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Bolik-Coulon N, Zachrdla M, Bouvignies G, Pelupessy P, Ferrage F. Comprehensive analysis of relaxation decays from high-resolution relaxometry. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 355:107555. [PMID: 37797558 DOI: 10.1016/j.jmr.2023.107555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Relaxometry consists in measuring relaxation rates over orders of magnitude of magnetic fields to probe motions of complex systems. High-resolution relaxometry (HRR) experiments can be performed on conventional high-field NMR magnets equipped with a sample shuttle. During the experiment, the sample shuttle transfers the sample between the high-field magnetic center and a chosen position in the stray field for relaxation during a variable delay, thus using the stray field as a variable field. As the relaxation delay occurs outside of the probe, HRR experiments cannot rely on the control of cross-relaxation pathways, which is standard in high-field relaxation pulse sequences. Thus, decay rates are not pure relaxation rates, which may impair a reliable description of the dynamics. Previously, we took into account cross-relaxation effects in the analysis of high-resolution relaxometry data by applying a correction factor to relaxometry decay rates in order to estimate relaxation rates. These correction factors were obtained from the iterative simulation of the relaxation decay while the sample lies outside of the probe and a preceding analysis of relaxation rates which relies on the approximation of a priori multi-exponential decays by mono-exponential functions. However, an analysis protocol matching directly experimental and simulated relaxometry decays should be more self consistent and more generally applicable as it can accommodate deviations from mono-exponential decays. Here, we introduce Matching INtensities for the Optimization of Timescales and Amplitudes of motions Under Relaxometry (MINOTAUR), a framework for the analysis of high-resolution relaxometry that takes as input the intensity decays at all fields. This approach uses the full relaxation matrix to calculate intensity decays, allowing complex relaxation pathways to be taken into account. Therefore, it eliminates the need for a correction of decay rates and for fitting multi-exponential decays with mono-exponential functions. The MINOTAUR software is designed as a flexible framework where relaxation matrices and spectral density functions corresponding to various models of motions can be defined on a case-by-case basis. The agreement with our previous analyses of protein side-chain dynamics from carbon-13 relaxation is excellent, while providing a more robust analysis tool. We expect MINOTAUR to become the tool of choice for the analysis of high-resolution relaxometry.
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Affiliation(s)
- Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.
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2
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Ellermann F, Saul P, Hövener JB, Pravdivtsev AN. Modern Manufacturing Enables Magnetic Field Cycling Experiments and Parahydrogen-Induced Hyperpolarization with a Benchtop NMR. Anal Chem 2023; 95:6244-6252. [PMID: 37018544 DOI: 10.1021/acs.analchem.2c03682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Benchtop NMR (btNMR) spectrometers are revolutionizing the way we use NMR and lowering the cost drastically. Magnetic field cycling (MFC) experiments with precise timing and control over the magnetic field, however, were hitherto not available on btNMRs, although some systems exist for high-field, high-resolution NMR spectrometers. Still, the need and potential for btNMR MFC is great─e.g., to perform and analyze parahydrogen-induced hyperpolarization, another method that has affected analytical chemistry and NMR beyond expectations. Here, we describe a setup that enables MFC on btNMRs for chemical analysis and hyperpolarization. Taking full advantage of the power of modern manufacturing, including computer-aided design, three-dimensional printing, and microcontrollers, the setup is easy to reproduce, highly reliable, and easy to adjust and operate. Within 380 ms, the NMR tube was shuttled reliably from the electromagnet to the NMR isocenter (using a stepper motor and gear rod). We demonstrated the power of this setup by hyperpolarizing nicotinamide using signal amplification by reversible exchange (SABRE), a versatile method to hyperpolarize a broad variety of molecules including metabolites and drugs. Here, the standard deviation of SABRE hyperpolarization was between 0.2 and 3.3%. The setup also allowed us to investigate the field dependency of the polarization and the effect of different sample preparation protocols. We found that redissolution of the activated and dried Ir catalyst always reduced the polarization. We anticipate that this design will greatly accelerate the ascension of MFC experiments for chemical analysis with btNMR─adding yet another application to this rapidly developing field.
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Affiliation(s)
- Frowin Ellermann
- Section for Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Schleswig-Holstein (UKSH), Kiel 24118, Germany
| | - Philip Saul
- Section for Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Schleswig-Holstein (UKSH), Kiel 24118, Germany
| | - Jan-Bernd Hövener
- Section for Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Schleswig-Holstein (UKSH), Kiel 24118, Germany
| | - Andrey N Pravdivtsev
- Section for Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Schleswig-Holstein (UKSH), Kiel 24118, Germany
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3
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How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation. Curr Opin Struct Biol 2022; 77:102459. [PMID: 36148743 DOI: 10.1016/j.sbi.2022.102459] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 07/29/2022] [Accepted: 08/05/2022] [Indexed: 12/14/2022]
Abstract
Nuclear magnetic resonance (NMR) spin relaxation experiments currently probe molecular motions on timescales from picoseconds to nanoseconds. The detailed interpretation of these motions in atomic detail benefits from complementarity with the results from molecular dynamics (MD) simulations. In this mini-review, we describe the recent developments in experimental techniques to study the backbone dynamics from 15N relaxation and side-chain dynamics from 13C relaxation, discuss the different analysis approaches from model-free to dynamics detectors, and highlight the many ways that NMR relaxation experiments and MD simulations can be used together to improve the interpretation and gain insights into protein dynamics.
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4
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Roberts MF, Hedstrom L. High Resolution 31P Field Cycling NMR Reveals Unsuspected Features of Enzyme-Substrate-Cofactor Dynamics. Front Mol Biosci 2022; 9:865519. [PMID: 35433832 PMCID: PMC9009223 DOI: 10.3389/fmolb.2022.865519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
The dynamic interactions of enzymes and substrates underpins catalysis, yet few techniques can interrogate the dynamics of protein-bound ligands. Here we describe the use of field cycling NMR relaxometry to measure the dynamics of enzyme-bound substrates and cofactors in catalytically competent complexes of GMP reductase. These studies reveal new binding modes unanticipated by x-ray crystal structures and reaction-specific dynamic networks. Importantly, this work demonstrates that distal interactions not usually considered part of the reaction coordinate can play an active role in catalysis. The commercialization of shuttling apparatus will make field cycling relaxometry more accessible and expand its use to additional nuclei, promising more intriguing findings to come.
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Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States
| | - Lizbeth Hedstrom
- Departments of Biology and Chemistry, Brandeis University, Waltham, MA, United States
- *Correspondence: Lizbeth Hedstrom,
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5
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Roberts MF, Cai J, V Natarajan S, Khan HM, Reuter N, Gershenson A, Redfield AG. Phospholipids in Motion: High-Resolution 31P NMR Field Cycling Studies. J Phys Chem B 2021; 125:8827-8838. [PMID: 34320805 DOI: 10.1021/acs.jpcb.1c02105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Diverse phospholipid motions are key to membrane function but can be quite difficult to untangle and quantify. High-resolution field cycling 31P NMR spin-lattice relaxometry, where the sample is excited at high field, shuttled in the magnet bore for low-field relaxation, then shuttled back to high field for readout of the residual magnetization, provides data on phospholipid dynamics and structure. This information is encoded in the field dependence of the 31P spin-lattice relaxation rate (R1). In the field range from 11.74 down to 0.003 T, three dipolar nuclear magnetic relaxation dispersions (NMRDs) and one due to 31P chemical shift anisotropy contribute to R1 of phospholipids. Extraction of correlation times and maximum relaxation amplitudes for these NMRDs provides (1) lateral diffusion constants for different phospholipids in the same bilayer, (2) estimates of how additives alter the motion of the phospholipid about its long axis, and (3) an average 31P-1H angle with respect to the bilayer normal, which reveals that polar headgroup motion is not restricted on a microsecond timescale. Relative motions within a phospholipid are also provided by comparing 31P NMRD profiles for specifically deuterated molecules as well as 13C and 1H field dependence profiles to that of 31P. Although this work has dealt exclusively with phospholipids in small unilamellar vesicles, these same NMRDs can be measured for phospholipids in micelles and nanodisks, making this technique useful for monitoring lipid behavior in a variety of structures and assessing how additives alter specific lipid motions.
