1
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Qi C, Mankinen O, Telkki VV, Hilty C. Measuring Protein-Ligand Binding by Hyperpolarized Ultrafast NMR. J Am Chem Soc 2024; 146:5063-5066. [PMID: 38373110 PMCID: PMC10910566 DOI: 10.1021/jacs.3c14359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/21/2024]
Abstract
Protein-ligand interactions can be detected by observing changes in the transverse relaxation rates of the ligand upon binding. The ultrafast NMR technique, which correlates the chemical shift with the transverse relaxation rate, allows for the simultaneous acquisition of R2 for carbon spins at different positions. In combination with dissolution dynamic nuclear polarization (D-DNP), where the signal intensity is enhanced by thousands of times, the R2 values of several carbon signals from unlabeled benzylamine are observable within a single scan. The hyperpolarized ultrafast chemical shift-R2 correlated experiment separates chemical shift encoding from the readout phase in the NMR pulse sequence, which allows it to beat the fundamental limit on the spectral resolution otherwise imposed by the sampling theorem. Applications enabled by the ability to measure multiple relaxation rates in a single scan include the study of structural properties of protein-ligand interactions.
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Affiliation(s)
- Chang Qi
- Chemistry
Department, Texas A&M University, College Station, Texas 77843-3255, United
States
| | - Otto Mankinen
- NMR
Research Unit, Faculty of Science, University
of Oulu, 90014 Oulu, Finland
| | - Ville-Veikko Telkki
- NMR
Research Unit, Faculty of Science, University
of Oulu, 90014 Oulu, Finland
| | - Christian Hilty
- Chemistry
Department, Texas A&M University, College Station, Texas 77843-3255, United
States
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2
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Wang Z, Guo D, Tu Z, Huang Y, Zhou Y, Wang J, Feng L, Lin D, You Y, Agback T, Orekhov V, Qu X. A Sparse Model-Inspired Deep Thresholding Network for Exponential Signal Reconstruction-Application in Fast Biological Spectroscopy. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023; 34:7578-7592. [PMID: 35120010 DOI: 10.1109/tnnls.2022.3144580] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The nonuniform sampling (NUS) is a powerful approach to enable fast acquisition but requires sophisticated reconstruction algorithms. Faithful reconstruction from partially sampled exponentials is highly expected in general signal processing and many applications. Deep learning (DL) has shown astonishing potential in this field, but many existing problems, such as lack of robustness and explainability, greatly limit its applications. In this work, by combining the merits of the sparse model-based optimization method and data-driven DL, we propose a DL architecture for spectra reconstruction from undersampled data, called MoDern. It follows the iterative reconstruction in solving a sparse model to build the neural network, and we elaborately design a learnable soft-thresholding to adaptively eliminate the spectrum artifacts introduced by undersampling. Extensive results on both synthetic and biological data show that MoDern enables more robust, high-fidelity, and ultrafast reconstruction than the state-of-the-art methods. Remarkably, MoDern has a small number of network parameters and is trained on solely synthetic data while generalizing well to biological data in various scenarios. Furthermore, we extend it to an open-access and easy-to-use cloud computing platform (XCloud-MoDern), contributing a promising strategy for further development of biological applications.
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3
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Negroni M, Kurzbach D. Missing Pieces in Structure Puzzles: How Hyperpolarized NMR Spectroscopy Can Complement Structural Biology and Biochemistry. Chembiochem 2023; 24:e202200703. [PMID: 36624049 DOI: 10.1002/cbic.202200703] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Structure determination lies at the heart of many biochemical research programs. However, the "giants": X-ray diffraction, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, among others, leave quite a few dark spots on the structural pictures drawn of proteins, nucleic acids, membranes, and other biomacromolecules. For example, structural models under physiological conditions or of short-lived intermediates often remain out of reach of the established experimental methods. This account frames the possibility of including hyperpolarized, that is, dramatically signal-enhanced NMR in existing workflows to fill these spots with detailed depictions. We highlight how integrating methods based on dissolution dynamic nuclear polarization can provide valuable complementary information about formerly inaccessible conformational spaces for many systems. A particular focus will be on hyperpolarized buffers to facilitate the NMR structure determination of challenging systems.
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Affiliation(s)
- Mattia Negroni
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
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4
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Dumez JN. NMR methods for the analysis of mixtures. Chem Commun (Camb) 2022; 58:13855-13872. [PMID: 36458684 PMCID: PMC9753098 DOI: 10.1039/d2cc05053f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/19/2022] [Indexed: 07/31/2023]
Abstract
NMR spectroscopy is a powerful approach for the analysis of mixtures. Its usefulness arises in large part from the vast landscape of methods, and corresponding pulse sequences, that have been and are being designed to tackle the specific properties of mixtures of small molecules. This feature article describes a selection of methods that aim to address the complexity, the low concentrations, and the changing nature that mixtures can display. These notably include pure-shift and diffusion NMR methods, hyperpolarisation methods, and fast 2D NMR methods such as ultrafast 2D NMR and non-uniform sampling. Examples or applications are also described, in fields such as reaction monitoring and metabolomics, to illustrate the relevance and limitations of different methods.
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5
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Pham P, Mandal R, Qi C, Hilty C. Interfacing Liquid State Hyperpolarization Methods with NMR Instrumentation. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100052. [PMID: 35530721 PMCID: PMC9070690 DOI: 10.1016/j.jmro.2022.100052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Advances in liquid state hyperpolarization methods have enabled new applications of high-resolution NMR spectroscopy. Utilizing strong signal enhancements from hyperpolarization allows performing NMR spectroscopy at low concentration, or with high time resolution. Making use of the high, but rapidly decaying hyperpolarization in the liquid state requires new techniques to interface hyperpolarization equipment with liquid state NMR spectrometers. This article highlights rapid injection, high resolution NMR spectroscopy with hyperpolarization produced by the techniques of dissolution dynamic nuclear polarization (D-DNP) and para-hydrogen induced polarization (PHIP). These are popular, albeit not the only methods to produce high polarization levels for liquid samples. Gas and liquid driven sample injection techniques are compatible with both of these hyperpolarization methods. The rapid sample injection techniques are combined with adapted NMR experiments working in a single, or small number of scans. They expand the application of liquid state hyperpolarization to spins with comparably short relaxation times, provide enhanced control over sample conditions, and allow for mixing experiments to study reactions in real time.
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6
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Lhoste C, Lorandel B, Praud C, Marchand A, Mishra R, Dey A, Bernard A, Dumez JN, Giraudeau P. Ultrafast 2D NMR for the analysis of complex mixtures. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:1-46. [PMID: 36113916 DOI: 10.1016/j.pnmrs.2022.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 06/15/2023]
Abstract
2D NMR is extensively used in many different fields, and its potential for the study of complex biochemical or chemical mixtures has been widely demonstrated. 2D NMR gives the ability to resolve peaks that overlap in 1D spectra, while providing both structural and quantitative information. However, complex mixtures are often analysed in situations where the data acquisition time is a crucial limitation, due to an ongoing chemical reaction or a moving sample from a hyphenated technique, or to the high-throughput requirement associated with large sample collections. Among the great diversity of available fast 2D methods, ultrafast (or single-scan) 2D NMR is probably the most general and versatile approach for complex mixture analysis. Indeed, ultrafast NMR has undergone an impressive number of methodological developments that have helped turn it into an efficient analytical tool, and numerous applications to the analysis of mixtures have been reported. This review first summarizes the main concepts, features and practical limitations of ultrafast 2D NMR, as well as the methodological developments that improved its analytical potential. Then, a detailed description of the main applications of ultrafast 2D NMR to mixture analysis is given. The two major application fields of ultrafast 2D NMR are first covered, i.e., reaction/process monitoring and metabolomics. Then, the potential of ultrafast 2D NMR for the analysis of hyperpolarized mixtures is described, as well as recent developments in oriented media. This review focuses on high-resolution liquid-state 2D experiments (including benchtop NMR) that include at least one spectroscopic dimension (i.e., 2D spectroscopy and DOSY) but does not cover in depth applications without spectral resolution and/or in inhomogeneous fields.
