecular Dynamics Simulation, Nuclear Magnetic Resonance, Biomolecular, Proteins, Time Factors, Physical and Theoretical Chemistry, Surfaces, Coatings and Films, Medicine (all), Work (thermodynamics), Nuclear Magnetic Resonance, 010402 general chemistry, 01 natural sciences, Power law, Coatings and Films, 03 medical and health sciences, Molecular dynamics, Nuclear magnetic resonance, Theoretical, Models, Materials Chemistry, Statistical physics, 030304 developmental biology, 0303 health sciences, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Chemistry, Stochastic process, Chemical shift, Relaxation (NMR), Resonance, 0104 chemical sciences, Surfaces, Correlation function (statistical mechanics), Biomolecular
Abstract: Fluctuations of NMR resonance frequency shifts and their relation with protein exchanging conformations are usually analyzed in terms of simple two-site jump processes. However, this description is unable to account for the presence of multiple time scale dynamics. In this work, we present an alternative model for the interpretation of the stochastic processes underlying these fluctuations of resonance frequencies. Time correlation functions of 15 N amide chemical shifts computed from molecular dynamics simulations (MD) were analyzed in terms of a transiently fractional diffusion process. The analysis of MD trajectories spanning dramatically different time scales (∼200 ns and 1 ms (Shaw, D. E.; et al. Science 2010, 330, 341−346)) allowed us to show that our model could capture the multiple scale structure of chemical shift fluctuations. Moreover, the predicted exchange contribution Rex to the NMR transverse relaxation rate is in qualitative agreement with experimental results. These observations suggest that the proposed fractional diffusion model may provide significative improvement to the analysis of NMR dispersion experiments. relaxation. 17 In this paper, we investigate the stochastic properties of the fluctuations of the nuclei frequencies at a more fundamental level. We present a combined analysis of chemical shift trajectories computed from a 1 ms MD trajectory of the small protein BPTI, 16 together with a short 200 ns simulation of the same protein performed by us in similar conditions. Chemical shift correlation functions computed from these trajectories are analyzed in terms of a transiently fractional diffusion process. We show that, when quality permits, data are consistent with a variable order fractional diffusion equation. 18 Moreover, in these favorable cases, similar fractional orders are found in both simulations. This suggests that in spite of the dramatically different sampling rates (2 ps and 25 ns) and lengths (200 ns and 1 ms), the same fractional structure of stochastic process underlying the chemical shift fluctuations can be identified. Such processes imply a distribution of time scales, as typically occurs in complex systems, 19 and associated with a power law decay of the correlation function. However, this kind of decay occurs at intermediate rather than asymptotically long
Published: 2014

29. Stochastic modeling of macromolecules in solution. I. Relaxation processes

Author: Daniel Abergel, Antonino Polimeno, Mirco Zerbetto, Dipartimento di Scienze Chimiche [Padova], Universita degli Studi di Padova, Laboratoire des biomolécules (LBM UMR 7203), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Physics, 010304 chemical physics, Continuum (measurement), Stochastic process, General Physics and Astronomy, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, symbols.namesake, 0103 physical sciences, Dissipative system, symbols, Fokker–Planck equation, Statistical physics, Physical and Theoretical Chemistry, Hamiltonian (quantum mechanics), Macromolecule
Abstract: International audience; A framework for the stochastic description of relaxation processes in flexible macro-molecules, including dissipative effects, is introduced, from an atomistic point of view. Projection-operator techniques are employed to obtain multidimensional Fokker-Planck operators governing the relaxation of internal coordinates and global degrees of freedom, and depending upon parameters fully recoverable from classic force fields (energetics) and continuum models (friction tensors). A hierarchy of approaches of different complexity is proposed in this unified context, aimed primarily at the interpretation of magnetic resonance relaxation experiments. In particular, a model based on a harmonic internal Hamiltonian is discussed as a test case.
Published: 2019