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Affiliation(s)
- Mary F Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jingfei Cai
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Sivanandam V Natarajan
- Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Hanif M Khan
- Department of Molecular Biology and Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
| | - Nathalie Reuter
- Department of Molecular Biology and Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Alfred G Redfield
- Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, Waltham, Massachusetts 02454, United States
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6
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Wang Z, Pisano S, Ghini V, Kadeřávek P, Zachrdla M, Pelupessy P, Kazmierczak M, Marquardsen T, Tyburn JM, Bouvignies G, Parigi G, Luchinat C, Ferrage F. Detection of Metabolite-Protein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Toward Interactomics by NMR. J Am Chem Soc 2021; 143:9393-9404. [PMID: 34133154 DOI: 10.1021/jacs.1c01388] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics, the systematic investigation of metabolites in biological fluids, cells, or tissues, reveals essential information about metabolism and diseases. Metabolites have functional roles in a myriad of biological processes, as substrates and products of enzymatic reactions but also as cofactors and regulators of large numbers of biochemical mechanisms. These functions involve interactions of metabolites with macromolecules. Yet, methods to systematically investigate these interactions are still scarce to date. In particular, there is a need for techniques suited to identify and characterize weak metabolite-macromolecule interactions directly in complex media such as biological fluids. Here, we introduce a method to investigate weak interactions between metabolites and macromolecules in biological fluids. Our approach is based on high-resolution NMR relaxometry and does not require any invasive procedure or separation step. We show that we can detect interactions between small and large molecules in human blood serum and quantify the size of the complex. Our work opens the way for investigations of metabolite (or other small molecules)-protein interactions in biological fluids for interactomics or pharmaceutical applications.
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Affiliation(s)
- Ziqing Wang
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Simone Pisano
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Veronica Ghini
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Pavel Kadeřávek
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Morgan Kazmierczak
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | | | - Jean-Max Tyburn
- Bruker BioSpin, 34 rue de l'Industrie BP 10002, 67166 Cedex Wissembourg, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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7
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Parigi G, Ravera E, Fragai M, Luchinat C. Unveiling protein dynamics in solution with field-cycling NMR relaxometry. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 124-125:85-98. [PMID: 34479712 DOI: 10.1016/j.pnmrs.2021.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Field-cycling NMR relaxometry is a well-established technique that can give information on molecular structure and dynamics of biological systems. It provides the nuclear relaxation rates as a function of the applied magnetic field, starting from fields as low as ~ 10-4 T up to about 1-3 T. The profiles so collected, called nuclear magnetic relaxation dispersion (NMRD) profiles, can be extended to include the relaxation rates at the largest fields achievable with high resolution NMR spectrometers. By exploiting this wide range of frequencies, the NMRD profiles can provide information on motions occurring on time scales from 10-6 to 10-9 s. 1H NMRD measurements have proved very useful also for the characterization of paramagnetic proteins, because they can help characterise a number of parameters including the number, distance and residence time of water molecules coordinated to the paramagnetic center, the reorientation correlation times and the electron spin relaxation time, and the electronic structure at the metal site.
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Affiliation(s)
- Giacomo Parigi
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy.
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy
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8
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Smith AA, Bolik-Coulon N, Ernst M, Meier BH, Ferrage F. How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution? JOURNAL OF BIOMOLECULAR NMR 2021; 75:119-131. [PMID: 33759077 PMCID: PMC8018934 DOI: 10.1007/s10858-021-00361-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
The dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments-where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution-seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the "detector" analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion.
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Affiliation(s)
- Albert A Smith
- Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstraße 16-18, 04107, Leipzig, Germany.
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Nicolas Bolik-Coulon
- Laboratoire des biomolécules, LBM, Département de Chimie, École normale superieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Matthias Ernst
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Fabien Ferrage
- Laboratoire des biomolécules, LBM, Département de Chimie, École normale superieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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9
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Zhukov I, Kiryutin A, Wang Z, Zachrdla M, Yurkovskaya A, Ivanov K, Ferrage F. Surprising absence of strong homonuclear coupling at low magnetic field explored by two-field nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:237-246. [PMID: 38111910 PMCID: PMC10726027 DOI: 10.5194/mr-1-237-2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2023]
Abstract
Strong coupling of nuclear spins, which is achieved when their scalar coupling 2 π J is greater than or comparable to the difference Δ ω in their Larmor precession frequencies in an external magnetic field, gives rise to efficient coherent longitudinal polarization transfer. The strong coupling regime can be achieved when the external magnetic field is sufficiently low, as Δ ω is reduced proportional to the field strength. In the present work, however, we demonstrate that in heteronuclear spin systems these simple arguments may not hold, since heteronuclear spin-spin interactions alter the Δ ω value. The experimental method that we use is two-field nuclear magnetic resonance (NMR), exploiting sample shuttling between the high field, at which NMR spectra are acquired, and the low field, where strong couplings are expected and at which NMR pulses can be applied to affect the spin dynamics. By using this technique, we generate zero-quantum spin coherences by means of a nonadiabatic passage through a level anticrossing and study their evolution at the low field. Such zero-quantum coherences mediate the polarization transfer under strong coupling conditions. Experiments performed with a 13 C -labeled amino acid clearly show that the coherent polarization transfer at the low field is pronounced in the 13 C spin subsystem under proton decoupling. However, in the absence of proton decoupling, polarization transfer by coherent processes is dramatically reduced, demonstrating that heteronuclear spin-spin interactions suppress the strong coupling regime, even when the external field is low. A theoretical model is presented, which can model the reported experimental results.
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Affiliation(s)
- Ivan V. Zhukov
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexey S. Kiryutin
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ziqing Wang
- Laboratoire des Biomolécules (LBM), Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Milan Zachrdla
- Laboratoire des Biomolécules (LBM), Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Alexandra V. Yurkovskaya
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Konstantin L. Ivanov
- International Tomography Center, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Fabien Ferrage
- Laboratoire des Biomolécules (LBM), Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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10
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Hall AMR, Cartlidge TAA, Pileio G. A temperature-controlled sample shuttle for field-cycling NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 317:106778. [PMID: 32650304 DOI: 10.1016/j.jmr.2020.106778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
We present a design for a temperature-controlled sample shuttle for use in NMR measurements at variable magnetic field strength. Accurate temperature control was achieved using a mixture of water-ethylene glycol as a heat transfer fluid, reducing temperature gradients across the sample to < 0.05 °C and minimising convection. Using the sample shuttle, we show how the longitudinal (T1) and singlet order (TS) relaxation time constants were measured for two molecules capable of supporting long-lived states, with new record lifetimes observed at low field and above ambient temperatures.
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Affiliation(s)
- Andrew M R Hall
- University of Southampton, Highfield Campus, Southampton SO17 1BJ, United Kingdom
| | - Topaz A A Cartlidge
- University of Southampton, Highfield Campus, Southampton SO17 1BJ, United Kingdom
| | - Giuseppe Pileio
- University of Southampton, Highfield Campus, Southampton SO17 1BJ, United Kingdom.
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11
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Rosenberg MM, Yao T, Patton GC, Redfield AG, Roberts MF, Hedstrom L. Enzyme-Substrate-Cofactor Dynamical Networks Revealed by High-Resolution Field Cycling Relaxometry. Biochemistry 2020; 59:2359-2370. [PMID: 32479091 PMCID: PMC8364753 DOI: 10.1021/acs.biochem.0c00212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The remarkable power and specificity of enzyme catalysis rely on the dynamic alignment of the enzyme, substrates, and cofactors, yet the role of dynamics has usually been approached from the perspective of the protein. We have been using an underappreciated NMR technique, subtesla high-resolution field cycling 31P NMR relaxometry, to investigate the dynamics of the enzyme-bound substrates and cofactor on guanosine-5'-monophosphate reductase (GMPR). GMPR forms two dead end, yet catalytically competent, complexes that mimic distinct steps in the catalytic cycle: E·IMP·NADP+ undergoes a partial hydride transfer reaction, while E·GMP·NADP+ undergoes a partial deamination reaction. A different cofactor conformation is required for each partial reaction. Here we report the effects of mutations designed to perturb cofactor conformation and ammonia binding with the goal of identifying the structural features that contribute to the distinct dynamic signatures of the hydride transfer and deamination complexes. These experiments suggest that Asp129 is a central cog in a dynamic network required for both hydride transfer and deamination. In contrast, Lys77 modulates the conformation and mobility of substrates and cofactors in a reaction-specific manner. Thr105 and Tyr318 are part of a deamination-specific dynamic network that includes the 2'-OH of GMP. These residues have comparatively little effect on the dynamic properties of the hydride transfer complex. These results further illustrate the potential of high-resolution field cycling NMR relaxometry for the investigation of ligand dynamics. In addition, exchange experiments indicate that NH3/NH4+ has a high affinity for the deamination complex but a low affinity for the hydride transfer complex, suggesting that the movement of ammonia may gate the cofactor conformational change. Collectively, these experiments reinforce the view that the enzyme, substrates, and cofactor are linked in intricate, reaction-specific, dynamic networks and demonstrate that distal portions of the substrates and cofactors are critical features in these networks.