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Affiliation(s)
- Célia Lhoste
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | | | - Clément Praud
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | - Achille Marchand
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | - Rituraj Mishra
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | - Arnab Dey
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
| | - Aurélie Bernard
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes F-44000, France
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7
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Residue-resolved monitoring of protein hyperpolarization at sub-second time resolution. Commun Chem 2021; 4:147. [PMID: 36697662 PMCID: PMC9814832 DOI: 10.1038/s42004-021-00587-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
Signal-enhancement techniques for NMR spectroscopy are important to amplify the weak resonances provided by nuclear spins. Recently, 'hyperpolarization' techniques have been intensively investigated. These provide nuclear spin states far from equilibrium yielding strong signal boosts up to four orders of magnitude. Here we propose a method for real-time NMR of 'hyperpolarized' proteins at residue resolution. The approach is based on dissolution dynamic nuclear polarization (d-DNP), which enables the use of hyperpolarized buffers that selectively boost NMR signals of solvent-exposed protein residues. The resulting spectral sparseness and signal enhancements enable recording of residue-resolved spectra at a 2 Hz sampling rate. Thus, we monitor the hyperpolarization level of different protein residues simultaneously under near-physiological conditions. We aim to address two points: 1) NMR experiments are often performed under conditions that increase sensitivity but are physiologically irrelevant; 2) long signal accumulation impedes fast real-time monitoring. Both limitations are of fundamental relevance to ascertain pharmacological relevance and study protein kinetics.
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8
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Yong JRJ, Hansen AL, Kupče Ē, Claridge TDW. Increasing sensitivity and versatility in NMR supersequences with new HSQC-based modules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 329:107027. [PMID: 34246882 DOI: 10.1016/j.jmr.2021.107027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 05/22/2023]
Abstract
The sensitivity-enhanced HSQC, as well as HSQC-TOCSY, experiments have been modified for incorporation into NOAH (NMR by Ordered Acquisition using 1H detection) supersequences, adding diversity for 13C and 15N modules. Importantly, these heteronuclear modules have been specifically tailored to preserve the magnetisation required for subsequent acquisition of other heteronuclear or homonuclear modules in a supersequence. In addition, we present protocols for optimally combining HSQC and HSQC-TOCSY elements within the same supersequences, yielding high-quality 2D spectra suitable for structure characterisation but with greatly reduced experiment durations. We further demonstrate that these time savings can translate to increased detection sensitivity per unit time.
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Affiliation(s)
- Jonathan R J Yong
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH 43210, USA
| | - Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, UK
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.
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9
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Kupče Ē, Frydman L, Webb AG, Yong JRJ, Claridge TDW. Parallel nuclear magnetic resonance spectroscopy. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00024-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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10
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Qiu T, Wang Z, Liu H, Guo D, Qu X. Review and prospect: NMR spectroscopy denoising and reconstruction with low-rank Hankel matrices and tensors. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:324-345. [PMID: 32797694 DOI: 10.1002/mrc.5082] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 05/16/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is an important analytical tool in chemistry, biology, and life science, but it suffers from relatively low sensitivity and long acquisition time. Thus, improving the apparent signal-to-noise ratio and accelerating data acquisition became indispensable. In this review, we summarize the recent progress on low-rank Hankel matrix and tensor methods, which exploit the exponential property of free-induction decay signals, to enable effective denoising and spectra reconstruction. We also outline future developments that are likely to make NMR spectroscopy a far more powerful technique.
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Affiliation(s)
- Tianyu Qiu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Zi Wang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Huiting Liu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Di Guo
- School of Computer and Information Engineering, Xiamen University of Technology, Xiamen, China
| | - Xiaobo Qu
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
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11
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Dumez JN. -Frequency-swept pulses for ultrafast spatially encoded NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 323:106817. [PMID: 33518177 DOI: 10.1016/j.jmr.2020.106817] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 06/12/2023]
Abstract
Ultrafast NMR based on spatial encoding yields arbitrary multidimensional spectra in a single scan. The dramatic acceleration afforded by spatial parallelisation makes it possible to capture transient species and processes, and has notably been applied to the monitoring of reactions and the analysis of hyperpolarised species. At the heart of ultrafast NMR lies the spatially sequential manipulation of nuclear spins. This is virtually always achieved by combining a swept radio-frequency pulse with a magnetic field gradient pulse. The dynamics of nuclear spins during these pulse sequence elements is key to understand and design ultrafast NMR experiments, and can often be described by surprisingly simple models. This article describes the spatial encoding of relaxation, chemical shift and diffusion in a common framework and discusses directions for future developments.
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12
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A 300-fold enhancement of imino nucleic acid resonances by hyperpolarized water provides a new window for probing RNA refolding by 1D and 2D NMR. Proc Natl Acad Sci U S A 2020; 117:2449-2455. [PMID: 31949004 DOI: 10.1073/pnas.1916956117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
NMR sensitivity-enhancement methods involving hyperpolarized water could be of importance for solution-state biophysical investigations. Hyperpolarized water (HyperW) can enhance the 1H NMR signals of exchangeable sites by orders of magnitude over their thermal counterparts, while providing insight into chemical exchange and solvent accessibility at a site-resolved level. As HyperW's enhancements are achieved by exploiting fast solvent exchanges associated with minimal interscan delays, possibilities for the rapid monitoring of chemical reactions and biomolecular (re)folding are opened. HyperW NMR can also accommodate heteronuclear transfers, facilitating the rapid acquisition of 2-dimensional (2D) 15N-1H NMR correlations, and thereby combining an enhanced spectral resolution with speed and sensitivity. This work demonstrates how these qualities can come together for the study of nucleic acids. HyperW injections were used to target the guanine-sensing riboswitch aptamer domain (GSRapt) of the xpt-pbuX operon in Bacillus subtilis Unlike what had been observed in proteins, where residues benefited of HyperW NMR only if/when sufficiently exposed to water, these enhancements applied to every imino resonance throughout the RNA. The >300-fold enhancements observed in the resulting 1H NMR spectra allowed us to monitor in real time the changes that GSRapt undergoes upon binding hypoxanthine, a high-affinity interaction leading to conformational refolding on a ∼1-s timescale at 36 °C. Structural responses could be identified for several nucleotides by 1-dimensional (1D) imino 1H NMR as well as by 2D HyperW NMR spectra acquired upon simultaneous injection of hyperpolarized water and hypoxanthine. The folding landscape revealed by this HyperW strategy for GSRapt, is briefly discussed.
