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Razew A, Laguri C, Vallet A, Bougault C, Kaus-Drobek M, Sabala I, Simorre JP. Staphylococcus aureus sacculus mediates activities of M23 hydrolases. Nat Commun 2023; 14:6706. [PMID: 37872144 PMCID: PMC10593780 DOI: 10.1038/s41467-023-42506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
Peptidoglycan, a gigadalton polymer, functions as the scaffold for bacterial cell walls and provides cell integrity. Peptidoglycan is remodelled by a large and diverse group of peptidoglycan hydrolases, which control bacterial cell growth and division. Over the years, many studies have focused on these enzymes, but knowledge on their action within peptidoglycan mesh from a molecular basis is scarce. Here, we provide structural insights into the interaction between short peptidoglycan fragments and the entire sacculus with two evolutionarily related peptidases of the M23 family, lysostaphin and LytM. Through nuclear magnetic resonance, mass spectrometry, information-driven modelling, site-directed mutagenesis and biochemical approaches, we propose a model in which peptidoglycan cross-linking affects the activity, selectivity and specificity of these two structurally related enzymes differently.
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Affiliation(s)
- Alicja Razew
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France
- International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106, Warsaw, Poland
| | - Cedric Laguri
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France
| | - Alicia Vallet
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France
| | - Catherine Bougault
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France
| | - Magdalena Kaus-Drobek
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106, Warsaw, Poland
| | - Izabela Sabala
- International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109, Warsaw, Poland.
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106, Warsaw, Poland.
| | - Jean-Pierre Simorre
- Universite Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 avenue des Martyrs-CS10090, Grenoble cedex 9, 38044, France.
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2
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Johann C, Wegner S, Althoff G, Struppe J. Automation in solid state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 355:107554. [PMID: 37717302 DOI: 10.1016/j.jmr.2023.107554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Automation in solid state NMR (ssNMR) requires appropriate hardware, from rotor loading mechanisms over highly stable rf-transmitters and probe circuitry to automatic tuning and matching capabilities including automatic magic angle adjustment for ssNMR probes. While these hardware capabilities are highly desirable and are, to various degrees, provided by manufacturers, we focus herein on automating experiment setup using radio frequency (rf) fields, which are key parameters in solid state NMR experiments. Specifically, these include spinlock fields during cross polarization (CP), or rf-fields for homo- or heteronuclear spin recoupling or decoupling. Often, these fields have specific relationships to the magic angle spinning (MAS) frequency. Relying on a well-maintained spectrometer, the experiment setup shifts from traditionally required optimization of rf-power values for each element of an experiment sequence to automatically setting all parameters correctly without any need for optimization. The proposed approach allows executing an experiment by reading its rf-amplitude requirements based on the actual MAS rotation frequency just before starting data acquisition, while all other hardware-related parameters are automatically provided through global tables and scripts. Under modest MAS frequencies, no further rf-power optimization is required while providing optimal sensitivity of better than 90% of the optimal signal to noise. Any optional parameter optimization relates only to adjusting rf-nutation frequencies to the requirements of the sample and the sample rotation frequency rather than the spectrometer hardware. Fast MAS CP experiments with MAS frequencies above 40 kHz require a semi-automated setup by optimizing Hartmann-Hahn (HH) matched rf-fields that are synchronously varied relative to the MAS-frequency. This allows for a significant reduction of setup steps by up to one order of magnitude for such experiments, avoiding the traditional grid search for optimal CPMAS conditions. The approach presented here can also be applied to decoupling or recoupling sequences, requiring rotor synchronized rf-fields, reducing the setup to a few steps addressing the spin system's properties rather than the spectrometer hardware. Our approach permits automating all basic solid state NMR experiments for high throughput analytical tasks.
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Affiliation(s)
- Christof Johann
- Buker Biospin Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | | | - Gerhard Althoff
- Buker Biospin Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States.