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Affiliation(s)
- Masha M. Rosenberg
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
| | - Tianjiong Yao
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
| | - Gregory C. Patton
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
| | - Alfred G. Redfield
- Department of Biochemistry, Brandeis University, MS009, 415 South Street, Waltham, MA 02453-9110 USA
| | - Mary F. Roberts
- Department of Chemistry, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467-9110 USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453-3808 USA
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12
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Bolik-Coulon N, Kadeřávek P, Pelupessy P, Dumez JN, Ferrage F, Cousin SF. Theoretical and computational framework for the analysis of the relaxation properties of arbitrary spin systems. Application to high-resolution relaxometry. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 313:106718. [PMID: 32234674 DOI: 10.1016/j.jmr.2020.106718] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
A wide variety of nuclear magnetic resonance experiments rely on the prediction and analysis of relaxation processes. Recently, innovative approaches have been introduced where the sample travels through a broad range of magnetic fields in the course of the experiment, such as dissolution dynamic nuclear polarization or high-resolution relaxometry. Understanding the relaxation properties of nuclear spin systems over orders of magnitude of magnetic fields is essential to rationalize the results of these experiments. For example, during a high-resolution relaxometry experiment, the absence of control of nuclear spin relaxation pathways during the sample transfers and relaxation delays leads to systematic deviations of polarization decays from an ideal mono-exponential decay with the pure longitudinal relaxation rate. These deviations have to be taken into account to describe quantitatively the dynamics of the system. Here, we present computational tools to (1) calculate analytical expressions of relaxation rates for a broad variety of spin systems and (2) use these analytical expressions to correct the deviations arising in high-resolution relaxometry experiments. These tools lead to a better understanding of nuclear spin relaxation, which is required to improve the sensitivity of many pulse sequences, and to better characterize motions in macromolecules.
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Affiliation(s)
- Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Pavel Kadeřávek
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | | | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Samuel F Cousin
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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13
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Jaseňáková Z, Zapletal V, Padrta P, Zachrdla M, Bolik-Coulon N, Marquardsen T, Tyburn JM, Žídek L, Ferrage F, Kadeřávek P. Boosting the resolution of low-field [Formula: see text] relaxation experiments on intrinsically disordered proteins with triple-resonance NMR. JOURNAL OF BIOMOLECULAR NMR 2020; 74:139-145. [PMID: 31960224 DOI: 10.1007/s10858-019-00298-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Improving our understanding of nanosecond motions in disordered proteins requires the enhanced sampling of the spectral density function obtained from relaxation at low magnetic fields. High-resolution relaxometry and two-field NMR measurements of relaxation have, so far, only been based on the recording of one- or two-dimensional spectra, which provide insufficient resolution for challenging disordered proteins. Here, we introduce a 3D-HNCO-based two-field NMR experiment for measurements of protein backbone [Formula: see text] amide longitudinal relaxation rates. The experiment provides accurate longitudinal relaxation rates at low field (0.33 T in our case) preserving the resolution and sensitivity typical for high-field NMR spectroscopy. Radiofrequency pulses applied on six different radiofrequency channels are used to manipulate the spin system at both fields. The experiment was demonstrated on the C-terminal domain of [Formula: see text] subunit of RNA polymerase from Bacillus subtilis, a protein with highly repetitive amino-acid sequence and very low dispersion of backbone chemical shifts.
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Affiliation(s)
- Zuzana Jaseňáková
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Vojtěch Zapletal
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Petr Padrta
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | | | - Jean-Max Tyburn
- Bruker BioSpin, 34 rue de l'Industrie BP 10002, 67166, Wissembourg Cedex, France
| | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science and Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
| | - Pavel Kadeřávek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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14
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Kadeřávek P, Bolik-Coulon N, Cousin SF, Marquardsen T, Tyburn JM, Dumez JN, Ferrage F. Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Nuclear Spin Relaxation. J Phys Chem Lett 2019; 10:5917-5922. [PMID: 31509419 DOI: 10.1021/acs.jpclett.9b02233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nuclear magnetic relaxation provides invaluable quantitative site-specific information on the dynamics of complex systems. Determining dynamics on nanosecond time scales requires relaxation measurements at low magnetic fields incompatible with high-resolution NMR. Here, we use a two-field NMR spectrometer to measure carbon-13 transverse and longitudinal relaxation rates at a field as low as 0.33 T (proton Larmor frequency 14 MHz) in specifically labeled side chains of the protein ubiquitin. The use of radiofrequency pulses enhances the accuracy of measurements as compared to high-resolution relaxometry approaches, where the sample is moved in the stray field of the superconducting magnet. Importantly, we demonstrate that accurate measurements at a single low magnetic field provide enough information to characterize complex motions on low nanosecond time scales, which opens a new window for the determination of site-specific nanosecond motions in complex systems such as proteins.
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Affiliation(s)
- Pavel Kadeřávek
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | - Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | - Samuel F Cousin
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | | | - Jean-Max Tyburn
- Bruker BioSpin , 34 rue de l'Industrie BP 10002, 67166 Wissembourg Cedex, France
| | | | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
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15
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Schanda P. Relaxing with liquids and solids - A perspective on biomolecular dynamics. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:180-186. [PMID: 31350165 PMCID: PMC7302934 DOI: 10.1016/j.jmr.2019.07.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 05/05/2019] [Accepted: 07/08/2019] [Indexed: 05/05/2023]
Affiliation(s)
- Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38000 Grenoble, France.
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16
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Ajoy A, Lv X, Druga E, Liu K, Safvati B, Morabe A, Fenton M, Nazaryan R, Patel S, Sjolander TF, Reimer JA, Sakellariou D, Meriles CA, Pines A. Wide dynamic range magnetic field cycler: Harnessing quantum control at low and high fields. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:013112. [PMID: 30709175 DOI: 10.1063/1.5064685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
We describe the construction of a fast field cycling device capable of sweeping a 4-order-of-magnitude range of magnetic fields, from ∼1 mT to 7 T, in under 700 ms, and which is further extendable to a 1 nT-7 T range. Central to this system is a high-speed sample shuttling mechanism between a superconducting magnet and a magnetic shield, with the capability to access arbitrary fields in between with high resolution. Our instrument serves as a versatile platform to harness the inherent dichotomy of spin dynamics on offer at low and high fields-in particular, the low anisotropy, fast spin manipulation, and rapid entanglement growth at low field as well as the long spin lifetimes, spin specific control, and efficient inductive measurement possible at high fields. Exploiting these complementary capabilities in a single device opens up applications in a host of problems in quantum control, sensing, and information storage, besides in nuclear hyperpolarization, relaxometry, and imaging. In particular, in this paper, we focus on the ability of the device to enable low-field hyperpolarization of 13C nuclei in diamond via optically pumped electronic spins associated with nitrogen vacancy defect centers.
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Affiliation(s)
- A Ajoy
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - X Lv
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - E Druga
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - K Liu
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - B Safvati
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - A Morabe
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - M Fenton
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - R Nazaryan
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - S Patel
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - T F Sjolander
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - J A Reimer
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - D Sakellariou
- Centre for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems (M2S), KU Leuven, Celestijnenlaan 200F P.O. Box 2461, 3001 Leuven, Belgium
| | - C A Meriles
- Department of Physics, CUNY-City College of New York, New York, New York 10031, USA
| | - A Pines
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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17
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Tayler MCD, Ward-Williams J, Gladden LF. NMR relaxation in porous materials at zero and ultralow magnetic fields. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 297:1-8. [PMID: 30316016 DOI: 10.1016/j.jmr.2018.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/28/2018] [Accepted: 09/29/2018] [Indexed: 06/08/2023]
Abstract
NMR detection in the ultralow-field regime (below 10 μT) was used to measure the nuclear spin relaxation rates of liquids imbibed into silica pellets with mean pore diameters in the 10-50 nm range. Heptane, formic acid and acetic acid were studied and relaxation rate data were compared with a conventional field-cycling NMR technique. Detection of 1H-13C spin coupling NMR signals at zero field (∼0.1 nT) allowed spectroscopic identification of molecules inside the porous material and unambiguous measurements of the chemistry-specific relaxation rates in liquid mixtures. In the case of molecules that contain 1H and 13C, spin-singlet state relaxation can provide additional information about the dynamics. Applications and future improvements to the methodology are discussed.
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Affiliation(s)
- Michael C D Tayler
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK.
| | - Jordan Ward-Williams
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
| | - Lynn F Gladden
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK
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18
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Roberts MF, Khan HM, Goldstein R, Reuter N, Gershenson A. Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes. Chem Rev 2018; 118:8435-8473. [DOI: 10.1021/acs.chemrev.8b00208] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Rebecca Goldstein
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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19
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Abstract
Many of the functions of biomacromolecules can be rationalized by the characterization of their conformational energy landscapes: the structures of the dominant states, transitions between states and motions within states. Nuclear magnetic resonance (NMR) spectroscopy is the technique of choice to study internal motions in proteins. The determination of motions on picosecond to nanosecond timescales requires the measurement of nuclear spin relaxation rates at multiple magnetic fields. High sensitivity and resolution are obtained only at high magnetic fields, so that, until recently, site-specific relaxation rates in biomolecules were only measured over a narrow range of high magnetic fields. This limitation was particularly striking for the quantification of motions on nanosecond timescales, close to the correlation time for overall rotational diffusion. High-resolution relaxometry is an emerging technique to investigate picosecond-nanosecond motions of proteins. This approach uses a high-field NMR spectrometer equipped with a sample shuttle device, which allows for the measurement of the relaxation rate constants at low magnetic fields, while preserving the sensitivity and resolution of a high-field NMR spectrometer. The combined analysis of high-resolution relaxometry and standard high-field relaxation data provides a more accurate description of the dynamics of proteins, in particular in the nanosecond range. The purpose of this chapter is to describe how to perform high-resolution relaxometry experiments and how to analyze the rates measured with this technique.