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13
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Jacquemmoz C, Giraud F, Dumez JN. Online reaction monitoring by single-scan 2D NMR under flow conditions. Analyst 2020; 145:478-485. [DOI: 10.1039/c9an01758e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-scan 2D NMR based on spatial encoding can be used to monitor chemical reactions with a flow unit in realistic reaction conditions.
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Affiliation(s)
| | - François Giraud
- ICSN
- CNRS UPR2301
- Univ. Paris Sud
- Université Paris-Saclay
- 91190 Gif sur Yvette
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14
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Nawrocka EK, Kasprzak P, Zawada K, Sadło J, Grochala W, Kazimierczuk K, Leszczyński PJ. Nonstationary Two-Dimensional Nuclear Magnetic Resonance: A Method for Studying Reaction Mechanisms in Situ. Anal Chem 2019; 91:11306-11315. [PMID: 31387347 DOI: 10.1021/acs.analchem.9b02414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear magnetic resonance spectroscopy (NMR) is a versatile tool of chemical analysis allowing one to determine structures of molecules with atomic resolution. Particularly informative are two-dimensional (2D) experiments that directly identify atoms coupled by chemical bonds or a through-space interaction. Thus, NMR could potentially be powerful tool to study reactions in situ and explain their mechanisms. Unfortunately, 2D NMR is very time-consuming and thus often cannot serve as a "snapshot" technique for in situ reaction monitoring. Particularly difficult is the case of spectra, in which resonance frequencies vary in the course of reaction. This leads to resolution and sensitivity loss, often hindering the detection of transient products. In this paper we introduce a novel approach to correct such nonstationary 2D NMR signals and raise the detection limits over 10 times. We demonstrate success of its application for studying the mechanism of the reaction of AgSO4-induced synthesis of diphenylmethane-type compounds. Several reactions occur in the studied mixture of benzene and toluene, all with rather low yield and leading to compounds with similar chemical shifts. Nevertheless, with the use of a proposed 2D NMR approach we were able to describe complex mechanisms of diphenylmethane formation involving AgSO4-induced toluene deprotonation and formation of benzyl carbocation, followed by nucleophilic attacks.
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Affiliation(s)
- Ewa Klaudia Nawrocka
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-089 Warsaw , Poland.,Centre of New Technologies , University of Warsaw , Banacha 2C , 02-097 Warsaw , Poland
| | - Paweł Kasprzak
- Centre of New Technologies , University of Warsaw , Banacha 2C , 02-097 Warsaw , Poland.,Department of Mathematical Methods in Physics, Faculty of Physics , University of Warsaw , Pasteura 5 , 02-093 Warsaw , Poland
| | - Katarzyna Zawada
- Department of Physical Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division , Medical University of Warsaw , Banacha 1 , 02-097 Warsaw , Poland
| | - Jarosław Sadło
- Institute of Nuclear Chemistry and Technology , Dorodna 16 , 03-195 Warsaw , Poland
| | - Wojciech Grochala
- Centre of New Technologies , University of Warsaw , Banacha 2C , 02-097 Warsaw , Poland
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15
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Urbańczyk M, Shchukina A, Gołowicz D, Kazimierczuk K. TReNDS-Software for reaction monitoring with time-resolved non-uniform sampling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:4-12. [PMID: 30255516 DOI: 10.1002/mrc.4796] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
NMR spectroscopy, used routinely for structure elucidation, has also become a widely applied tool for process and reaction monitoring. However, the most informative of NMR methods-correlation experiments-are often useless in this kind of applications. The traditional sampling of a multidimensional FID is usually time-consuming, and thus, the reaction-monitoring toolbox was practically limited to 1D experiments (with rare exceptions, e.g., single-scan or fast-sampling experiments). Recently, the technique of time-resolved non-uniform sampling (TR-NUS) has been proposed, which allows to use standard multidimensional pulse sequences preserving the temporal resolution close to that achievable in 1D experiments. However, the method existed only as a prototype and did not allow on-the-fly processing during the reaction. In this paper, we introduce TReNDS: free, user-friendly software kit for acquisition and processing of TR-NUS data. The program works on Bruker, Agilent, and Magritek spectrometers, allowing to carry out up to four experiments with interleaved TR-NUS. The performance of the program is demonstrated on the example of enzymatic hydrolysis of sucrose.
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Affiliation(s)
- Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Spektrino Sp. z o.o., Warsaw, Poland
- NMR Research Unit, University of Oulu, Oulu, Finland
| | | | - Dariusz Gołowicz
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
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16
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Dumez JN. Spatial encoding and spatial selection methods in high-resolution NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:101-134. [PMID: 30527133 DOI: 10.1016/j.pnmrs.2018.08.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/01/2018] [Accepted: 08/01/2018] [Indexed: 06/09/2023]
Abstract
A family of high-resolution NMR methods share the common concept of acquiring in parallel different sub-experiments in different spatial regions of the NMR tube. These spatial encoding and spatial selection methods were for the most part introduced independently from each other and serve different purposes, but they share common ingredients, often derived from magnetic resonance imaging, and they all benefit from a greatly improved time-efficiency. This review article provides a description of several spatial encoding and spatial selection methods, including single-scan multidimensional experiments (ultrafast 2D NMR, DOSY, Z spectroscopy, inversion recovery and Laplace NMR), pure shift and selective refocusing experiments (including Zangger-Sterk decoupling, G-SERF and PSYCHE), a Z filter, and fast-pulsing slice-selective experiments. Some key elements for spatial parallelisation are introduced and when possible a common framework is used for the analysis of each method. Sensitivity considerations are discussed, and a selection of applications is analysed to illustrate which questions can be answered thanks to spatial encoding and spatial selection methods, and discuss the perspectives for future developments and applications.
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Affiliation(s)
- Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France.
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17
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Concilio MG, Jacquemmoz C, Boyarskaya D, Masson G, Dumez JN. Ultrafast Maximum-Quantum NMR Spectroscopy for the Analysis of Aromatic Mixtures. Chemphyschem 2018; 19:3310-3317. [PMID: 30239108 DOI: 10.1002/cphc.201800667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 12/24/2022]
Abstract
Maximum-quantum (MaxQ) NMR experiments have been introduced to overcome issues related to peak overlap and high spectral density in the NMR spectra of aromatic mixtures. In MaxQ NMR, spin systems are separated on the basis of the highest-quantum coherence that they can form. MaxQ experiments are however time consuming and methods have been introduced to accelerate them. In this article, we demonstrate the ultrafast, single-scan acquisition of MaxQ NMR spectra using spatial encoding of the multiple-quantum dimension. So far, the spatial encoding methodology has been applied only for the encoding of up to double-quantum coherences, and here we show that it can be extended to higher coherence orders, to yield a massive reduction of the acquisition time of multi-quantum spectra of aromatic mixtures, and also to monitor chemical reactions.