30. Structure, Dynamics and Thermodynamics of the Human Centrin 2/hSfi1 Complex

Author: Geoffrey Bodenhausen, Liliane Assairi, Liliane Mouawad, Constantin T. Craescu, Daniel Abergel, Fatiha Kateb, Yves Blouquit, Juan Martinez-Sanz, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Biomolécules : synthèse, structure et mode d'action (UMR 8642) (BIOSYMA), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Curie [Paris], Imagerie intégrative de la molécule à l'organisme, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences et d'ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Université Pierre et Marie Curie - Paris 6 (UPMC), Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), and École normale supérieure - Paris (ENS-PSL)
Subjects: Models, Molecular, Magnetic Resonance Spectroscopy, human centrin 2, Cell Cycle Proteins, Peptide, Crystallography, X-Ray, Protein Structure, Secondary, 0302 clinical medicine, Structural Biology, Sfi1, chemistry.chemical_classification, 0303 health sciences, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Hydrogen bond, Backbone Dynamics, Solutions, Biochemistry, Thermodynamics, Molecular-Cloning, Two-dimensional nuclear magnetic resonance spectroscopy, Heteronuclear single quantum coherence spectroscopy, Protein Binding, Repetitive Sequences, Amino Acid, DNA repair, Quantum Nmr-Spectroscopy, Excision-Repair, Molecular Sequence Data, Calorimetry, Biology, Group-C Protein, 03 medical and health sciences, multiple-quantum relaxation, Chlamydomonas-Reinhardtii, Mitotic Spindle Poles, Humans, Chemical-Shift Modulations, Amino Acid Sequence, Molecular Biology, 030304 developmental biology, Binding Sites, Cross-Correlated Relaxation, Calcium-Binding Proteins, Itc, Nmr, chemistry, Centrosome, Centrin, Pole Body Duplication, Biophysics, Calcium, Peptides, 030217 neurology & neurosurgery, Nucleotide excision repair
Abstract: Centrin, an EF-hand calcium-binding protein, has been shown to be involved in the duplication of centrosomes, and Sfi1 (Suppressor of fermentation-induced loss of stress resistance protein 1) is one of its centrosomal targets. There are three isoforms of human centrin, but here we only considered centrin 2 (HsCen2). This protein has the ability to bind to any of the similar to 25 repeats of human Sfi1 (hSfi1) with more or less affinity. In this study, we mainly focused on the 17th repeat (R17-hSfi1-20), which presents the highest level of similarity with a well-studied 17-residue peptide (P17-XPC) from human xeroderma pigmentosum complementation group C protein, another centrin target for DNA repair. The only known structure of HsCen2 was resolved in complex with P17-XPC. The 20-residue peptide R17-hSfi1-20 exhibits the motif L8L4W1, which is the reverse of the XPC motif, W1L4L8. Consequently, the dipole of the helix formed by this motif has a reverse orientation. We wished to ascertain the impact of this reversal on the structure, dynamics and affinity of centrin. To address this question, we determined the structure of C-HsCen2 [the C-terminal domain of HsCen2 (T94-Y172)] in complex with R17-hSfi1-20 and monitored its dynamics by NMR, after having verified that the N-terminal domain of HsCen2 does not interact with the peptide The structure shows that the binding mode is similar to that of P17-XPC. However, we observed a 2 -angstrom translation of the R17-hSfi1-20 helix along its axis, inducing less anchorage in the protein and the disruption of a hydrogen bond between a tryptophan residue in the peptide and a well-conserved nearby glutamate in C+HsCen2. NMR dynamic studies of the complex strongly suggested the existence of an unusual calcium secondary binding mode in calcium-binding loop III made possible by the uncommon residue composition of this loop. The secondary metal site is only populated at high calcium concentration and depends on the type of bound ligand. (C) 2009 Elsevier Ltd. All rights reserved
Published: 2010

31. Generating spin turbulence through nonlinear excitation in liquid-state NMR

Author: Daniel Abergel, Alain Louis-Joseph, and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Nuclear and High Energy Physics, Magnetic Resonance Spectroscopy, Field (physics), Radio Waves, Biophysics, Chaotic, 02 engineering and technology, Sensitivity and Specificity, 01 natural sciences, Biochemistry, Magnetics, Magnetization, 0103 physical sciences, 010306 general physics, Spin-½, Physics, Radiation, Condensed matter physics, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Turbulence, Equipment Design, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Liquid Crystals, Computational physics, Kinetics, Nonlinear system, Radiation damping, Nonlinear Dynamics, Bloch equations, Electronics, 0210 nano-technology
Abstract: International audience; Chaotic dynamics of a water magnetization in a 600 MHz NMR spectrometer was generated by a radiation damping-based electronic feedback. Erratic induction signal was observed for several tens of seconds. The analysis of the data shows that this chaotic behaviour can be ascribed to spin turbulence in the sample and that a simpler model based on the three-dimensional Bloch equations modified to include a feedback field may not account for the experimental data.
Published: 2009