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20
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Rosenberg MM, Redfield AG, Roberts MF, Hedstrom L. Dynamic Characteristics of Guanosine-5'-monophosphate Reductase Complexes Revealed by High-Resolution 31P Field-Cycling NMR Relaxometry. Biochemistry 2018; 57:3146-3154. [PMID: 29547266 DOI: 10.1021/acs.biochem.8b00142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability of enzymes to modulate the dynamics of bound substrates and cofactors is a critical feature of catalysis, but the role of dynamics has largely been approached from the perspective of the protein. Here, we use an underappreciated NMR technique, subtesla high-resolution field-cycling 31P NMR relaxometry, to interrogate the dynamics of enzyme bound substrates and cofactors in guanosine-5'-monophosphate reductase (GMPR). These experiments reveal distinct binding modes and dynamic profiles associated with the 31P nuclei in the Michaelis complexes for the deamination and hydride transfer steps of the catalytic cycle. Importantly, the substrate is constrained and the cofactor is more dynamic in the deamination complex E·GMP·NADP+, whereas the substrate is more dynamic and the cofactor is constrained in the hydride transfer complex E·IMP·NADP+. The presence of D2O perturbed the relaxation of the 31P nuclei in E·IMP·NADP+ but not in E·GMP·NADP+, providing further evidence of distinct binding modes with different dynamic properties. dIMP and dGMP are poor substrates, and the dynamics of the cofactor complexes of dGMP/dIMP are disregulated relative to GMP/IMP. The substrate 2'-OH interacts with Asp219, and mutation of Asp219 to Ala decreases the value of Vmax by a factor of 30. Counterintuitively, loss of Asp219 makes both substrates and cofactors less dynamic. These observations suggest that the interactions between the substrate 2'-OH and Asp219 coordinate the dynamic properties of the Michaelis complexes, and these dynamics are important for progression through the catalytic cycle.
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Affiliation(s)
- Masha M Rosenberg
- Department of Biology , Brandeis University , MS009, 415 South Street , Waltham , Massachusetts 02453-9110 , United States
| | - Alfred G Redfield
- Department of Biochemistry , Brandeis University , MS009, 415 South Street , Waltham , Massachusetts 02453-9110 , United States
| | - Mary F Roberts
- Department of Chemistry , Boston College , 140 Commonwealth Avenue , Chestnut Hill , Massachusetts 02467-9110 , United States
| | - Lizbeth Hedstrom
- Department of Biology , Brandeis University , MS009, 415 South Street , Waltham , Massachusetts 02453-9110 , United States.,Department of Chemistry , Brandeis University , 415 South Street , Waltham , Massachusetts 02453-3808 , United States
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21
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Korb JP. Multiscale nuclear magnetic relaxation dispersion of complex liquids in bulk and confinement. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 104:12-55. [PMID: 29405980 DOI: 10.1016/j.pnmrs.2017.11.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 10/29/2017] [Accepted: 11/01/2017] [Indexed: 06/07/2023]
Abstract
The nuclear magnetic relaxation dispersion (NMRD) technique consists of measurement of the magnetic-field dependence of the longitudinal nuclear-spin-lattice relaxation rate 1/T1. Usually, the acquisition of the NMRD profiles is made using a fast field cycling (FFC) NMR technique that varies the magnetic field and explores a very large range of Larmor frequencies (10 kHz < ω0/(2π) <40 MHz). This allows extensive explorations of the fluctuations to which nuclear spin relaxation is sensitive. The FFC technique thus offers opportunities on multiple scales of both time and distance for characterizing the molecular dynamics and transport properties of complex liquids in bulk or embedded in confined environments. This review presents the principles, theories and applications of NMRD for characterizing fundamental properties such as surface correlation times, diffusion coefficients and dynamical surface affinity (NMR wettability) for various confined liquids. The basic longitudinal and transverse relaxation equations are outlined for bulk liquids. The nuclear relaxation of a liquid confined in pores is considered in detail in order to find the biphasic fast exchange relations for a liquid at proximity of a solid surface. The physical-chemistry of liquids at solid surfaces induces striking differences between NMRD profiles of aprotic and protic (water) liquids embedded in calibrated porous disordered materials. A particular emphasis of this review concerns the extension of FFC NMR relaxation to industrial applications. For instance, it is shown that the FFC technique is sufficiently rapid for following the progressive setting of cement-based materials (plasters, cement pastes, concretes). The technique also allows studies of the dynamics of hydrocarbons in proximity of asphaltene nano-aggregates and macro-aggregates in heavy crude oils as a function of the concentration of asphaltenes. It also gives new information on the wettability of petroleum fluids (brine and oil) embedded in shale oil rocks. It is useful for understanding the relations and correlations between NMR relaxation times T1 and T2, diffusion coefficients D, and viscosity η of heavy crude oils. This is of particular importance for interpreting T1, T2, 2D T1-T2 and D-T2 correlation spectra that could be obtained down-hole, thus giving a valuable tool for investigating in situ the molecular dynamics of petroleum fluids. Another domain of interest concerns biological applications. This is of particular importance for studying the complex dynamical spectrum of a folded polymeric structure that may span many decades in frequency or time. A direct NMRD characterization of water diffusional dynamics is presented at the protein interface. NMR experiments using a shuttle technique give results well above the frequency range accessible via the FFC technique; examples of this show protein dynamics over a range from fast and localized motions to slow and delocalized collective motions involving the whole protein. This review ends by an interpretation of the origin of the proton magnetic field dependence of T1 for different biological tissues of animals; this includes a proposal for interpreting in vivo MRI data from human brain at variable magnetic fields, where the FFC relaxation analysis suggests that brain white-matter is distinct from grey-matter, in agreement with diffusion-weighted MRI imaging.
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Affiliation(s)
- Jean-Pierre Korb
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, Université de Paris Saclay, 91128 Palaiseau Cedex, France; Sorbonne Universités, UPMC Univ. Paris 06, CNRS, PHENIX Laboratory, F-75005 Paris, France.
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22
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Salvi N, Abyzov A, Blackledge M. Atomic resolution conformational dynamics of intrinsically disordered proteins from NMR spin relaxation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:43-60. [PMID: 29157493 DOI: 10.1016/j.pnmrs.2017.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 05/08/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful experimental approaches for investigating the conformational behaviour of intrinsically disordered proteins (IDPs). IDPs represent a significant fraction of all proteomes, and, despite their importance for understanding fundamental biological processes, the molecular basis of their activity still remains largely unknown. The functional mechanisms exploited by IDPs in their interactions with other biomolecules are defined by their intrinsic dynamic modes and associated timescales, justifying the considerable interest over recent years in the development of technologies adapted to measure and describe this behaviour. NMR spin relaxation delivers information-rich, site-specific data reporting on conformational fluctuations occurring throughout the molecule. Here we review recent progress in the use of 15N relaxation to identify local backbone dynamics and long-range chain-like motions in unfolded proteins.
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Affiliation(s)
- Nicola Salvi
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France
| | - Anton Abyzov
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France.
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23
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Gräsing D, Bielytskyi P, Céspedes-Camacho IF, Alia A, Marquardsen T, Engelke F, Matysik J. Field-cycling NMR with high-resolution detection under magic-angle spinning: determination of field-window for nuclear hyperpolarization in a photosynthetic reaction center. Sci Rep 2017; 7:12111. [PMID: 28935961 PMCID: PMC5608766 DOI: 10.1038/s41598-017-10413-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/09/2017] [Indexed: 11/09/2022] Open
Abstract
Several parameters in NMR depend on the magnetic field strength. Field-cycling NMR is an elegant way to explore the field dependence of these properties. The technique is well developed for solution state and in relaxometry. Here, a shuttle system with magic-angle spinning (MAS) detection is presented to allow for field-dependent studies on solids. The function of this system is demonstrated by exploring the magnetic field dependence of the solid-state photochemically induced nuclear polarization (photo-CIDNP) effect. The effect allows for strong nuclear spin-hyperpolarization in light-induced spin-correlated radical pairs (SCRPs) under solid-state conditions. To this end, 13C MAS NMR is applied to a photosynthetic reaction center (RC) of the purple bacterium Rhodobacter (R.) sphaeroides wildtype (WT). For induction of the effect in the stray field of the magnet and its subsequent observation at 9.4 T under MAS NMR conditions, the sample is shuttled by the use of an aerodynamically driven sample transfer technique. In the RC, we observe the effect down to 0.25 T allowing to determine the window for the occurrence of the effect to be between about 0.2 and 20 T.