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Affiliation(s)
- Maria Grazia Concilio
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Corentin Jacquemmoz
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Dina Boyarskaya
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Géraldine Masson
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Univ. Paris Sud, Université Paris-Saclay Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
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18
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Szekely O, Armony G, Olsen GL, Bigman LS, Levy Y, Fass D, Frydman L. Identification and Rationalization of Kinetic Folding Intermediates for a Low-Density Lipoprotein Receptor Ligand-Binding Module. Biochemistry 2018; 57:4776-4787. [PMID: 29979586 DOI: 10.1021/acs.biochem.8b00466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many mutations that cause familial hypercholesterolemia localize to ligand-binding domain 5 (LA5) of the low-density lipoprotein receptor, motivating investigation of the folding and misfolding of this small, disulfide-rich, calcium-binding domain. LA5 folding is known to involve non-native disulfide isomers, yet these folding intermediates have not been structurally characterized. To provide insight into these intermediates, we used nuclear magnetic resonance (NMR) to follow LA5 folding in real time. We demonstrate that misfolded or partially folded disulfide intermediates are indistinguishable from the unfolded state when focusing on the backbone NMR signals, which provide information on the formation of only the final, native state. However, 13C labeling of cysteine side chains differentiated transient intermediates from the unfolded and native states and reported on disulfide bond formation in real time. The cysteine pairings in a dominant intermediate were identified using 13C-edited three-dimensional NMR, and coarse-grained molecular dynamics simulations were used to investigate the preference of this disulfide set over other non-native arrangements. The transient population of LA5 species with particular non-native cysteine connectitivies during folding supports the conclusion that cysteine pairing is not random and that there is a bias toward certain structural ensembles during the folding process, even prior to the binding of calcium.
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Affiliation(s)
- Or Szekely
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Gad Armony
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Gregory Lars Olsen
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Lavi S Bigman
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Yaakov Levy
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Deborah Fass
- Department of Structural Biology , Weizmann Institute of Science , Rehovot 7610001 , Israel
| | - Lucio Frydman
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 7610001 , Israel
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19
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Huang Y, Yang Y, Cai S, Chen Z, Zhan H, Li C, Tan C, Chen Z. General Two-Dimensional Absorption-Mode J-Resolved NMR Spectroscopy. Anal Chem 2017; 89:12646-12651. [DOI: 10.1021/acs.analchem.7b02740] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yuqing Huang
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Yu Yang
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuhui Cai
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhiwei Chen
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Haolin Zhan
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Chen Li
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Chunhua Tan
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhong Chen
- Department of Electronic
Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance,
State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, Fujian 361005, China
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20
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Ikeya T, Ban D, Lee D, Ito Y, Kato K, Griesinger C. Solution NMR views of dynamical ordering of biomacromolecules. Biochim Biophys Acta Gen Subj 2017; 1862:287-306. [PMID: 28847507 DOI: 10.1016/j.bbagen.2017.08.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND To understand the mechanisms related to the 'dynamical ordering' of macromolecules and biological systems, it is crucial to monitor, in detail, molecular interactions and their dynamics across multiple timescales. Solution nuclear magnetic resonance (NMR) spectroscopy is an ideal tool that can investigate biophysical events at the atomic level, in near-physiological buffer solutions, or even inside cells. SCOPE OF REVIEW In the past several decades, progress in solution NMR has significantly contributed to the elucidation of three-dimensional structures, the understanding of conformational motions, and the underlying thermodynamic and kinetic properties of biomacromolecules. This review discusses recent methodological development of NMR, their applications and some of the remaining challenges. MAJOR CONCLUSIONS Although a major drawback of NMR is its difficulty in studying the dynamical ordering of larger biomolecular systems, current technologies have achieved considerable success in the structural analysis of substantially large proteins and biomolecular complexes over 1MDa and have characterised a wide range of timescales across which biomolecular motion exists. While NMR is well suited to obtain local structure information in detail, it contributes valuable and unique information within hybrid approaches that combine complementary methodologies, including solution scattering and microscopic techniques. GENERAL SIGNIFICANCE For living systems, the dynamic assembly and disassembly of macromolecular complexes is of utmost importance for cellular homeostasis and, if dysregulated, implied in human disease. It is thus instructive for the advancement of the study of the dynamical ordering to discuss the potential possibilities of solution NMR spectroscopy and its applications. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Teppei Ikeya
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Donghan Lee
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Yutaka Ito
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0373, Japan; CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Koichi Kato
- Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabe-dori 3-1, Mizuho-ku, Nagoya 467-8603, Japan
| | - Christian Griesinger
- Department of Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
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21
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Michalik-Onichimowska A, Kern S, Riedel J, Panne U, King R, Maiwald M. "Click" analytics for "click" chemistry - A simple method for calibration-free evaluation of online NMR spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 277:154-161. [PMID: 28288418 DOI: 10.1016/j.jmr.2017.02.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/23/2017] [Accepted: 02/25/2017] [Indexed: 06/06/2023]
Abstract
Driven mostly by the search for chemical syntheses under biocompatible conditions, so called "click" chemistry rapidly became a growing field of research. The resulting simple one-pot reactions are so far only scarcely accompanied by an adequate optimization via comparably straightforward and robust analysis techniques possessing short set-up times. Here, we report on a fast and reliable calibration-free online NMR monitoring approach for technical mixtures. It combines a versatile fluidic system, continuous-flow measurement of 1H spectra with a time interval of 20s per spectrum, and a robust, fully automated algorithm to interpret the obtained data. As a proof-of-concept, the thiol-ene coupling between N-boc cysteine methyl ester and allyl alcohol was conducted in a variety of non-deuterated solvents while its time-resolved behaviour was characterized with step tracer experiments. Overlapping signals in online spectra during thiol-ene coupling could be deconvoluted with a spectral model using indirect hard modeling and were subsequently converted to either molar ratios (using a calibration-free approach) or absolute concentrations (using 1-point calibration). For various solvents the kinetic constant k for pseudo-first order reaction was estimated to be 3.9h-1 at 25°C. The obtained results were compared with direct integration of non-overlapping signals and showed good agreement with the implemented mass balance.
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Affiliation(s)
- Aleksandra Michalik-Onichimowska
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstaetter-Str. 11, D-12489 Berlin, Germany; Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Zum Groβen Windkanal 6, 12489 Berlin, Germany
| | - Simon Kern
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstaetter-Str. 11, D-12489 Berlin, Germany
| | - Jens Riedel
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstaetter-Str. 11, D-12489 Berlin, Germany
| | - Ulrich Panne
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstaetter-Str. 11, D-12489 Berlin, Germany; Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany; School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Zum Groβen Windkanal 6, 12489 Berlin, Germany
| | - Rudibert King
- Department Measurement and Control, Institute of Process Engineering, Berlin University of Technology, Hardenbergstr. 36a, 10623 Berlin, Germany
| | - Michael Maiwald
- Bundesanstalt für Materialforschung und -prüfung (BAM), Richard-Willstaetter-Str. 11, D-12489 Berlin, Germany.