32. Toward Quantitative Measurements of Enzyme Kinetics by Dissolution Dynamic Nuclear Polarization

Author: Emeric Miclet, Geoffrey Bodenhausen, Jonas Milani, Sami Jannin, Daniel Abergel, Aurélien Bornet, Université Pierre et Marie Curie - Paris 6 (UPMC), Synthèse, Structure et Fonction de Molécules Bioactives (SSFMB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences et d'ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL)-Batochime, Swiss National Science Foundation, Ecole Polytechnique Federale de Lausanne (EPFL), Swiss Commission for Technology and Innovation (CTI), Bruker BioSpin Switzerland AG, French CNRS, and European Research Council (ERC)
Subjects: chemistry.chemical_classification, Hexokinase, Kinetics, Catalysis, chemistry.chemical_compound, Enzyme, Biochemistry, chemistry, Glucose 6-phosphate, Biophysics, General Materials Science, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Enzyme kinetics, Physical and Theoretical Chemistry, Polarization (electrochemistry), Dissolution
Abstract: International audience; Dissolution dynamic nuclear polarization (D-DNP) experiments enabled us to study the kinetics of the enzymatic phosphorylation reaction of glucose to form glucose-6-phosphate (G6P) by hexokinase (HK), with or without the presence of an excess of G6P, which is known to be an inhibitor of the enzyme. Against all expectations, our observations demonstrate that the phosphorylation of both alpha and beta glucose anomers occurs with comparable kinetics. The catalytic constant of the reaction was estimated based on a simple kinetic model tailored for hyperpolarized systems.
Published: 2015

33. Slow Backbone Dynamics of the C-Terminal Fragment of Human Centrin 2 in Complex with a Target Peptide Probed by Cross-Correlated Relaxation in Multiple-Quantum NMR Spectroscopy

Author: Geoffrey Bodenhausen, Constantin T. Craescu, Daniel Abergel, Fatiha Kateb, Patricia Duchambon, and Yves Blouquit
Subjects: Models, Molecular, DNA Repair, Fragment (computer graphics), Chemistry, Calcium-Binding Proteins, Dynamics (mechanics), Relaxation (NMR), Cell Cycle Proteins, Target peptide, Nuclear magnetic resonance spectroscopy, Biochemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Structure-Activity Relationship, Crystallography, Terminal (electronics), Centrin, Humans, Transverse relaxation-optimized spectroscopy, Nuclear Magnetic Resonance, Biomolecular, DNA Damage
Abstract: The C-terminal domain of human centrin 2 (C-HsCen2) strongly binds to P1-XPC, a peptide comprising 17 amino acids with a NWKLLAKGLLIRERLKR sequence. This peptide corresponds to residues N847-R863 of XPC, a protein involved in the recognition of damaged DNA during the initial step of the nucleotide excision repair pathway. The slow internal dynamics of the protein backbone in the C-HsCen-P1-XPC complex was studied by measuring the relaxation rates of zero- and double-quantum coherences involving neighboring pairs of carbonyl 13C and amide 15N nuclei. These relaxation rates, which reflect dynamics on time scales in the range of micro- to milliseconds, vary significantly along the protein backbone. Analysis of the relaxation rates at different CaCl2 concentrations and ionic strengths shows that these slow motions are mainly affected by the binding of a Ca2+ ion to the lower-affinity EF-hand III. Moreover, we discuss the possible functional role of residues that undergo differential exchange in the formation of HsCen homodimers.
Published: 2006

34. A Markov Model for Relaxation and Exchange in NMR Spectroscopy

Author: Daniel Abergel and Arthur G. Palmer
Subjects: Physics, Magnetic Resonance Spectroscopy, Laplace transform, Condensed matter physics, Markov chain, Kinetics, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, Markov model, 01 natural sciences, Markov Chains, 030218 nuclear medicine & medical imaging, 0104 chemical sciences, Surfaces, Coatings and Films, Perturbation expansion, 03 medical and health sciences, 0302 clinical medicine, Lattice (order), Materials Chemistry, Statistical physics, Physical and Theoretical Chemistry, Resolvent
Abstract: A two-state Markov noise process for lattice fluctuations and chemical exchange dynamics is used to derive a stochastic Liouville equation describing the evolution of the spin-density operator in nuclear magnetic resonance spectroscopy. Relaxation through lattice fluctuations and chemical exchange processes is incorporated into the theory at the same fundamental level, and the results are valid for all time scales provided that lattice fluctuations are much faster than chemical exchange kinetics. Time-scale separation emerges as an essential feature from the lowest-order perturbation expansion of the average resolvent in the Laplace domain.
Published: 2005