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Affiliation(s)
- Daniel Gräsing
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103, Leipzig, Germany
| | - Pavlo Bielytskyi
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103, Leipzig, Germany
| | - Isaac F Céspedes-Camacho
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103, Leipzig, Germany.,Escuela de Química, Tecnológico de Costa Rica, Sede Central, 30101, Cartago, Costa Rica
| | - A Alia
- Institut für Medizinische Physik und Biophysik, Universität Leipzig, Härtelstr. 16-18, D-04107, Leipzig, Germany.,Leiden Institute of Chemistry, 2333, Leiden, The Netherlands
| | | | - Frank Engelke
- Bruker BioSpin GmbH, Silberstreifen 4, D-76287, Rheinstetten, Germany
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, D-04103, Leipzig, Germany.
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24
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Dynamical regimes of lipids in additivated liposomes with enhanced elasticity: A field-cycling NMR relaxometry approach. Biophys Chem 2017; 228:38-46. [DOI: 10.1016/j.bpc.2017.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/14/2017] [Accepted: 06/20/2017] [Indexed: 11/22/2022]
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25
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Morozova OB, Yurkovskaya AV, Vieth HM, Sosnovsky DV, Ivanov KL. Light-induced spin hyperpolarisation in condensed phase. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1363923] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Olga B. Morozova
- Laboratory of Magnetic and Spin Phenomena, International Tomography Center SB RAS, Novosibirsk, 630090, Russia
- Laboratory of Magnetic Resonance in Chemistry, Biology and Medicine, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Alexandra V. Yurkovskaya
- Laboratory of Magnetic and Spin Phenomena, International Tomography Center SB RAS, Novosibirsk, 630090, Russia
- Laboratory of Magnetic Resonance in Chemistry, Biology and Medicine, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Hans-Martin Vieth
- Laboratory of Magnetic and Spin Phenomena, International Tomography Center SB RAS, Novosibirsk, 630090, Russia
- Department of Physics, Free University of Berlin, Berlin, 14195, Germany
| | - Denis V. Sosnovsky
- Laboratory of Magnetic and Spin Phenomena, International Tomography Center SB RAS, Novosibirsk, 630090, Russia
- Laboratory of Magnetic Resonance in Chemistry, Biology and Medicine, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Konstantin L. Ivanov
- Laboratory of Magnetic and Spin Phenomena, International Tomography Center SB RAS, Novosibirsk, 630090, Russia
- Laboratory of Magnetic Resonance in Chemistry, Biology and Medicine, Novosibirsk State University, Novosibirsk, 630090, Russia
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26
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Ultra-wide range field-dependent measurements of the relaxivity of Gd 1-xEu xVO 4 nanoparticle contrast agents using a mechanical sample-shuttling relaxometer. Sci Rep 2017; 7:44770. [PMID: 28317892 PMCID: PMC5357940 DOI: 10.1038/srep44770] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/14/2017] [Indexed: 11/17/2022] Open
Abstract
The current trend for Magnetic Resonance Imaging points towards higher magnetic fields. Even though sensitivity and resolution are increased in stronger fields, T1 contrast is often reduced, and this represents a challenge for contrast agent design. Field-dependent measurements of relaxivity are thus important to characterize contrast agents. At present, the field-dependent curves of relaxivity are usually carried out in the field range of 0 T to 2 T, using fast field cycling relaxometers. Here, we employ a high-speed sample shuttling device to switch the magnetic fields experienced by the nuclei between virtually zero field, and the center of any commercial spectrometer. We apply this approach on rare-earth (mixed Gadolinium-Europium) vanadate nanoparticles, and obtain the dispersion curves from very low magnetic field up to 11.7 T. In contrast to the relaxivity profiles of Gd chelates, commonly used for clinical applications, which display a plateau and then a decrease for increasing magnetic fields, these nanoparticles provide maximum contrast enhancement for magnetic fields around 1–1.5 T. These field-dependent curves are fitted using the so-called Magnetic Particle (MP) model and the extracted parameters discussed as a function of particle size and composition. We finally comment on the new possibilities offered by this approach.
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27
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Dalvit C, Piotto M. 19 F NMR transverse and longitudinal relaxation filter experiments for screening: a theoretical and experimental analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:106-114. [PMID: 27514284 DOI: 10.1002/mrc.4500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
Ligand-based 19 F NMR screening represents an efficient approach for performing binding assays. The high sensitivity of the methodology to receptor binding allows the detection of weak affinity ligands. The observable NMR parameters that are typically used are the 19 F transverse relaxation rate and isotropic chemical shift. However, there are few cases where the 19 F longitudinal relaxation rate should also be used. A theoretical and experimental analysis of the 19 F NMR transverse and longitudinal relaxation rates at different magnetic fields is presented along with proposed methods for improving the sensitivity and dynamic range of these experiments applied to fragment-based screening. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Claudio Dalvit
- Faculty of Science, University of Neuchatel, Neuchatel, Switzerland
- IDD/SDI, Sanofi, Vitry-sur-Seine, France
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28
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Chou CY, Chu M, Chang CF, Yu T, Huang TH, Sakellariou D. High sensitivity high-resolution full range relaxometry using a fast mechanical sample shuttling device and a cryo-probe. JOURNAL OF BIOMOLECULAR NMR 2016; 66:187-194. [PMID: 27744623 DOI: 10.1007/s10858-016-0066-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
Field-dependent NMR studies of bio-molecular systems using a sample shuttling hardware operating on a high-field NMR apparatus have provided valuable structural and dynamic information. We have recently published a design of a compact sample transportation device, called "field-cycler", which was installed in a commercial spectrometer and which provided highly precise positioning and stability during high speed shuttling. In this communication, we demonstrate the first use of a sample shuttling device on a commercial high field standard bore NMR spectrometer, equipped with a commercial triple resonance cryogenically cooled NMR probe. The performance and robustness of the hardware operating in 1D and 2D field cycling experiments, as well as the impact of the sample shuttling time on the signal intensity are discussed.
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Affiliation(s)
- Ching-Yu Chou
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191, Gif-Sur-Yvette, France
- Laboratoire des Biomolécules, Département de Chimie, UMR7203 CNRS-UPMC-ENS, Ecole Normale Supérieure, 24 Rue Lhomond, 75005, Paris Cedex 05, France
- Field Cycling Technology Ltd., 10F., No.136, Chaiqiao Rd., Xiangshan, Hsinchu, 300, Taiwan, ROC
| | - Minglee Chu
- Institute of Physics, Academia Sinica, Taipei, Taiwan, ROC
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Tsunai Yu
- Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan, ROC
| | - Tai-Huang Huang
- Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan, ROC.
| | - Dimitris Sakellariou
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191, Gif-Sur-Yvette, France
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29
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Gradziel CS, Jordan PA, Jewel D, Dufort FJ, Miller SJ, Chiles TC, Roberts MF. d-3-Deoxy-dioctanoylphosphatidylinositol induces cytotoxicity in human MCF-7 breast cancer cells via a mechanism that involves downregulation of the D-type cyclin-retinoblastoma pathway. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1861:1808-1815. [PMID: 27600289 PMCID: PMC5115159 DOI: 10.1016/j.bbalip.2016.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/24/2016] [Accepted: 09/01/2016] [Indexed: 11/29/2022]
Abstract
Phosphatidylinositol analogs (PIAs) were originally designed to bind competitively to the Akt PH domain and prevent membrane translocation and activation. d-3-Deoxy-dioctanoylphosphatidylinositol (d-3-deoxy-diC8PI), but not compounds with altered inositol stereochemistry (e.g., l-3-deoxy-diC8PI and l-3,5-dideoxy-diC8PI), is cytotoxic. However, high resolution NMR field cycling relaxometry shows that both cytotoxic and non-toxic PIAs bind to the Akt1 PH domain at the site occupied by the cytotoxic alkylphospholipid perifosine. This suggests that another mechanism for cytotoxicity must account for the difference in efficacy of the synthetic short-chain PIAs. In MCF-7 breast cancer cells, with little constitutively active Akt, d-3-deoxy-diC8PI (but not l-compounds) decreases viability concomitant with increased cleavage of PARP and caspase 9, indicative of apoptosis. d-3-Deoxy-diC8PI also induces a decrease in endogenous levels of cyclins D1 and D3 and blocks downstream retinoblastoma protein phosphorylation. siRNA-mediated depletion of cyclin D1, but not cyclin D3, reduces MCF-7 cell proliferation. Thus, growth arrest and cytotoxicity induced by the soluble d-3-deoxy-diC8PI occur by a mechanism that involves downregulation of the D-type cyclin-pRb pathway independent of its interaction with Akt. This ability to downregulate D-type cyclins contributes, at least in part, to the anti-proliferative activity of d-3-deoxy-diC8PI and may be a common feature of other cytotoxic phospholipids.
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Affiliation(s)
- Cheryl S Gradziel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Peter A Jordan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA.
| | - Delilah Jewel
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
| | - Fay J Dufort
- Department of Biology, Higgins Hall, 140 Commonwealth Avenue, Boston College, Chestnut Hill, MA, USA.
| | - Scott J Miller
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA.
| | - Thomas C Chiles
- Department of Biology, Higgins Hall, 140 Commonwealth Avenue, Boston College, Chestnut Hill, MA, USA.
| | - Mary F Roberts
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA.