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22
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Jaiswal SK, Tejo Prakash N, Prakash R. 1H NMR Based Quantification of Ethyl Ester in Biodiesel: A Comparative Study of Product-Dependent Derivations. ACTA ACUST UNITED AC 2016. [DOI: 10.1080/22297928.2016.1246977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Dass R, Kasprzak P, Koźmiński W, Kazimierczuk K. Artifacts in time-resolved NUS: A case study of NOE build-up curves from 2D NOESY. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:108-116. [PMID: 26896866 DOI: 10.1016/j.jmr.2016.01.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 06/05/2023]
Abstract
Multidimensional NMR spectroscopy requires time-consuming sampling of indirect dimensions and so is usually used to study stable samples. However, dynamically changing compounds or their mixtures commonly occur in problems of natural science. Monitoring them requires the use multidimensional NMR in a time-resolved manner - in other words, a series of quick spectra must be acquired at different points in time. Among the many solutions that have been proposed to achieve this goal, time-resolved non-uniform sampling (TR-NUS) is one of the simplest. In a TR-NUS experiment, the signal is sampled using a shuffled random schedule and then divided into overlapping subsets. These subsets are then processed using one of the NUS reconstruction methods, for example compressed sensing (CS). The resulting stack of spectra forms a temporal "pseudo-dimension" that shows the changes caused by the process occurring in the sample. CS enables the use of small subsets of data, which minimizes the averaging of the effects studied. Yet, even within these limited timeframes, the sample undergoes certain changes. In this paper we discuss the effect of varying signal amplitude in a TR-NUS experiment. Our theoretical calculations show that the variations within the subsets lead to t1-noise, which is dependent on the rate of change of the signal amplitude. We verify these predictions experimentally. As a model case we choose a novel 2D TR-NOESY experiment in which mixing time is varied in parallel with shuffled NUS in the indirect dimension. The experiment, performed on a sample of strychnine, provides a near-continuous NOE build-up curve, whose shape closely reflects the t1-noise level. 2D TR-NOESY reduces the measurement time compared to the conventional approach and makes it possible to verify the theoretical predictions about signal variations during TR-NUS.
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Affiliation(s)
- Rupashree Dass
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paweł Kasprzak
- Department of Mathematical Methods in Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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24
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Herrera A, Fernández-Valle E, Martínez-Álvarez R, Molero-Vílchez D, Pardo-Botero ZD, Sáez-Barajas E. Monitoring organic reactions by UF-NMR spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:952-970. [PMID: 25998506 DOI: 10.1002/mrc.4240] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 02/26/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
Standard 2D NMR experiments suffer from the many t1 increments needed for spectra with sufficient digital resolution in the indirect dimension. Despite the different methodological approaches to overcome this problem, these increments have prevented studies of fast reactions. The development of ultrafast NMR (UF-NMR) has decisively speeded up the time scale of standard NMR to allow the study of organic reactions as they happen in real time to reveal mechanistic details. This mini-review summarizes the results achieved in monitoring organic reactions through this exciting technique.
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Affiliation(s)
- Antonio Herrera
- CAI-RMN, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Química Orgánica I, Facultad de Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Roberto Martínez-Álvarez
- Departamento de Química Orgánica I, Facultad de Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Zulay D Pardo-Botero
- CAI-RMN, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Química Orgánica I, Facultad de Químicas, Universidad Complutense de Madrid, Madrid, Spain
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25
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Akoka S, Giraudeau P. Fast hybrid multi-dimensional NMR methods based on ultrafast 2D NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:986-94. [PMID: 25825866 DOI: 10.1002/mrc.4237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 05/13/2023]
Abstract
Conventional multi-dimensional (nD) NMR experiments are characterized by inherent long acquisition durations, while ultrafast (UF) NMR makes it possible to reduce to a few hundreds of milliseconds the overall acquisition duration of a complete nD NMR dataset. Although extremely promising for a number of specific applications, the UF strategy suffers from significant limitations compared with its conventional counterpart. The main limitations concern the sensitivity, the resolution, and the accessible spectral width. However, when the targeted applications are compatible with an acquisition duration between a few seconds and a few minutes, hybrid UF techniques can be used to improve the performance of UF nD NMR while remaining faster than conventional acquisitions. Much better results in terms of signal-to-noise ratio can be achieved with the multi-scan single-shot approach or with interleaved acquisitions. Even more, for the same experimental duration, and in the case of homonuclear 2D NMR, the multi-scan single-shot approach has a much higher precision than conventional 2D NMR. Interleaved 2D NMR overcomes the drawbacks of single-scan UF NMR in terms of spectral width and provides spectra for which the quality is not significantly different from that obtained with conventional 2D NMR. Finally, high spectral qualities have been demonstrated from hybrid conventional/UF 3D approaches capable of recording a whole 3D spectrum in the time needed to record a conventional 2D spectrum. This mini-review aims at describing the principles, the recent advances and the latest applications of these hybrid techniques. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Serge Akoka
- EBSI Team, Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), CNRS, UMR 6230, Université de Nantes, LUNAM Université
| | - Patrick Giraudeau
- EBSI Team, Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), CNRS, UMR 6230, Université de Nantes, LUNAM Université
- Institut Universitaire de France, 1 rue Descartes, 75005, Paris Cedex 5, France
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26
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Gal M, Frydman L. Multidimensional NMR spectroscopy in a single scan. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:971-985. [PMID: 26249041 DOI: 10.1002/mrc.4271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 06/04/2023]
Abstract
Multidimensional NMR has become one of the most widespread spectroscopic tools available to study diverse structural and functional aspects of organic and biomolecules. A main feature of multidimensional NMR is the relatively long acquisition times that these experiments demand. For decades, scientists have been working on a variety of alternatives that would enable NMR to overcome this limitation, and deliver its data in shorter acquisition times. Counting among these methodologies is the so-called ultrafast (UF) NMR approach, which in principle allows one to collect arbitrary multidimensional correlations in a single sub-second transient. By contrast to conventional acquisitions, a main feature of UF NMR is a spatiotemporal manipulation of the spins that imprints the chemical shift and/or J-coupling evolutions being sought, into a spatial pattern. Subsequent gradient-based manipulations enable the reading out of this information and its multidimensional correlation into patterns that are identical to those afforded by conventional techniques. The current review focuses on the fundamental principles of this spatiotemporal UF NMR manipulation, and on a few of the methodological extensions that this form of spectroscopy has undergone during the years.
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Affiliation(s)
- Maayan Gal
- Migal Galilee Institute of Research Ltd, 11016, Kiryat Shmona, Israel
| | - Lucio Frydman
- Chemical Physics Department, Weizmann Institute of Science, 76100, Rehovot, Israel
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27
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Hilty C, Ragavan M. Application of blind source separation to real-time dissolution dynamic nuclear polarization. Anal Chem 2015; 87:1004-8. [PMID: 25506716 DOI: 10.1021/ac503475c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The use of a blind source separation (BSS) algorithm is demonstrated for the analysis of time series of nuclear magnetic resonance (NMR) spectra. This type of data is obtained commonly from experiments, where analytes are hyperpolarized using dissolution dynamic nuclear polarization (D-DNP), both in in vivo and in vitro contexts. High signal gains in D-DNP enable rapid measurement of data sets characterizing the time evolution of chemical or metabolic processes. BSS is based on an algorithm that can be applied to separate the different components contributing to the NMR signal and determine the time dependence of the signals from these components. This algorithm requires minimal prior knowledge of the data, notably, no reference spectra need to be provided, and can therefore be applied rapidly. In a time-resolved measurement of the enzymatic conversion of hyperpolarized oxaloacetate to malate, the two signal components are separated into computed source spectra that closely resemble the spectra of the individual compounds. An improvement in the signal-to-noise ratio of the computed source spectra is found compared to the original spectra, presumably resulting from the presence of each signal more than once in the time series. The reconstruction of the original spectra yields the time evolution of the contributions from the two sources, which also corresponds closely to the time evolution of integrated signal intensities from the original spectra. BSS may therefore be an approach for the efficient identification of components and estimation of kinetics in D-DNP experiments, which can be applied at a high level of automation.
