1
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Heinrich G, Kondratiuk M, Gooßen LJ, Wiesenfeldt MP. Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy. Nat Protoc 2024; 19:1529-1556. [PMID: 38409535 DOI: 10.1038/s41596-023-00951-3] [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: 03/01/2023] [Accepted: 11/16/2023] [Indexed: 02/28/2024]
Abstract
The instrumental analysis of reaction mixtures is usually the rate-determining step in the optimization of chemical processes. Traditionally, reactions are analyzed by gas chromatography, HPLC or quantitative NMR spectroscopy on high-field spectrometers. However, chromatographic methods require elaborate work-up and calibration protocols, and high-field NMR spectrometers are expensive to purchase and operate. This protocol describes an inexpensive and highly effective analysis method based on low-field benchtop NMR spectroscopy. Its key feature is the use of fluorine-labeled model substrates that, because of the wide chemical shift range and high sensitivity of 19F, enable separate, quantitative detection of product and by-product signals even on low-field, permanent magnet spectrometers. An external lock/shim device obviates the need for deuterated solvents, permitting the direct, noninvasive measurement of crude reaction mixtures with minimal workup. The low field-strength facilitates a homogeneous excitation over a wide chemical shift range, minimizing systematic integration errors. The addition of the optimal amount of the nonshifting relaxation agent tris(acetylacetonato) iron(III) minimizes relaxation delays at full resolution, reducing the analysis time to 32 s per sample. The correct choice of processing parameters is also crucial. A step-by-step guideline is provided, the influence of all parameters, including adjustments needed when using high-field spectrometers, is discussed and potential pitfalls are highlighted. The wide applicability of the analytical protocol for reaction optimization is illustrated by three examples: a Buchwald-Hartwig amination, a Suzuki coupling and a C-H arylation reaction.
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Affiliation(s)
- G Heinrich
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - M Kondratiuk
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - L J Gooßen
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - M P Wiesenfeldt
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
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2
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González-Delgado JM, Thompson PM, Andrałojć W, Gdaniec Z, Ghiladi RA, Franzen S. Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes. J Phys Chem B 2024; 128:3383-3397. [PMID: 38563384 DOI: 10.1021/acs.jpcb.3c07176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.
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Affiliation(s)
| | - Peter M Thompson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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3
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Koppe J, Pell AJ. Structure Determination and Refinement of Paramagnetic Materials by Solid-State NMR. ACS PHYSICAL CHEMISTRY AU 2023; 3:419-433. [PMID: 37780542 PMCID: PMC10540298 DOI: 10.1021/acsphyschemau.3c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 10/03/2023]
Abstract
Paramagnetism in solid-state materials has long been considered an additional challenge for structural investigations by using solid-state nuclear magnetic resonance spectroscopy (ssNMR). The strong interactions between unpaired electrons and the surrounding atomic nuclei, on the one hand, are complex to describe, and on the other hand can cause fast decaying signals and extremely broad resonances. However, significant progress has been made over the recent years in developing both theoretical models to understand and calculate the frequency shifts due to paramagnetism and also more sophisticated experimental protocols for obtaining high-resolution ssNMR spectra. While the field is continuously moving forward, to date, the combination of state-of-the-art numerical and experimental techniques enables us to obtain high-quality data for a variety of systems. This involves the determination of several ssNMR parameters that represent different contributions to the frequency shift in paramagnetic solids. These contributions encode structural information on the studied material on various length scales, ranging from crystal morphologies, to the mid- and long-range order, down to the local atomic bonding environment. In this perspective, the different ssNMR parameters characteristic for paramagnetic materials are discussed with a focus on their interpretation in terms of structure. This includes a summary of studies that have explored the information content of these ssNMR parameters, mostly to complement experimental data from other methods, e.g., X-ray diffraction. The presented overview aims to demonstrate how far ssNMR has hitherto been able to determine and refine the structures of materials and to discuss where it currently falls short of its full potential. We attempt to highlight how much further ssNMR can be pushed to determine and refine structure to deliver a comprehensive structural characterization of paramagnetic materials comparable to what is to date achieved by the combined effort of electron microscopy, diffraction, and spectroscopy.