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3
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Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR. J Am Chem Soc 2023; 145:10700-10711. [PMID: 37140345 DOI: 10.1021/jacs.3c01200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts.
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Affiliation(s)
- Laura Troussicot
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria
| | - Alicia Vallet
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
| | - Mikael Molin
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Department of Life Sciences, Chalmers University of Technology, SE-405 30 Göteborg, Sweden
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | - Paul Schanda
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria
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4
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Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. J Struct Biol X 2022; 7:100079. [PMID: 36578472 PMCID: PMC9791609 DOI: 10.1016/j.yjsbx.2022.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.
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5
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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6
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Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nat Commun 2022; 13:1927. [PMID: 35395851 PMCID: PMC8993905 DOI: 10.1038/s41467-022-29423-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/14/2022] [Indexed: 02/07/2023] Open
Abstract
Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution.
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Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.,ICSN, CNRS UPR2301, Univ. Paris-Saclay, Gif-sur-Yvette, France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.,Celonic AG, Eulerstrasse 55, 4051, Basel, Switzerland
| | - Duccio Malinverni
- Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.,Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,i3S, Instituto de Investigacao e Inovacao em Saude, Universidade do Porto, Porto, Portugal
| | - Matteo Paloni
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Iva Sučec
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Juan Pablo Bustamante
- Instituto de Bioingenieria y Bioinformatica, IBB (CONICET-UNER), Oro Verde, Entre Rios, Argentina
| | - Alessandro Barducci
- Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France. .,Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.
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7
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Lends A, Berbon M, Habenstein B, Nishiyama Y, Loquet A. Protein resonance assignment by solid-state NMR based on 1H-detected 13C double-quantum spectroscopy at fast MAS. JOURNAL OF BIOMOLECULAR NMR 2021; 75:417-427. [PMID: 34813018 DOI: 10.1007/s10858-021-00386-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Solid-state NMR spectroscopy is a powerful technique to study insoluble and non-crystalline proteins and protein complexes at atomic resolution. The development of proton (1H) detection at fast magic-angle spinning (MAS) has considerably increased the analytical capabilities of the technique, enabling the acquisition of 1H-detected fingerprint experiments in few hours. Here an approach based on double-quantum (DQ) 13C spectroscopy, detected on 1H, is proposed for fast MAS regime (> 60 kHz) to perform the sequential assignment of insoluble proteins of small size, without any specific deuteration requirement. By combining two three-dimensional 1H detected experiments correlating a 13C DQ dimension respectively to its intra-residue and sequential 15 N-1H pairs, a sequential walk through DQ (Ca + CO) resonance is obtained. The approach takes advantage of fast MAS to achieve an efficient sensitivity and the addition of a DQ dimension provides spectral features useful for the resonance assignment process.
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Affiliation(s)
- Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
| | - Mélanie Berbon
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Birgit Habenstein
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa, 230-0045, Japan.
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo, 196-8558, Japan.
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
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8
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Tognetti J, Trent Franks W, Gallo A, Lewandowski JR. Accelerating 15N and 13C R 1 and R 1ρ relaxation measurements by multiple pathway solid-state NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 331:107049. [PMID: 34508920 DOI: 10.1016/j.jmr.2021.107049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Magic angle spinning (MAS) Solid-state NMR is a powerful technique to probe dynamics of biological systems at atomic resolution. R1 and R1ρ relaxation measurements can provide detailed insight on amplitudes and time scales of motions, especially when information from several different site-specific types of probes is combined. However, such experiments are time-consuming to perform. Shortening the time necessary to record relaxation data for different nuclei will greatly enhance practicality of such approaches. Here, we present staggered acquisition experiments to acquire multiple relaxation experiments from a single excitation to reduce the overall experimental time. Our strategy enables one to collect 15N and 13C relaxation data in a single experiment in a fraction of the time necessary for two separate experiments, with the same signal to noise ratio.
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Affiliation(s)
- Jacqueline Tognetti
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom; Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom; Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Angelo Gallo
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom.
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