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Affiliation(s)
- Christian Hilty
- Department of Chemistry and ‡Department of Biochemistry and Biophysics, Texas A&M University , College Station, Texas 77843, United States
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28
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Fernández-Valle ME, Martínez-Álvarez R, Molero-Vílchez D, Pardo ZD, Sáez-Barajas E, Herrera A. 2D Ultrafast HMBC 1H,31P: Obtaining Mechanistic Details on the Michaelis–Arbuzov Reaction. J Org Chem 2014; 80:799-805. [DOI: 10.1021/jo502253p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Roberto Martínez-Álvarez
- Departamento
de Química Orgánica I, Facultad de Químicas, Universidad Complutense, 28040 Madrid, Spain
| | | | - Zulay D. Pardo
- Departamento
de Química Orgánica I, Facultad de Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Elena Sáez-Barajas
- CAI
de RMN y RSE, Facultad de Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Antonio Herrera
- Departamento
de Química Orgánica I, Facultad de Químicas, Universidad Complutense, 28040 Madrid, Spain
- CAI
de RMN y RSE, Facultad de Químicas, Universidad Complutense, 28040 Madrid, Spain
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29
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Wei Z, Yang J, Lin L, Liu G, Lin Y, Chen Z. Reverse detection for spectral width improvements in spatially encoded dimensions of ultrafast two-dimensional NMR spectra. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:680-685. [PMID: 25102814 DOI: 10.1002/mrc.4117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 06/20/2014] [Accepted: 07/06/2014] [Indexed: 06/03/2023]
Abstract
Recently, the spatially encoded technique has been broadly used in the fast analyses of chemical systems and real-time detections of chemical reactions. In spatially encoded ultrafast 2D spectra, spectral widths and resolution in spatially encoded dimensions are contradictive, leading to the risk of insufficient spectral widths when providing satisfactory resolution values for all resonances. Here, a method named as reverse detection is proposed to improve the spectral width in the spatially encoded dimension. Experimental results show that spectral width improvements are at least twofold with reverse detection solely, and more improvements can be expected along with the gradient-controlled folding method. The proposed method can be applied to almost any spatially encoded scheme with echo planar spectroscopic imaging--like detection module and may promote wide applications of ultrafast 2D spectroscopy techniques in chemical analyses.
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Affiliation(s)
- Zhiliang Wei
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for the Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen, 361005, China
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30
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Brächer A, Hoch S, Albert K, Kost HJ, Werner B, von Harbou E, Hasse H. Thermostatted micro-reactor NMR probe head for monitoring fast reactions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 242:155-161. [PMID: 24650728 DOI: 10.1016/j.jmr.2014.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/10/2014] [Accepted: 02/13/2014] [Indexed: 06/03/2023]
Abstract
A novel nuclear magnetic resonance (NMR) probe head for monitoring fast chemical reactions is described. It combines micro-reaction technology with capillary flow NMR spectroscopy. Two reactants are fed separately into the probe head where they are effectively mixed in a micro-mixer. The mixed reactants then pass through a capillary NMR flow cell that is equipped with a solenoidal radiofrequency coil where the NMR signal is acquired. The whole flow path of the reactants is thermostatted using the liquid FC-43 (perfluorotributylamine) so that exothermic and endothermic reactions can be studied under almost isothermal conditions. The set-up enables kinetic investigation of reactions with time constants of only a few seconds. Non-reactive mixing experiments carried out with the new probe head demonstrate that it facilitates the acquisition of constant highly resolved NMR signals suitable for quantification of different species in technical mixtures. Reaction kinetic measurements on a test system are presented that prove the applicability of the novel NMR probe head for monitoring fast reactions.
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Affiliation(s)
- A Brächer
- University of Kaiserslautern, Kaiserslautern, Germany
| | - S Hoch
- University of Kaiserslautern, Kaiserslautern, Germany
| | - K Albert
- Eberhard Karls University, Tübingen, Germany
| | - H J Kost
- Institut für Mikrotechnik Mainz GmbH, Mainz, Germany
| | - B Werner
- Institut für Mikrotechnik Mainz GmbH, Mainz, Germany
| | - E von Harbou
- University of Kaiserslautern, Kaiserslautern, Germany.
| | - H Hasse
- University of Kaiserslautern, Kaiserslautern, Germany
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31
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Lee JH, Okuno Y, Cavagnero S. Sensitivity enhancement in solution NMR: emerging ideas and new frontiers. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:18-31. [PMID: 24656077 PMCID: PMC3967054 DOI: 10.1016/j.jmr.2014.01.005] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/14/2014] [Accepted: 01/17/2014] [Indexed: 05/05/2023]
Abstract
Modern NMR spectroscopy has reached an unprecedented level of sophistication in the determination of biomolecular structure and dynamics at atomic resolution in liquids. However, the sensitivity of this technique is still too low to solve a variety of cutting-edge biological problems in solution, especially those that involve viscous samples, very large biomolecules or aggregation-prone systems that need to be kept at low concentration. Despite the challenges, a variety of efforts have been carried out over the years to increase sensitivity of NMR spectroscopy in liquids. This review discusses basic concepts, recent developments and future opportunities in this exciting area of research.
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Affiliation(s)
- Jung Ho Lee
- Department of Chemistry and Biophysics Program, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
| | - Yusuke Okuno
- Department of Chemistry and Biophysics Program, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
| | - Silvia Cavagnero
- Department of Chemistry and Biophysics Program, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA.
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Ahola S, Telkki VV. Ultrafast two-dimensional NMR relaxometry for investigating molecular processes in real time. Chemphyschem 2014; 15:1687-92. [PMID: 24634359 DOI: 10.1002/cphc.201301117] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Indexed: 11/07/2022]
Abstract
Nuclear spin-lattice (T1) and spin-spin (T2) relaxation times provide versatile information about the dynamics and structure of substances, such as proteins, polymers, porous media, and so forth. Multidimensional experiments increase the information content and resolution of NMR relaxometry, but they also multiply the measurement time. To overcome this issue, we present an efficient strategy for a single-scan measurement of a 2D T1-T2 correlation map. The method shortens the experimental time by one to three orders of magnitude as compared to the conventional method, offering an unprecedented opportunity to study molecular processes in real-time. We demonstrate that, despite the tremendous speed-up, the T1-T2 correlation maps determined by the single-scan method are in good agreement with the maps measured by the conventional method. The concept of the single-scan T1-T2 correlation experiment is applicable to a broad range of other multidimensional relaxation and diffusion experiments.