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Affiliation(s)
- Jonas Koppe
- Centre
de RMN à Très Hauts Champs de Lyon (UMR 5082 −
CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon (UMR 5082 −
CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
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4
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Radhakrishnan S, Smet S, Chandran CV, Sree SP, Duerinckx K, Vanbutsele G, Martens JA, Breynaert E. Prediction of Cu Zeolite NH 3-SCR Activity from Variable Temperature 1H NMR Spectroscopy. Molecules 2023; 28:6456. [PMID: 37764230 PMCID: PMC10537069 DOI: 10.3390/molecules28186456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Selective catalytic reduction (SCR) of NOx by ammonia is one of the dominant pollution abatement technologies for near-zero NOx emission diesel engines. A crucial step in the reduction of NOx to N2 with Cu zeolite NH3-SCR catalysts is the generation of a multi-electron donating active site, implying the permanent or transient dimerization of Cu ions. Cu atom mobility has been implicated by computational chemistry as a key factor in this process. This report demonstrates how variable temperature 1H NMR reveals the Cu induced generation of sharp 1H resonances associated with a low concentration of sites on the zeolite. The onset temperature of the appearance of these signals was found to strongly correlate with the NH3-SCR activity and was observed for a range of catalysts covering multiple frameworks (CHA, AEI, AFX, ERI, ERI-CHA, ERI-OFF, *BEA), with different Si/Al ratios and different Cu contents. The results point towards universal applicability of variable temperature NMR to predict the activity of a Cu-zeolite SCR catalyst. The unique relationship of a spectroscopic feature with catalytic behavior for zeolites with different structures and chemical compositions is exceptional in heterogeneous catalysis.
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Affiliation(s)
- Sambhu Radhakrishnan
- Centre for Surface Chemistry and Catalysis—Characterization and Application Team (COK-KAT), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
- NMR/X-ray Platform for Convergence Research (NMRCoRe), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
| | - Sam Smet
- Centre for Surface Chemistry and Catalysis—Characterization and Application Team (COK-KAT), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
| | - C. Vinod Chandran
- Centre for Surface Chemistry and Catalysis—Characterization and Application Team (COK-KAT), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
- NMR/X-ray Platform for Convergence Research (NMRCoRe), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
| | - Sreeprasanth Pulinthanathu Sree
- Centre for Surface Chemistry and Catalysis—Characterization and Application Team (COK-KAT), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
| | - Karel Duerinckx
- Centre for Surface Chemistry and Catalysis—Characterization and Application Team (COK-KAT), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
- NMR/X-ray Platform for Convergence Research (NMRCoRe), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
| | - Gina Vanbutsele
- Centre for Surface Chemistry and Catalysis—Characterization and Application Team (COK-KAT), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
| | - Johan A. Martens
- Centre for Surface Chemistry and Catalysis—Characterization and Application Team (COK-KAT), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
- NMR/X-ray Platform for Convergence Research (NMRCoRe), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
| | - Eric Breynaert
- Centre for Surface Chemistry and Catalysis—Characterization and Application Team (COK-KAT), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
- NMR/X-ray Platform for Convergence Research (NMRCoRe), KU Leuven, Celestijnenlaan 200F Box 2461, 3001 Heverlee, Belgium
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5
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Bara‐Estaún A, Harder MC, Lyall CL, Lowe JP, Suturina E, Hintermair U. Paramagnetic Relaxation Agents for Enhancing Temporal Resolution and Sensitivity in Multinuclear FlowNMR Spectroscopy. Chemistry 2023; 29:e202300215. [PMID: 36946535 PMCID: PMC10962566 DOI: 10.1002/chem.202300215] [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: 01/21/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/23/2023]
Abstract
Sensitivity in FlowNMR spectroscopy for reaction monitoring often suffers from low levels of pre-magnetisation due to limited residence times of the sample in the magnetic field. While this in-flow effect is tolerable for high sensitivity nuclei such as 1 H and 19 F, it significantly reduces the signal-to-noise ratio in 31 P and 13 C spectra, making FlowNMR impractical for low sensititvity nuclei at low concentrations. Paramagnetic relaxation agents (PRAs), which enhance polarisation and spin-lattice relaxation, could eliminate the adverse in-flow effect and improve the signal-to-noise ratio. Herein, [Co(acac)3 ], [Mn(acac)3 ], [Fe(acac)3 ], [Cr(acac)3 ], [Ni(acac)2 ]3, [Gd(tmhd)3 ] and [Cr(tmhd)3 ] are investigated for their effectiveness in improving signal intensity per unit time in FlowNMR applications under the additional constraint of chemical inertness towards catalytically active transition metal complexes. High-spin Cr(III) acetylacetonates emerged as the most effective compounds, successfully reducing 31 P T1 values four- to five-fold at PRA concentrations as low as 10 mM without causing adverse line broadening. Whereas [Cr(acac)3 ] showed signs of chemical reactivity with a mixture of triphenylphosphine, triphenylphosphine oxide and triphenylphosphate over the course of several hours at 80° C, the bulkier [Cr(tmhd)3 ] was stable and equally effective as a PRA under these conditions. Compatibility with a range of representative transition metal complexes often used in homogeneous catalysis has been investigated, and application of [Cr(tmhd)3 ] in significantly improving 1 H and 31 P{1 H} FlowNMR data quality in a Rh-catalysed hydroformylation reaction has been demonstrated. With the PRA added, 13 C relaxation times were reduced more than six-fold, allowing quantitative reaction monitoring of substrate consumption and product formation by 13 C{1 H} FlowNMR spectroscopy at natural abundance.