35. A simple model for NMR relaxation in the presence of internal motions with dynamical coupling

Author: Daniel Abergel and Geoffrey Bodenhausen
Subjects: Physics, Coupling, Nuclear magnetic resonance, Classical mechanics, Order (biology), Simple (abstract algebra), Differential equation, Ordinary differential equation, General Physics and Astronomy, Limit (mathematics), Physical and Theoretical Chemistry, Small amplitude
Abstract: In this paper some effects of dynamical coupling between two interaction-carrying vectors on the internal auto- and cross-correlation functions are investigated in the limit of small amplitude motions. A linearized Langevin approach allows the derivation of explicit expressions for these correlation functions and for the corresponding order parameters. [on SciFinder (R)]
Published: 2004

36. Cross-correlated relaxation in NMR of macromolecules in the presence of fast and slow internal dynamics

Author: Boris E. Vugmeister, Geoffrey Bodenhausen, Liliya Vugmeyster, Philippe Pelupessy, and Daniel Abergel
Subjects: Physics, Coupling (physics), Work (thermodynamics), Condensed matter physics, Chemical physics, Dynamics (mechanics), Relaxation (NMR), Internal rotation, General Engineering, Energy Engineering and Power Technology, Spin relaxation, Macromolecule
Abstract: We present an anal. of correlation and spectral d. functions involved in autorelaxation and cross-correlated relaxation in the magnetic resonance of macromols. Internal dynamics of the macromol. are described in terms of 2 distinct fluctuation processes with different, slow and fast, correlation times. The approach developed in this work takes into account the possible coupling between both fluctuating internal processes. [on SciFinder (R)]
Published: 2004

37. Nonlinear dynamics of a magnetization subject to RF feedback field: new experimental evidence

Author: Jean-Yves Lallemand, Alain Louis-Joseph, and Daniel Abergel
Subjects: Magnetization, Nonlinear system, Amplitude, Radiation damping, Field (physics), law, Bloch equations, General Chemical Engineering, General Chemistry, Maser, Radiation, Computational physics, law.invention
Abstract: In a recent study, the dynamics of large magnetization subject to a RF feedback field from the detection circuit of the probe was investigated both theoretically and experimentally. A simple model including non-linear modification of the Bloch equations allowed us to predict the occurrence of repeated bursts of NMR transverse magnetization during evolution (named self-sustained maser pulses). However, the decay of the amplitude of these repeated maser pulses with a characteristic time 4T1 predicted by this simple model could not be observed and the experiments showed a regime of non-attenuated self-sustained maser pulses. This was interpreted as a direct consequence of B0 inhomogeneities. In this paper we present new experimental evidence that support this assumption and that further demonstrate the role of B0 inhomogeneity. To cite this article : A. Louis-Joseph et al., C. R. Chimie 7 (2004).
Published: 2004

38. An average-magnetization analysis of R 1ρ relaxation outside of the fast exchange limit

Author: Daniel Abergel, Oleg Trott, and Arthur G. Palmer
Subjects: Physics, Operator (physics), Mathematical analysis, Biophysics, Condensed Matter Physics, Rotating reference frame, Interpretation (model theory), Magnetization, Matrix (mathematics), Quantum mechanics, Relaxation (physics), Limit (mathematics), Physical and Theoretical Chemistry, Molecular Biology, Eigenvalues and eigenvectors
Abstract: Approximate expressions for the NMR spin relaxation rate constant in the rotating frame of reference R 1ρ are derived for two-site chemical exchange by consideration of the evolution of the average density operator using the stochastic Liouville equation. R 1ρ is obtained as a linearized approximation to the largest (least negative) eigenvalue of the matrix describing the evolution of the average density operator in the long-term limit. The expressions obtained are more accurate than existing expressions when exchange is not fast and the populations of the exchanging sites are close to equal. The new expressions for R 1ρ facilitate the interpretation of chemical exchange phenomena in proteins and other biological macromolecules.
Published: 2003