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30
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Rosenberg MM, Redfield AG, Roberts MF, Hedstrom L. Substrate and Cofactor Dynamics on Guanosine Monophosphate Reductase Probed by High Resolution Field Cycling 31P NMR Relaxometry. J Biol Chem 2016; 291:22988-22998. [PMID: 27613871 PMCID: PMC5087720 DOI: 10.1074/jbc.m116.739516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 08/31/2016] [Indexed: 12/31/2022] Open
Abstract
Guanosine-5'-monophosphate reductase (GMPR) catalyzes the reduction of GMP to IMP and ammonia with concomitant oxidation of NADPH. Here we investigated the structure and dynamics of enzyme-bound substrates and cofactors by measuring 31P relaxation rates over a large magnetic field range using high resolution field cycling NMR relaxometry. Surprisingly, these experiments reveal differences in the low field relaxation profiles for the monophosphate of GMP compared with IMP in their respective NADP+ complexes. These complexes undergo partial reactions that mimic different steps in the overall catalytic cycle. The relaxation profiles indicate that the substrate monophosphates have distinct interactions in E·IMP·NADP+ and E·GMP·NADP+ complexes. These findings were not anticipated by x-ray crystal structures, which show identical interactions for the monophosphates of GMP and IMP in several inert complexes. In addition, the motion of the cofactor is enhanced in the E·GMP·NADP+ complex. Last, the motions of the substrate and cofactor are coordinately regulated; the cofactor has faster local motions than GMP in the deamination complex but is more constrained than IMP in that complex, leading to hydride transfer. These results show that field cycling can be used to investigate the dynamics of protein-bound ligands and provide new insights into how portions of the substrate remote from the site of chemical transformation promote catalysis.
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Affiliation(s)
| | | | - Mary F Roberts
- the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467-3860
| | - Lizbeth Hedstrom
- From the Departments of Biology,
- Chemistry, Brandeis University, Waltham, Massachusetts 02453 and
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31
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Pravdivtsev AN, Yurkovskaya AV, Petrov PA, Ivanov KL. A Site-Specific Study of the Magnetic Field-Dependent Proton Spin Relaxation of an Iridium N-Heterocyclic Carbene Complex. Z PHYS CHEM 2016. [DOI: 10.1515/zpch-2016-0849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
We report a study of proton spin relaxation of an Iridium N-heterocyclic carbene complex [Ir(COD)(IMes)Cl] complex (where COD=1,5-cyclooctadiene, Imes=1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene). This compound is a pre-catalyst of the most efficient complex allowing the signal amplification by reversible exchange (SABRE) effect, relevant for enhancing weak signals in nuclear magnetic resonance (NMR). An important feature of the study is a combination of relaxation measurements over a wide field range with high-resolution NMR detection. As a result, we are able to measure nuclear magnetic relaxation dispersion (NMRD) curves in the field range 0.1 mT–16.4 T (corresponding to the frequency range 4 kHz–700 MHz) for individual protons in the complex under study. This attractive possibility enables determination of the motional correlation times, τc
, for the individual protons by analyzing the features in the NMRD curves (increase of the relaxation times) appearing at the magnetic fields where ωτc
≈1 (here ω is the proton Larmor precession frequency at a given field strength). The following correlation times were determined: (1.3±0.1) ns for the protons of imidazol-2-ylidene, (0.96±0.1) ns for the ortho-protons of two phenyl moieties and (0.95±0.2) ns for the protons of methyl groups. Additionally, we report low-field features coming from “strong coupling” of the protons. One should note that such features must not be misinterpreted by associating them with motional features. From the low-field features we obtain consistent estimates for the proton spin-spin interactions. The analysis of motional correlation times is also of importance for interpretation of spin order transfer from parahydrogen to various substrates in transient organometallic complexes (termed the SABRE effect) at high magnetic field.
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Affiliation(s)
- Andrey N. Pravdivtsev
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3A, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Alexandra V. Yurkovskaya
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3A, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Pavel A. Petrov
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
- Nikolaev Institute of Inorganic Chemistry, Siberian Branch of the Russian Academy of Science, Institutskaya 3, Novosibirsk 630090, Russian Federation
| | - Konstantin L. Ivanov
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3A, Novosibirsk 630090, Russian Federation
- Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
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32
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Cousin SF, Kadeřávek P, Haddou B, Charlier C, Marquardsen T, Tyburn JM, Bovier PA, Engelke F, Maas W, Bodenhausen G, Pelupessy P, Ferrage F. Recovering Invisible Signals by Two-Field NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Samuel F. Cousin
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Pavel Kadeřávek
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Baptiste Haddou
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR, 8640 Pasteur; 75005 Paris France
| | - Cyril Charlier
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
- Laboratory of Chemical Physics, NIDDK, NIH; Bethesda MD 20892 USA
| | | | - Jean-Max Tyburn
- Bruker BioSpin; 34 rue de l'Industrie BP 10002 67166 Wissembourg Cedex France
| | | | - Frank Engelke
- Bruker BioSpin GmbH; Silberstreifen 4 76287 Rheinstetten Germany
| | | | - Geoffrey Bodenhausen
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Philippe Pelupessy
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Fabien Ferrage
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
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33
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Cousin SF, Kadeřávek P, Haddou B, Charlier C, Marquardsen T, Tyburn JM, Bovier PA, Engelke F, Maas W, Bodenhausen G, Pelupessy P, Ferrage F. Recovering Invisible Signals by Two-Field NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:9886-9. [DOI: 10.1002/anie.201602978] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Samuel F. Cousin
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Pavel Kadeřávek
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Baptiste Haddou
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR, 8640 Pasteur; 75005 Paris France
| | - Cyril Charlier
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
- Laboratory of Chemical Physics, NIDDK, NIH; Bethesda MD 20892 USA
| | | | - Jean-Max Tyburn
- Bruker BioSpin; 34 rue de l'Industrie BP 10002 67166 Wissembourg Cedex France
| | | | - Frank Engelke
- Bruker BioSpin GmbH; Silberstreifen 4 76287 Rheinstetten Germany
| | | | - Geoffrey Bodenhausen
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Philippe Pelupessy
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
| | - Fabien Ferrage
- Department of Chemistry, Ecole Normale Supérieure; PSL Research University; 24 rue Lhomond 75005 Paris France
- Sorbonne Universités, UPMC Univ Paris 06, LBM; 4 place Jussieu 75005 Paris France
- CNRS, UMR 7203 LBM; 75005 Paris France
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34
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Steele RM, Korb JP, Ferrante G, Bubici S. New applications and perspectives of fast field cycling NMR relaxometry. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:502-9. [PMID: 25855084 DOI: 10.1002/mrc.4220] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 12/17/2014] [Accepted: 01/19/2015] [Indexed: 05/08/2023]
Abstract
The field cycling NMR relaxometry method (also known as fast field cycling (FFC) when instruments employing fast electrical switching of the magnetic field are used) allows determination of the spin-lattice relaxation time (T1 ) continuously over five decades of Larmor frequency. The method can be exploited to observe the T1 frequency dependence of protons, as well as any other NMR-sensitive nuclei, such as (2) H, (13) C, (31) P, and (19) F in a wide range of substances and materials. The information obtained is directly correlated with the physical/chemical properties of the compound and can be represented as a 'nuclear magnetic resonance dispersion' curve. We present some recent academic and industrial applications showing the relevance of exploiting FFC NMR relaxometry in complex materials to study the molecular dynamics or, simply, for fingerprinting or quality control purposes. The basic nuclear magnetic resonance dispersion features are outlined in representative examples of magnetic resonance imaging (MRI) contrast agents, porous media, proteins, and food stuffs. We will focus on the new directions and perspectives for the FFC technique. For instance, the introduction of the latest Wide Bore FFC NMR relaxometers allows probing, for the first time, of the dynamics of confined surface water contained in the macro-pores of carbonate rock cores. We also evidence the use of the latest field cycling technology with a new cryogen-free variable-field electromagnet, which enhances the range of available frequencies in the 2D T1 -T2 correlation spectrum for separating oil and water in crude oil. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Jean-Pierre Korb
- Physique de la Matière Condensée, Ecole Polytechnique-CNRS, 91128, Palaiseau, France
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35
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Kiryutin AS, Pravdivtsev AN, Ivanov KL, Grishin YA, Vieth HM, Yurkovskaya AV. A fast field-cycling device for high-resolution NMR: Design and application to spin relaxation and hyperpolarization experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 263:79-91. [PMID: 26773525 DOI: 10.1016/j.jmr.2015.11.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 06/05/2023]
Abstract
A device for performing fast magnetic field-cycling NMR experiments is described. A key feature of this setup is that it combines fast switching of the external magnetic field and high-resolution NMR detection. The field-cycling method is based on precise mechanical positioning of the NMR probe with the mounted sample in the inhomogeneous fringe field of the spectrometer magnet. The device enables field variation over several decades (from 100μT up to 7T) within less than 0.3s; progress in NMR probe design provides NMR linewidths of about 10(-3)ppm. The experimental method is very versatile and enables site-specific studies of spin relaxation (NMRD, LLSs) and spin hyperpolarization (DNP, CIDNP, and SABRE) at variable magnetic field and at variable temperature. Experimental examples of such studies are demonstrated; advantages of the experimental method are described and existing challenges in the field are outlined.