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Affiliation(s)
- Alejandro Bara‐Estaún
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
| | - Marie C. Harder
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
| | - Catherine L. Lyall
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
| | - John P. Lowe
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
| | - Elizaveta Suturina
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
| | - Ulrich Hintermair
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
- Institute for SustainabilityUniversity of BathBathBA2 7AYUnited Kingdom
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6
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Umegawa Y, Shimonishi T, Tsuchikawa H, Murata M. LnDOTA-d 8 , a versatile chemical-shift thermometer for 2 H solid-state NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:1005-1013. [PMID: 35938541 DOI: 10.1002/mrc.5303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
2 H solid-state nuclear magnetic resonance (NMR) is a method for examining the mobility and orientation of molecules in the field of biophysics. In studies on lipid bilayer membranes, 2 H NMR is often adopted to detect a phase transition from the gel to the liquid-crystal phase, which is observed as a change in spectral shape, and to evaluate the ordering of lipid alkyl chains using quadrupole coupling values. Because the mobility of membrane lipids is highly temperature dependent, precise temperature control is a prerequisite for evaluating the physical properties of membranes. Generally, NMR instruments monitor the temperature of the variable temperature (VT) gas. The temperature inside the sample tube and the VT gas match only when the heat generated by the radio frequency (rf) pulse emitted from the coil or magic angle spinning is significantly lower than the cooling capacity of the VT gas. In other words, the sample temperature inside the tube depends on the measurement method. Therefore, in this study, we took advantage of temperature-dependent changes in the chemical shift of a paramagnetic metal-ligand complex. We designed and synthesized a deuterated ligand complex and evaluated its temperature dependence as a thermometer for 2 H solid-state NMR spectroscopy. We chose Tb, Dy, Ho, and Er as the paramagnetic central metals. We then measured the 2 H NMR spectrum of each metal complex and confirmed the 2 H chemical shift to be temperature dependent. Furthermore, with the use of the thermometer molecule with Er, we succeeded in accurately evaluating the segmental melting of an alkyl chain in lipid bilayers with 0.1°C accuracy.
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Affiliation(s)
- Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- JST ERATO, Lipid Active Structure Project and Project Research Center for Fundamental Science, Osaka University, Osaka, Japan
| | - Takeshi Shimonishi
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
- JST ERATO, Lipid Active Structure Project and Project Research Center for Fundamental Science, Osaka University, Osaka, Japan
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7
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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8
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Klug CA, Swift MW, Miller JB, Lyons JL, Albert A, Laskoski M, Hangarter CM. High resolution solid state NMR in paramagnetic metal-organic frameworks. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 120:101811. [PMID: 35792451 DOI: 10.1016/j.ssnmr.2022.101811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/06/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
We study the metal-organic framework (MOF) ZIF-67 with 1H and 13C nuclear magnetic resonance (NMR). In addition to the usual orbital chemical shifts, we observe spinning sideband manifolds in the NMR spectrum due to hyperfine interactions of the paramagnetic cobalt with 1H and 13C. Both orbital and paramagnetic chemical shifts are in good agreement with values calculated from first principles, allowing high-confidence assignment of the observed peaks to specific sites within the MOF. Our measured resonance shifts, line shapes, and spin lattice relaxation rates are also consistent with calculated values. We show that molecules in the pores of the MOF can exhibit high-resolution NMR spectra with fast spin lattice relaxation rates due to dipole-dipole couplings to the Co2+ nodes in the ZIF-67 lattice, showcasing NMR spectroscopy as a powerful tool for identification and characterization of "guests" that may be hosted by the MOF in electrochemical and catalytic applications.