39. On the use of the stochastic Liouville equation in nuclear magnetic resonance: Application toR1? relaxation in the presence of exchange

Author: Arthur G. Palmer and Daniel Abergel
Subjects: Physics, Millisecond, Spins, Relaxation (NMR), General Chemistry, Kinetic energy, Rotating reference frame, Frame of reference, Microsecond, Nuclear magnetic resonance, Quantum mechanics, Master equation, Physical and Theoretical Chemistry, Spectroscopy
Abstract: The nuclear magnetic resonance (NMR) spin relaxation rate constant in the rotating frame of reference R1ρ provides information on microsecond to millisecond (μs-ms) timescale kinetic processes that stochastically modulate the resonance frequencies of nuclear spins in molecules. Expressions for R1ρ are presented for two-site chemical exchange using both the conventional perturbation approach for evolution of the density operator in the interaction frame of reference and the stochastic Liouville equation (SLE) for evolution of the average density operator in the rotating frame of reference. The former approach is limited to the fast-exchange regime, in which the chemical exchange kinetics are faster than the frequency difference between spins in the two sites. The latter approach provides approximate expressions for R1ρ that are accurate when chemical exchange is not fast. Expressions for R1ρ that are accurate over the widest range of experimental conditions facilitate the interpretation of chemical exchange phenomena. © 2003 Wiley Periodicals, Inc. Concepts Magn Reson Part A 19A: 134–148, 2003.
Published: 2003

40. Chaotic solutions of the feedback driven Bloch equations

Author: Daniel Abergel
Subjects: Physics, Nonlinear system, Magnetization, Classical mechanics, Radiation damping, Field (physics), Bloch equations, Quantum mechanics, Demagnetizing field, Attractor, Chaotic, General Physics and Astronomy
Abstract: Recent acute manifestations of nonlinear spin behaviour in high field NMR spectroscopy of liquids have been observed. These were caused by collective effects, such as demagnetizing field effects or back action from the probe (radiation damping or radiation damping-based electronic feedback). These findings motivated the present study, in which the dynamics of a magnetization undergoing the effect of a radiation-damping based feedback field from the probe was numerically investigated. The existence of chaotic attractors is demonstrated and the type of transition to chaos investigated for various sets of parameters.
Published: 2002

41. Communication: Dissolution DNP reveals a long-lived deuterium spin state imbalance in methyl groups

Author: Daniel Abergel, Aditya Jhajharia, Dennis Kurzbach, James G. Kempf, Emmanuelle M. M. Weber, and Geoffrey Bodenhausen
Subjects: education.field_of_study, 010304 chemical physics, Spin states, Spins, Dynamic nuclear polarisation, Population, Relaxation (NMR), Analytical chemistry, General Physics and Astronomy, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, chemistry.chemical_compound, chemistry, Deuterium, Chemical physics, 0103 physical sciences, Condensed Matter::Strongly Correlated Electrons, Physical and Theoretical Chemistry, education, Methyl group
Abstract: We report the generation and observation of long-lived spin states in deuterated methyl groups by dissolution DNP. These states are based on population imbalances between manifolds of spin states corresponding to irreducible representations of the C3v point group and feature strongly dampened quadrupolar relaxation. Their lifetime depends on the activation energies of methyl group rotation. With dissolution DNP, we can reduce the deuterium relaxation rate by a factor up to 20, thereby extending the experimentally available time window. The intrinsic limitation of NMR spectroscopy of quadrupolar spins by short relaxation times can thus be alleviated.
Published: 2017