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Affiliation(s)
- Alexey S Kiryutin
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3a, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Andrey N Pravdivtsev
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3a, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia
| | - Konstantin L Ivanov
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3a, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia
| | - Yuri A Grishin
- Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Science, Institutskaya 3, Novosibirsk 630090, Russia
| | - Hans-Martin Vieth
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3a, Novosibirsk 630090, Russia; Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany.
| | - Alexandra V Yurkovskaya
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3a, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia
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36
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Gossuin Y, Serhan Z, Sandiford L, Henrard D, Marquardsen T, de Rosales RTM, Sakellariou D, Ferrage F. Sample Shuttling Relaxometry of Contrast Agents: NMRD Profiles above 1 T with a Single Device. APPLIED MAGNETIC RESONANCE 2016; 47:237-246. [PMID: 26941480 PMCID: PMC4761365 DOI: 10.1007/s00723-015-0751-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Indexed: 06/05/2023]
Abstract
Nuclear magnetic relaxation dispersion (NMRD) profiles are essential tools to evaluate the efficiency and investigate the properties of magnetic compounds used as contrast agents for magnetic resonance imaging (MRI), namely gadolinium chelates and superparamagnetic iron oxide particles. These curves represent the evolution of proton relaxation rates with the magnetic field. NMRD profiles are unparalleled to probe extensively the spectral density function involved in the relaxation of water in the presence of the paramagnetic ion or the magnetic nanoparticles. This makes such profiles an excellent test of the adequacy of a theoretical relaxation model and allow for a predictive approach to the development and optimization of contrast agents. From a practical point of view they also allow to evaluate the efficiency of a contrast agent in a certain range of magnetic fields. Nowadays, these curves are recorded with commercial fast field cycling devices, often limited to a maximum Larmor frequency of 40 MHz (0.94 T). In this article, relaxation data were acquired on a wide range of magnetic fields, from 3.5 × 10-4 to 14 T, for a gadolinium-based contrast agent and for PEGylated iron oxide nanoparticles. We show that the low-field NMRD curves can be completed with high-field data obtained on a shuttle apparatus device using the superconductive magnet of a high-field spectrometer. This allows a better characterization of the contrast agents at relevant magnetic fields for clinical and preclinical MRI, but also refines the experimental data that could be used for the validation of relaxation models.
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Affiliation(s)
- Yves Gossuin
- />Biomedical Physics Department, University of Mons, 24, Avenue du Champ de Mars, 7000 Mons, Belgium
| | - Zeinab Serhan
- />Département de Chimie, École Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005 Paris, France
- />Sorbonne Universités UPMC Univ Paris 06, LBM, 4 place Jussieu, 75005 Paris, France
- />UMR 7203 LBM, CNRS, 75005 Paris, France
| | - Lydia Sandiford
- />Division of Imaging Sciences and Biomedical Engineering, St. Thomas’ Hospital, King’s College London, London, SE1 7EH UK
| | - Daniel Henrard
- />Biomedical Physics Department, University of Mons, 24, Avenue du Champ de Mars, 7000 Mons, Belgium
| | | | - Rafael T. M. de Rosales
- />Division of Imaging Sciences and Biomedical Engineering, St. Thomas’ Hospital, King’s College London, London, SE1 7EH UK
| | - Dimitrios Sakellariou
- />Laboratoire Structure et Dynamique par Résonance Magnétique, CEA Saclay, DSM, IRAMIS, UMR CEA/CNRS 3685, NIMBE, 91191 Gif-sur-Yvette Cedex, France
| | - Fabien Ferrage
- />Département de Chimie, École Normale Supérieure - PSL Research University, 24 rue Lhomond, 75005 Paris, France
- />Sorbonne Universités UPMC Univ Paris 06, LBM, 4 place Jussieu, 75005 Paris, France
- />UMR 7203 LBM, CNRS, 75005 Paris, France
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37
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Charlier C, Cousin SF, Ferrage F. Protein dynamics from nuclear magnetic relaxation. Chem Soc Rev 2016; 45:2410-22. [DOI: 10.1039/c5cs00832h] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein dynamics are explored by a variety of methods designed to measure nuclear magnetic relaxation rates.
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Affiliation(s)
- Cyril Charlier
- École Normale Supérieure-PSL Research University
- Département de Chimie
- 75005 Paris
- France
- Sorbonne Universités
| | - Samuel F. Cousin
- École Normale Supérieure-PSL Research University
- Département de Chimie
- 75005 Paris
- France
- Sorbonne Universités
| | - Fabien Ferrage
- École Normale Supérieure-PSL Research University
- Département de Chimie
- 75005 Paris
- France
- Sorbonne Universités
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38
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Cousin SF, Charlier C, Kadeřávek P, Marquardsen T, Tyburn JM, Bovier PA, Ulzega S, Speck T, Wilhelm D, Engelke F, Maas W, Sakellariou D, Bodenhausen G, Pelupessy P, Ferrage F. High-resolution two-field nuclear magnetic resonance spectroscopy. Phys Chem Chem Phys 2016; 18:33187-33194. [DOI: 10.1039/c6cp05422f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two-field NMR provides correlations of nuclear spins at the most favourable magnetic fields in a single experiment.
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Affiliation(s)
- Samuel F. Cousin
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Cyril Charlier
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Pavel Kadeřávek
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | | | | | | | | | | | | | | | | | | | - Geoffrey Bodenhausen
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Philippe Pelupessy
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - Fabien Ferrage
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
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39
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Pravdivtsev AN, Yurkovskaya AV, Vieth HM, Ivanov KL. High resolution NMR study of T₁ magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide. J Chem Phys 2015; 141:155101. [PMID: 25338911 DOI: 10.1063/1.4897336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nuclear Magnetic Relaxation Dispersion (NMRD) of protons was studied in the pentapeptide Met-enkephalin and the amino acids, which constitute it. Experiments were run by using high-resolution Nuclear Magnetic Resonance (NMR) in combination with fast field-cycling, thus enabling measuring NMRD curves for all individual protons. As in earlier works, Papers I-III, pronounced effects of intramolecular scalar spin-spin interactions, J-couplings, on spin relaxation were found. Notably, at low fields J-couplings tend to equalize the apparent relaxation rates within networks of coupled protons. In Met-enkephalin, in contrast to the free amino acids, there is a sharp increase in the proton T1-relaxation times at high fields due to the changes in the regime of molecular motion. The experimental data are in good agreement with theory. From modelling the relaxation experiments we were able to determine motional correlation times of different residues in Met-enkephalin with atomic resolution. This allows us to draw conclusions about preferential conformation of the pentapeptide in solution, which is also in agreement with data from two-dimensional NMR experiments (rotating frame Overhauser effect spectroscopy). Altogether, our study demonstrates that high-resolution NMR studies of magnetic field-dependent relaxation allow one to probe molecular mobility in biomolecules with atomic resolution.
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Affiliation(s)
| | | | - Hans-Martin Vieth
- Institut für Experimentalphysik, Freie Universität Berlin Arnimallee 14, 14195 Berlin, Germany
| | - Konstantin L Ivanov
- International Tomography Center, Institutskaya 3a, Novosibirsk 630090, Russia
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40
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Morozova OB, Yurkovskaya AV. Assessment of Nanosecond Time Scale Motions in Native and Non-Native States of Ubiquitin. J Phys Chem B 2015; 119:12644-52. [DOI: 10.1021/acs.jpcb.5b07333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olga B. Morozova
- International Tomography Center of SB RAS, Institutskaya
3a, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova 2, Novosibirsk, 630090, Russia
| | - Alexandra V. Yurkovskaya
- International Tomography Center of SB RAS, Institutskaya
3a, Novosibirsk, 630090, Russia
- Novosibirsk State University, Pirogova 2, Novosibirsk, 630090, Russia
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41
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Wei Y, Stec B, Redfield AG, Weerapana E, Roberts MF. Phospholipid-binding sites of phosphatase and tensin homolog (PTEN): exploring the mechanism of phosphatidylinositol 4,5-bisphosphate activation. J Biol Chem 2014; 290:1592-606. [PMID: 25429968 DOI: 10.1074/jbc.m114.588590] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The lipid phosphatase activity of the tumor suppressor phosphatase and tensin homolog (PTEN) is enhanced by the presence of its biological product, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This enhancement is suggested to occur via the product binding to the N-terminal region of the protein. PTEN effects on short-chain phosphoinositide (31)P linewidths and on the full field dependence of the spin-lattice relaxation rate (measured by high resolution field cycling (31)P NMR using spin-labeled protein) are combined with enzyme kinetics with the same short-chain phospholipids to characterize where PI(4,5)P2 binds on the protein. The results are used to model a discrete site for a PI(4,5)P2 molecule close to, but distinct from, the active site of PTEN. This PI(4,5)P2 site uses Arg-47 and Lys-13 as phosphate ligands, explaining why PTEN R47G and K13E can no longer be activated by that phosphoinositide. Placing a PI(4,5)P2 near the substrate site allows for proper orientation of the enzyme on interfaces and should facilitate processive catalysis.