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Affiliation(s)
- Susanna Ahola
- Department of Physics, NMR Research Group, University of Oulu, P.O.Box 3000, FIN-90014 (Finland)
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33
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Mayzel M, Rosenlöw J, Isaksson L, Orekhov VY. Time-resolved multidimensional NMR with non-uniform sampling. JOURNAL OF BIOMOLECULAR NMR 2014; 58:129-39. [PMID: 24435565 PMCID: PMC3929766 DOI: 10.1007/s10858-013-9811-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/30/2013] [Indexed: 05/11/2023]
Abstract
Time-resolved experiments demand high resolution both in spectral dimensions and in time of the studied kinetic process. The latter requirement traditionally prohibits applications of the multidimensional experiments, which, although capable of providing invaluable information about structure and dynamics and almost unlimited spectral resolution, require too lengthy data collection. Our work shows that the problem has a solution in using modern methods of NMR data collection and signal processing. A continuous fast pulsing three-dimensional experiment is acquired using non-uniform sampling during full time of the studied reaction. High sensitivity and time-resolution of a few minutes is achieved by simultaneous processing of the full data set with the multi-dimensional decomposition. The method is verified and illustrated in realistic simulations and by measuring deuterium exchange rates of amide protons in ubiquitin. We applied the method for characterizing kinetics of in vitro phosphorylation of two tyrosine residues in an intrinsically disordered cytosolic domain of the B cell receptor protein CD79b. Signals of many residues including tyrosines in both phosphorylated and unmodified forms of CD79b are found in a heavily crowded region of 2D ¹H-¹⁵N correlation spectrum and the significantly enhanced spectral resolution provided by the 3D time-resolved approach was essential for the quantitative site-specific analysis.
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Affiliation(s)
- Maxim Mayzel
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Joakim Rosenlöw
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Linnéa Isaksson
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Vladislav Y. Orekhov
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
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34
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Wu Y, D'Agostino C, Holland DJ, Gladden LF. In situ study of reaction kinetics using compressed sensing NMR. Chem Commun (Camb) 2014; 50:14137-40. [DOI: 10.1039/c4cc06051b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CS-NMR improves the temporal resolution of conventional multi-dimensional NMR for species identification and study of reaction kinetics.
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Affiliation(s)
- Yuting Wu
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge, UK
| | - Carmine D'Agostino
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge, UK
| | - Daniel J. Holland
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge, UK
| | - Lynn F. Gladden
- Department of Chemical Engineering and Biotechnology
- University of Cambridge
- Cambridge, UK
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35
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Giraudeau P, Frydman L. Ultrafast 2D NMR: an emerging tool in analytical spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:129-61. [PMID: 25014342 PMCID: PMC5040491 DOI: 10.1146/annurev-anchem-071213-020208] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago, a so-called ultrafast (UF) approach was proposed, capable of delivering arbitrary 2D NMR spectra involving any kind of homo- or heteronuclear correlation, in a single scan. During the intervening years, the performance of this subsecond 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool experiencing an expanded scope of applications. This review summarizes the principles and main developments that have contributed to the success of this approach and focuses on applications that have been recently demonstrated in various areas of analytical chemistry--from the real-time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications.
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Affiliation(s)
- Patrick Giraudeau
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation, UMR 6230, Université de Nantes, 44322 Nantes Cedex 03, France;
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36
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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37
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Ultrafast localized two-dimensional magnetic resonance correlated spectroscopy via spatially encoded technique. Magn Reson Med 2013; 71:903-10. [DOI: 10.1002/mrm.24731] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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38
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Donovan KJ, Frydman L. HyperSPASM NMR: a new approach to single-shot 2D correlations on DNP-enhanced samples. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 225:115-9. [PMID: 23159821 PMCID: PMC5035685 DOI: 10.1016/j.jmr.2012.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/10/2012] [Accepted: 10/15/2012] [Indexed: 05/05/2023]
Abstract
Dissolution DNP experiments are limited to a single or at most a few scans, before the non-Boltzmann magnetization has been consumed. This makes it impractical to record 2D NMR data by conventional, t(1)-incremented schemes. Here a new approach termed HyperSPASM to establish 2D heteronuclear correlations in a single scan is reported, aimed at dealing with this kind of challenge. The HyperSPASM experiment relies on imposing an amplitude-modulation of the data by a single Δt(1) indirect-domain evolution time, and subsequently monitoring the imparted encoding on separate echo and anti-echo pathway signals within a single continuous acquisition. This is implemented via the use of alternating, switching, coherence selection gradients. As a result of these manipulations the phase imparted by a heteronucleus over its indirect domain evolution can be accurately extracted, and 2D data unambiguously reconstructed with a single-shot excitation. The nature of this sequence makes the resulting experiment particularly well suited for collecting indirectly-detected HSQC data on hyperpolarized samples. The potential of the ensuing HyperSPASM method is exemplified with natural-abundance hyperpolarized correlations on model systems.
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39
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Queiroz LHK, Giraudeau P, dos Santos FAB, de Oliveira KT, Ferreira AG. Real-time mechanistic monitoring of an acetal hydrolysis using ultrafast 2D NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50:496-501. [PMID: 22615138 DOI: 10.1002/mrc.3827] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 04/04/2012] [Accepted: 04/22/2012] [Indexed: 06/01/2023]
Abstract
Ultrafast (UF) 2D NMR makes it possible to obtain a 2D NMR spectrum in less than a second. Here, UF-HSQC experiments are used for the real-time mechanistic study of an acetal hydrolysis at ¹³C natural abundance, and it is possible to characterize the presence of the hemiacetal, an intermediate with a well-known short lifetime. The assignments are confirmed and rationalized by quantum calculations of ¹H and ¹³C NMR chemical shifts and natural bonding orbital analysis.
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Affiliation(s)
- Luiz H K Queiroz
- Laboratório de Ressonância Magnética Nuclear, Departamento de Química, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, Brazil.
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40
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Pardo ZD, Olsen GL, Fernández-Valle ME, Frydman L, Martínez-Álvarez R, Herrera A. Monitoring mechanistic details in the synthesis of pyrimidines via real-time, ultrafast multidimensional NMR spectroscopy. J Am Chem Soc 2012; 134:2706-15. [PMID: 22283498 DOI: 10.1021/ja210154g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent years have witnessed unprecedented advances in the development of fast multidimensional NMR acquisition techniques. This progress could open valuable new opportunities for the elucidation of chemical and biochemical processes. This study demonstrates one such capability, with the first real-time Two-dimensional (2D) dynamic analysis of a complex organic reaction relying on unlabeled substrates. Implementing such measurements required the development of new ultrafast 2D methods, capable of monitoring multiple spectral regions of interest as the reaction progressed. The alternate application of these acquisitions in an interleaved, excitation-optimized fashion, allowed us to extract new structural and dynamic insight concerning the reaction between aliphatic ketones and triflic anhydride in the presence of nitriles to yield alkylpyrimidines. Up to 2500 2D NMR data sets were thus collected over the course of this nearly 100 min long reaction, in an approach resembling that used in functional magnetic resonance imaging. With the aid of these new frequency-selective low-gradient strength experiments, supplemented by chemical shift calculations of the spectral coordinates observed in the 2D heteronuclear correlations, previously postulated intermediates involved in the alkylpyrimidine formation process could be confirmed, and hitherto undetected ones were revealed. The potential and limitations of the resulting methods are discussed.