42. On the reliability of NMR relaxation data analyses: A Markov Chain Monte Carlo approach

Author: Antonino Polimeno, Daniel Abergel, Eloi P. Coutant, Andrea Volpato, and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Nuclear and High Energy Physics, Magnetic Resonance Spectroscopy, Bayesian probability, Monte Carlo method, Biophysics, Biochemistry, Sensitivity and Specificity, Pattern Recognition, Automated, symbols.namesake, Computer Simulation, Statistical physics, Mathematics, Markov chain mixing time, Models, Statistical, Markov chain, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Model selection, Reproducibility of Results, Markov chain Monte Carlo, Condensed Matter Physics, Markov Chains, Data Interpretation, Statistical, symbols, Curve fitting, Marginal distribution, Monte Carlo Method, Algorithms
Abstract: International audience; : The analysis of NMR relaxation data is revisited along the lines of a Bayesian approach. Using a Markov Chain Monte Carlo strategy of data fitting, we investigate conditions under which relaxation data can be effectively interpreted in terms of internal dynamics. The limitations to the extraction of kinetic parameters that characterize internal dynamics are analyzed, and we show that extracting characteristic time scales shorter than a few tens of ps is very unlikely. However, using MCMC methods, reliable estimates of the marginal probability distributions and estimators (average, standard deviations, etc.) can still be obtained for subsets of the model parameters. Thus, unlike more conventional strategies of data analysis, the method avoids a model selection process. In addition, it indicates what information may be extracted from the data, but also what cannot.
Published: 2014

43. The stochastic Bloch equations driven by a coloured noise

Author: Jean-Yves Lallemand and Daniel Abergel
Subjects: Physics, General Physics and Astronomy, Binary number, Markov process, Limiting case (mathematics), White noise, symbols.namesake, Amplitude, Bloch equations, Quantum mechanics, symbols, Statistical physics, Physical and Theoretical Chemistry, Special case, Noise (radio)
Abstract: In this Letter, the lagged cross-moments and cross-spectra of the Bloch equations driven by a radiofrequency field whose amplitude is fluctuating randomly with Markovian statistics are calculated. Exact expressions for the lineshape are derived in the special case of a Markovian binary noise. The limiting case of white noise is investigated and compared with results found in the literature.
Published: 1998

44. A new concept for selective excitation in NMR

Author: Daniel Abergel, Jean-Yves Lallemand, and Alain Louis-Joseph
Subjects: Nuclear magnetic resonance, Chemistry, General Physics and Astronomy, Pulse duration, Physical and Theoretical Chemistry, Selective excitation, Atomic physics
Abstract: The new NMR concept of selective excitation generated by pulses whose envelope is slaved to that of a signal originating from the sample is described. It is shown that these kinds of pulses exhibit interesting features such as a sort of auto-calibration of the pulse length and phase. These particular features are discussed and experimental evidence is given. Illustration of the use of slaved pulses is demonstrated in the case of 1D transient NOE by selective inversion.
Published: 1996

45. Large-Scale Production of Microcrystals and Precipitates of Proteins and Their Complexes

Author: José Enrique Herbert-Pucheta, Geoffrey Bodenhausen, Luminita Duma, Yves Blouquit, Liliane Assairi, Monique Chan-Huot, Jean-Baptiste Charbonnier, Daniel Abergel, Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de Biologie Structurale et Radiobiologie (LBSR), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Imagerie intégrative de la molécule à l'organisme, Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Agence Nationale de la Recherche [ANR-09-BLAN-0111-01], and network of Tres Grands Equipements de Resonance Magnetique Nucleaire a Tres Hauts Champs (TGE RMN THC), CNRS [3050]
Subjects: chemistry.chemical_classification, 0303 health sciences, Chemistry, Biomolecule, Peptide, General Chemistry, Nuclear magnetic resonance spectroscopy, 010402 general chemistry, Condensed Matter Physics, 01 natural sciences, 0104 chemical sciences, 03 medical and health sciences, chemistry.chemical_compound, Crystallography, Centrin, General Materials Science, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Lysozyme, 030304 developmental biology
Abstract: International audience; The optimum conditions for the formation of plate-like and urchin-like microcrystals of biomolecules and their transfer to rotors for solid-state NMR spectroscopy depend on a variety of factors, of which minimizing the manipulation of the microcrystals and storing the sample for several months at 277 K (4 degrees C) play an important role. Three biological systems were investigated: Hen Egg-White (HEW) lysozyme (129 residues), the lengthened C-terminal domain (LCter) of Human centrin 2 (89 residues), and the complex between the C-terminal domain (Cter) of Human centrin 2 (79 residues) and the P17-XPC peptide (17 residues).
Published: 2012

46. Probing Structural and Motional Features of C-terminal Part of the Human Centrin 2/P17-XPC Microcrystalline Complex by Solid-State NMR Spectroscopy