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Affiliation(s)
- Yang Wei
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
| | - Boguslaw Stec
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
| | - Alfred G Redfield
- the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454
| | - Eranthie Weerapana
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
| | - Mary F Roberts
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
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42
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Ivanov KL, Pravdivtsev AN, Yurkovskaya AV, Vieth HM, Kaptein R. The role of level anti-crossings in nuclear spin hyperpolarization. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 81:1-36. [PMID: 25142733 DOI: 10.1016/j.pnmrs.2014.06.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/11/2014] [Accepted: 06/13/2014] [Indexed: 05/22/2023]
Abstract
Nuclear spin hyperpolarization is an important resource for increasing the sensitivity of NMR spectroscopy and MRI. Signal enhancements can be as large as 3-4 orders of magnitude. In hyperpolarization experiments, it is often desirable to transfer the initial polarization to other nuclei of choice, either protons or insensitive nuclei such as (13)C and (15)N. This situation arises primarily in Chemically Induced Dynamic Nuclear Polarization (CIDNP), Para-Hydrogen Induced Polarization (PHIP), and the related Signal Amplification By Reversible Exchange (SABRE). Here we review the recent literature on polarization transfer mechanisms, in particular focusing on the role of Level Anti-Crossings (LACs) therein. So-called "spontaneous" polarization transfer may occur both at low and high magnetic fields. In addition, transfer of spin polarization can be accomplished by using especially designed pulse sequences. It is now clear that at low field spontaneous polarization transfer is primarily due to coherent spin-state mixing under strong coupling conditions. However, thus far the important role of LACs in this process has not received much attention. At high magnetic field, polarization may be transferred by cross-relaxation effects. Another promising high-field technique is to generate the strong coupling condition by spin locking using strong radio-frequency fields. Here, an analysis of polarization transfer in terms of LACs in the rotating frame is very useful to predict which spin orders are transferred depending on the strength and frequency of the B1 field. Finally, we will examine the role of strong coupling and LACs in magnetic-field dependent nuclear spin relaxation and the related topic of long-lived spin-states.
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Affiliation(s)
- Konstantin L Ivanov
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3a, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Andrey N Pravdivtsev
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3a, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia
| | - Alexandra V Yurkovskaya
- International Tomography Center, Siberian Branch of the Russian Academy of Science, Institutskaya 3a, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia
| | - Hans-Martin Vieth
- Freie Universität Berlin, Institut für Experimentalphysik, Arnimallee 14, Berlin 14195, Germany
| | - Robert Kaptein
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands.
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43
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Gradziel CS, Wang Y, Stec B, Redfield AG, Roberts MF. Cytotoxic amphiphiles and phosphoinositides bind to two discrete sites on the Akt1 PH domain. Biochemistry 2014; 53:462-72. [PMID: 24383815 DOI: 10.1021/bi401720v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The mechanism of binding of two promising anticancer agents (the cytotoxic alkylphospholipids perifosine and miltefosine) to the Akt PH domain is investigated by high-resolution field-cycling (31)P nuclear magnetic resonance (NMR) spectroscopy using a spin-labeled recombinant PH domain. These results strongly indicate that there are two discrete amphiphile binding sites on the domain: (i) the cationic site that binds phosphoinositides and some alkylphospholipids and (ii) a second site that is occupied by only the alkylphospholipids. The identification of this second site for amphiphiles on the Akt1 PH domain provides a new target for drug development as well as insights into the regulation of the activity of the intact Akt1 protein. The field-cycling NMR methodology could be used to define discrete phospholipid or amphiphile binding sites on a wide variety of peripheral membrane proteins.
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Affiliation(s)
- Cheryl S Gradziel
- Department of Chemistry, Boston College , Chestnut Hill, Massachusetts 02467, United States
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44
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Charlier C, Khan SN, Marquardsen T, Pelupessy P, Reiss V, Sakellariou D, Bodenhausen G, Engelke F, Ferrage F. Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry. J Am Chem Soc 2013; 135:18665-72. [PMID: 24228712 PMCID: PMC3865798 DOI: 10.1021/ja409820g] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Understanding
the molecular determinants underlying protein function
requires the characterization of both structure and dynamics at atomic
resolution. Nuclear relaxation rates allow a precise characterization
of protein dynamics at the Larmor frequencies of spins. This usually
limits the sampling of motions to a narrow range of frequencies corresponding
to high magnetic fields. At lower fields one cannot achieve sufficient
sensitivity and resolution in NMR. Here, we use a fast shuttle device
where the polarization builds up and the signals are detected at high
field, while longitudinal relaxation takes place at low fields 0.5
< B0 < 14.1 T. The sample is propelled
over a distance up to 50 cm by a blowgun-like system in about 50 ms.
The analysis of nitrogen-15 relaxation in the protein ubiquitin over
such a wide range of magnetic fields offers unprecedented insights
into molecular dynamics. Some key regions of the protein feature structural
fluctuations on nanosecond time scales, which have so far been overlooked
in high-field relaxation studies. Nanosecond motions in proteins may
have been underestimated by traditional high-field approaches, and
slower supra-τc motions that have no effect on relaxation
may have been overestimated. High-resolution relaxometry thus opens
the way to a quantitative characterization of nanosecond motions in
proteins.
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Affiliation(s)
- Cyril Charlier
- Laboratoire des Biomolécules, Département de Chimie, UMR 7203 CNRS-UPMC-ENS, Ecole Normale Supérieure , 24 Rue Lhomond, 75231 Paris Cedex 05, France
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45
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Cai J, Guo S, Lomasney JW, Roberts MF. Ca2+-independent binding of anionic phospholipids by phospholipase C δ1 EF-hand domain. J Biol Chem 2013; 288:37277-88. [PMID: 24235144 DOI: 10.1074/jbc.m113.512186] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recombinant EF-hand domain of phospholipase C δ1 has a moderate affinity for anionic phospholipids in the absence of Ca(2+) that is driven by interactions of cationic and hydrophobic residues in the first EF-hand sequence. This region of PLC δ1 is missing in the crystal structure. The relative orientation of recombinant EF with respect to the bilayer, established with NMR methods, shows that the N-terminal helix of EF-1 is close to the membrane interface. Specific mutations of EF-1 residues in full-length PLC δ1 reduce enzyme activity but not because of disturbing partitioning of the protein onto vesicles. The reduction in enzymatic activity coupled with vesicle binding studies are consistent with a role for this domain in aiding substrate binding in the active site once the protein is transiently anchored at its target membrane.
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Affiliation(s)
- Jingfei Cai
- From the Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467 and
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46
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Cheng J, Goldstein R, Gershenson A, Stec B, Roberts MF. The cation-π box is a specific phosphatidylcholine membrane targeting motif. J Biol Chem 2013; 288:14863-73. [PMID: 23576432 DOI: 10.1074/jbc.m113.466532] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Peripheral membrane proteins can be targeted to specific organelles or the plasma membrane by differential recognition of phospholipid headgroups. Although molecular determinants of specificity for several headgroups, including phosphatidylserine and phosphoinositides are well defined, specific recognition of the headgroup of the zwitterionic phosphatidylcholine (PC) is less well understood. In cytosolic proteins the cation-π box provides a suitable receptor for choline recognition and binding through the trimethylammonium moiety. In PC, this moiety might provide a sufficient handle to bind to peripheral proteins via a cation-π cage, where the π systems of two or more aromatic residues are within 4-5 Å of the quaternary amine. We prove this hypothesis by engineering the cation-π box into secreted phosphatidylinositol-specific phospholipase C from Staphylococcus aureus, which lacks specific PC recognition. The N254Y/H258Y variant selectively binds PC-enriched vesicles, and x-ray crystallography reveals N254Y/H258Y binds choline and dibutyroylphosphatidylcholine within the cation-π motif. Such simple PC recognition motifs could be engineered into a wide variety of secondary structures providing a generally applicable method for specific recognition of PC.
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Affiliation(s)
- Jiongjia Cheng
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
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47
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Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for investigating the dynamics of biomolecules since it provides a description of motion that is comprehensive, site-specific, and relatively non-invasive. In particular, the study of protein dynamics has benefited from sustained methodological advances in NMR that have expanded the scope and time scales of accessible motion. Yet, many of these advances may not be well known to the more general physical chemistry community. Accordingly, this Perspective provides a glimpse of some of the more powerful methods in liquid state NMR that are helping reshape our understanding of functional motions of proteins.
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Affiliation(s)
- J W Peng
- Department of Chemistry and Biochemistry & Department of Physics University of Notre Dame, Notre Dame, IN 46556
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