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Affiliation(s)
- Zulay D Pardo
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
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41
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Bardaro MF, Varani G. Examining the relationship between RNA function and motion using nuclear magnetic resonance. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:122-32. [PMID: 22180312 DOI: 10.1002/wrna.108] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological function of proteins and nucleic acids relies on their complex structures, yet dynamics provides an additional layer of functional adaptability. Numerous studies have demonstrated that RNA is only able to perform the multitude of functions for which it is responsible by readily changing its conformation in response to binding of proteins or small molecules. Examination of RNA dynamics is therefore essential to understanding its biological function. Nuclear magnetic resonance (NMR) has emerged as a leading technique for the examination of RNA motion and conformational transitions. It can examine domain motions as well as motion with atomic level resolution over a wide range of time scales. This review examines how NMR spectroscopy can be applied to examine the relationship between function and dynamics in RNA.
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42
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Ziarek JJ, Peterson FC, Lytle BL, Volkman BF. Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Methods Enzymol 2011; 493:241-75. [PMID: 21371594 PMCID: PMC3635485 DOI: 10.1016/b978-0-12-381274-2.00010-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the last 15 years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like compounds because of its ability to identify binding sites, affinities, and ligand poses at the level of individual amino acids without necessarily solving the structure of the protein-ligand complex. However, it can also provide structures of flexible proteins and low-affinity (K(d)>10(-6)M) complexes, which often fail to crystallize. This chapter emphasizes a throughput-focused protocol that aims to identify practical aspects of binding site characterization, automated and semiautomated NMR assignment methods, and structure determination of protein-ligand complexes by NMR.
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Affiliation(s)
- Joshua J. Ziarek
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, 53226 USA
| | - Francis C. Peterson
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, 53226 USA
| | - Betsy L. Lytle
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, 53226 USA
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin, 53226 USA
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43
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Tal A, Frydman L. Single-scan multidimensional magnetic resonance. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:241-92. [PMID: 20667401 DOI: 10.1016/j.pnmrs.2010.04.001] [Citation(s) in RCA: 200] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 03/23/2010] [Indexed: 05/16/2023]
Affiliation(s)
- Assaf Tal
- The Department of Chemical Physics, Weizmann Institute of Science, Israel
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44
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Gal M, Frydman L. Single-scan 2D NMR correlations by multiple coherence transfers. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 203:311-315. [PMID: 20149697 DOI: 10.1016/j.jmr.2009.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 10/28/2009] [Indexed: 05/28/2023]
Abstract
A new scheme for the acquisition of heteronuclear 2D correlations in NMR spectroscopy within a single scan, is proposed and demonstrated. The principles of this new scheme resemble those of Mansfield's "k-space walk" proposal, in the sense that they rely on repetitively transferring spin coherences back-and-forth between the two spin systems to be correlated. It is shown that if properly executed, these transfers enable the equivalent of a continuous sampling of the time-domain space supporting a 2D heteronuclear single-quantum correlation NMR spectrum. Details on how to execute the resulting "time-domain walk" experiments are given, and examples comparing it against conventional and other single-scan 2D acquisition alternatives are shown. Advantages, opportunities, and main drawbacks of this new ultrafast approach to 2D NMR, are briefly discussed.
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Affiliation(s)
- Maayan Gal
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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45
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Herrera A, Fernández-Valle E, Gutiérrez EM, Martínez-Álvarez R, Molero D, Pardo ZD, Sáez E. 2D Ultrafast HMBC: A Valuable Tool for Monitoring Organic Reactions. Org Lett 2009; 12:144-7. [DOI: 10.1021/ol902532f] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonio Herrera
- Departamento de Química Orgánica and CAI de RMN Facultad de Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Encarnación Fernández-Valle
- Departamento de Química Orgánica and CAI de RMN Facultad de Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Eva M. Gutiérrez
- Departamento de Química Orgánica and CAI de RMN Facultad de Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Roberto Martínez-Álvarez
- Departamento de Química Orgánica and CAI de RMN Facultad de Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Dolores Molero
- Departamento de Química Orgánica and CAI de RMN Facultad de Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Zulay D. Pardo
- Departamento de Química Orgánica and CAI de RMN Facultad de Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Elena Sáez
- Departamento de Química Orgánica and CAI de RMN Facultad de Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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46
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Herrera A, Fernández-Valle E, Martínez-Álvarez R, Molero D, Pardo Z, Sáez E, Gal M. Real-Time Monitoring of Organic Reactions with Two-Dimensional Ultrafast TOCSY NMR Spectroscopy. Angew Chem Int Ed Engl 2009; 48:6274-7. [DOI: 10.1002/anie.200902387] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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47
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Herrera A, Fernández-Valle E, Martínez-Álvarez R, Molero D, Pardo Z, Sáez E, Gal M. Real-Time Monitoring of Organic Reactions with Two-Dimensional Ultrafast TOCSY NMR Spectroscopy. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Mishkovsky M, Frydman L. Principles and Progress in Ultrafast Multidimensional Nuclear Magnetic Resonance. Annu Rev Phys Chem 2009; 60:429-48. [DOI: 10.1146/annurev.physchem.040808.090420] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mor Mishkovsky
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel;
| | - Lucio Frydman
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel;
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49
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Chan SJ, Howe AG, Hook JM, Harper JB. (79)Br NMR spectroscopy as a practical tool for kinetic analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:342-347. [PMID: 19189283 DOI: 10.1002/mrc.2401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
(79)Br NMR spectroscopy has been used to monitor a series of reactions in which the bromide ion is produced, including the Menschutkin reaction of pyridine with a range of substituted benzyl bromides and a Heck coupling process. In cases where the process could also be monitored using (1)H NMR spectroscopy, the kinetic analyses using heteronuclear magnetic resonance spectroscopy were shown to be completely consistent. Both the utility of the process in following reactions which may be difficult to analyse using other techniques and the practical limitations associated with solvent choice are discussed.
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Affiliation(s)
- Si Jia Chan
- School of Chemistry, University of New South Wales, Sydney NSW 2052, Australia
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50
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Guyett P, Glushka J, Gu X, Bar-Peled M. Real-time NMR monitoring of intermediates and labile products of the bifunctional enzyme UDP-apiose/UDP-xylose synthase. Carbohydr Res 2009; 344:1072-8. [PMID: 19375693 DOI: 10.1016/j.carres.2009.03.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 03/17/2009] [Accepted: 03/23/2009] [Indexed: 11/25/2022]
Abstract
The conversion of UDP-alpha-d-glucuronic acid to UDP-alpha-d-xylose and UDP-alpha-d-apiose by a bifunctional potato enzyme UDP-apiose/UDP-xylose synthase was studied using real-time nuclear magnetic resonance (NMR) spectroscopy. UDP-alpha-d-glucuronic acid is converted via the intermediate uridine 5'-beta-l-threo-pentapyranosyl-4''-ulose diphosphate to UDP-alpha-d-apiose and simultaneously to UDP-alpha-d-xylose. The UDP-alpha-d-apiose that is formed is unstable and is converted to alpha-d-apio-furanosyl-1,2-cyclic phosphate and UMP. High-resolution real-time NMR spectroscopy is a powerful tool for the direct and quantitative characterization of previously undetected transient and labile components formed during a complex enzyme-catalyzed reaction.
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Affiliation(s)
- Paul Guyett
- Complex Carbohydrate Research Center, and BioEnergy Science Center, 315 Riverbend Road, University of Georgia, Athens, GA 30602, USA
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