Author: Geoffrey Bodenhausen, José Enrique Herbert-Pucheta, Luminita Duma, Piotr Tekely, Daniel Abergel, Jean-Baptiste Charbonnier, Liliane Assairi, Monique Chan-Huot, Yves Blouquit, Université Pierre et Marie Curie - Paris 6 (UPMC), Imagerie intégrative de la molécule à l'organisme, and Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Models, Molecular, Protein Conformation, Movement, Molecular Sequence Data, Cell Cycle Proteins, Crystallography, X-Ray, 010402 general chemistry, 01 natural sciences, 03 medical and health sciences, Protein structure, Materials Chemistry, Humans, Amino Acid Sequence, Physical and Theoretical Chemistry, Spectroscopy, Nuclear Magnetic Resonance, Biomolecular, Protein secondary structure, 030304 developmental biology, 0303 health sciences, Chemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Calcium-Binding Proteins, Resonance (chemistry), 0104 chemical sciences, Surfaces, Coatings and Films, NMR spectra database, Crystallography, Solid-state nuclear magnetic resonance, Centrin, Peptides, Magnetic dipole–dipole interaction, Protein Binding
Abstract: International audience; An insight into structural and motional features of the C-terminal part of the Human Centrin 2 in complex with the peptide P17-XPC was obtained by using complementary solid-state NMR methods. We demonstrate that the experimental conditions and procedures of sample crystallization determine not only the quality of solid-state NMR spectra but can also dramatically modify the dynamic state of water molecules and the internal mobility of the protein. Two-dimensional (2D) 13C - 13C and 15N - 15N correlation spectra reveal intra- and inter-residue dipolar connectivities and provide partial, site-specific assignments of 13C and 15N resonance signals. The secondary structure of the C-ter HsCen2 /P17-XPC complex in a microcrystalline state appears similar to that found in solution. Conformational flexibility is probed through relaxation-compensated measurements of dipolar order parameters that exploit the dynamics of cross-polarization in multidimensional experiments. The extracted dipolar coupling constants and relevant order parameters reveal increased backbone flexibility of the loops except for residues involved in coordination with the Ca2+ cation that stabilizes the hydrophobic pocket containing the peptide P17-XPC.
Published: 2012

47. Improvements in Radiation-Damping Control in High-Resolution NMR

Author: Jean-Yves Lallemand, Alain Louis-Joseph, Claire Carlotti, and Daniel Abergel
Subjects: High resolution nmr, Radiation damping, Nuclear magnetic resonance, Field (physics), Chemistry, General Engineering, Pulse sequence, Sample (graphics), Computational physics
Abstract: OUr goeal was to create a magnetization-dependent field in the sample, which exactly compensates the existing radiation-damping field.
Published: 1995

48. Towards the Characterization of Fractional Stochastic Processes Underlying Methyl Dynamics in Proteins

Author: Paolo Calligari, Daniel Abergel, and Université Pierre et Marie Curie - Paris 6 (UPMC)
Subjects: Materials Chemistry2506 Metals and Alloys, Movement, Structure (category theory), Probability density function, Molecular Dynamics Simulation, 010402 general chemistry, Methylation, 01 natural sciences, Coatings and Films, Computational chemistry, Matrix Metalloproteinase 12, 0103 physical sciences, Materials Chemistry, Side chain, Statistical physics, Physical and Theoretical Chemistry, Physics, Stochastic Processes, 010304 chemical physics, Ubiquitin, Stochastic process, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Dynamics (mechanics), Carbon, Markov Chains, 0104 chemical sciences, Surfaces, Coatings and Films, Connection (mathematics), Surfaces, Fractals, Hydrogen, Brownian dynamics, Continuous-time random walk
Abstract: International audience; In this article, we investigate the multiple scale structure of methyl side chain dynamics in proteins. We show that the orientational correlation functions of CH3 methyl groups are well described by a fractional Brownian dynamics model. Typical angular correlation functions involved in NMR relaxation were computed from MD simulations performed on two different proteins. These correlation functions were shown to be very well fitted by a fractional Ornstein-Uhlenbeck process in the presence of a effective local potentials at the C-H and C-C methyl bonds. In addition, our analysis highlights the presence of the asymptotic power law decay of the waiting time probability density of the stochastic process involved, thereby illustrating the connection between approaches based on fractional diffusion equations and the continuous time random walk (CTRW).
Published: 2012

49. Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics

Author: Geoffrey Bodenhausen, Jamal Ouazzani, Gilmar F. Salgado, Paolo Calligari, Philippe Pelupessy, Daniel Abergel, Philippe Lopes, Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences et d'ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), and Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: Conformational Entropy, Relaxation, Secondary, Magnetic Resonance Spectroscopy, Protozoan Proteins, Protein dynamics, Ligands, 01 natural sciences, Biochemistry, Protein Structure, Secondary, Molecular dynamics, Nuclear magnetic resonance, Structural Biology, Protein Interaction Mapping, chemistry.chemical_classification, Principal Component Analysis, 0303 health sciences, biology, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Pentose-Phosphate Pathway, Relaxation (NMR), Backbone Dynamics, Model-Free Approach, Conformational entropy, Ligand (biochemistry), Molecular dynamics simulations (MD), Time-Scale Dynamics, Protein Binding, Protein Structure, Globular protein, Trypanosoma brucei brucei, Molecular Dynamics Simulation, Trypanosoma brucei, Intrinsic Dynamics, 010402 general chemistry, 6-phospho-gluconolactonase (6PGL), NMR, Binding Sites, Carboxylic Ester Hydrolases, Computational Biology, Gluconates, Holoenzymes, Structure-Activity Relationship, Molecular Biology, 03 medical and health sciences, Delocalized electron, 030304 developmental biology, Binding, biology.organism_classification, Nmr Relaxation, 0104 chemical sciences, chemistry, Enzyme Catalysis
Abstract: Nuclear magnetic resonance is used to investigate the backbone dynamics in 6-phosphogluconolactonase from Trypanosoma brucei (Tb6PGL) with (holo-) and without (apo-) 6-phosphogluconic acid as ligand. Relaxation data were analyzed using the model-free approach and reduced spectral density mapping. Comparison of predictions, based on 77 ns molecular dynamics simulations, with the observed relaxation rates gives insight into dynamical properties of the protein and their alteration on ligand binding. Data indicate dynamics changes in the vicinity of the binding site. More interesting is the presence of perturbations located in remote regions of this well-structured globular protein in which no large-amplitude motions are involved. This suggests that delocalized changes in dynamics that occur upon binding could be a general feature of proteintarget interactions. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.
Published: 2012

50. From NMR relaxation to fractional Brownian dynamics in proteins: results from a virtual experiment

Author: Vania Calandrini, Gerald R. Kneller, Daniel Abergel, Paolo Calligari, Institut Laue-Langevin (ILL), Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Synchrotron SOLEIL (SSOLEIL), Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), ILL, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, and Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)
Subjects: Materials Chemistry2506 Metals and Alloys, Magnetic Resonance Spectroscopy, Overfitting, Molecular Dynamics Simulation, 010402 general chemistry, 01 natural sciences, Carboxylic Ester Hydrolases, Nitrogen Isotopes, Water, Physical and Theoretical Chemistry, Surfaces, Coatings and Films, Coatings and Films, Molecular dynamics, 0103 physical sciences, Materials Chemistry, Statistical physics, Spectroscopy, 010304 chemical physics, Basis (linear algebra), Chemistry, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Spectrum (functional analysis), Relaxation (NMR), 0104 chemical sciences, Magnetic field, Surfaces, Brownian dynamics
Abstract: International audience; In a recent simulation study [J. Chem. Phys. 2010, 133, 145101], it has been shown that the time correlation functions probed by nuclear magnetic resonance (NMR) relaxation spectroscopy of proteins are well described by a fractional Brownian dynamics model, which accounts for the wide spectrum of relaxation rates characterizing their internal dynamics. Here, we perform numerical experiments to explore the possibility of using this model directly in the analysis of experimental NMR relaxation data. Starting from a molecular dynamics simulation of the 266 residue protein 6PGL in explicit water, we construct virtual (15)N R(1), R(2), and NOE relaxation rates at two different magnetic fields, including artificial noise, and test how far the parameters obtained from a fit of the model to the virtual experimental data coincide with those obtained from an analysis of the MD time correlation functions that have been used to construct these data. We show that in most cases, close agreement is found. Acceptance or rejection of parameter values obtained from relaxation rates are discussed on a physical basis, therefore avoiding overfitting.
Published: 2011

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