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Affiliation(s)
- C A Klug
- Chemistry Division, U.S. Naval Research Laboratory, Washington, DC, USA.
| | - M W Swift
- Materials Science Division, U.S. Naval Research Laboratory, Washington, DC, USA
| | - J B Miller
- Chemistry Division, U.S. Naval Research Laboratory, Washington, DC, USA
| | - J L Lyons
- Materials Science Division, U.S. Naval Research Laboratory, Washington, DC, USA
| | - A Albert
- Chemistry Division, U.S. Naval Research Laboratory, Washington, DC, USA
| | - M Laskoski
- Chemistry Division, U.S. Naval Research Laboratory, Washington, DC, USA
| | - C M Hangarter
- Chemistry Division, U.S. Naval Research Laboratory, Washington, DC, USA
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9
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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10
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Di Mauro GM, La Rosa C, Condorelli M, Ramamoorthy A. Benchmarks of SMA-Copolymer Derivatives and Nanodisc Integrity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3113-3121. [PMID: 33645999 DOI: 10.1021/acs.langmuir.0c03554] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Poly(styrene-co-maleic acid) or SMA and its derivatives, a family of synthetic amphipathic copolymers, are increasingly used to directly solubilize cell membranes to functionally reconstitute membrane proteins in native-like copolymer-lipid nanodiscs. Although these copolymers act, de facto, like a "macromolecular detergent", the polymer-based lipid-nanodiscs has been demonstrated to be an excellent membrane mimetic for structural and functional studies of membrane proteins and their complexes by a variety of biophysical and biochemical approaches. In many studies reported in the literature, the choice of the right SMA formulation can depend on a number of factors, and the experimental conditions are typically developed according to a trial-and-error process since each studied system requires adapted protocols. While increasing number of nanodisc-forming copolymers are reported to be useful and they provide flexibilities in optimizing the sample preparation conditions, it is important to develop a systematic protocol that can be used for various applications. In this context, there is a vital necessity of benchmarking the performances of existing copolymer formulations, assessing crucial parameters for the successful extraction, isolation, and stabilization of membrane proteins. In this study, we compare both copolymers and copolymer-lipid nanodiscs obtained by SMA-EA with a set of anionic XIRAN copolymer formulations commercially available under the names of SL25010 P, SL30010 P, and SL40005 P. The reported results show how the critical micellar concentration (c.m.c.) of each copolymer is significantly altered in the presence of lipids and confirms the existence of an equilibrium between nanodisc-bound and "free" or "micellar" copolymer chains in the solution. We believe that these findings can be exploited to optimize studies that involve the necessity of special copolymers, which would not only simplify the applications but also broaden the scope of polymer-based nanodiscs.
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Affiliation(s)
- Giacomo M Di Mauro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Carmelo La Rosa
- Department of Chemistry, University of Catania, Catania 95125, Italy
| | | | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
- Biophysics and Chemistry Department, Macromolecular Science and Engineering, and Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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11
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Tennant T, Hulme MC, Robertson TBR, Sutcliffe OB, Mewis RE. Benchtop NMR analysis of piperazine-based drugs hyperpolarised by SABRE. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:1151-1159. [PMID: 31945193 DOI: 10.1002/mrc.4999] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Piperazine-based drugs, such as N-benzylpiperazine (BZP), became attractive in the 2000s due to possessing effects similar to amphetamines. Herein, BZP, in addition to its pyridyl analogues, 2-, 3-, and 4-pyridylmethylpiperidine (2-PMP, 3-PMP, and 4-PMP respectively) was subjected to the hyperpolarisation technique Signal Amplification By Reversible Exchange (SABRE) in order to demonstrate the use of this technique to detect these piperazine-based drugs. Although BZP was not hyperpolarised via SABRE, 2-PMP, 3-PMP, and 4-PMP were, with the ortho- and meta-pyridyl protons of 4-PMP showing the largest enhancement of 313-fold and 267-fold, respectively, in a 1.4-T detection field, following polarisation transfer at Earth's magnetic field. In addition to the freebase, 4-PMP.3HCl was also appraised by SABRE and was found not to polarise, however, the addition of increasing equivalents of triethylamine (TEA) produced the freebase, with a maximum enhancement observed upon the addition of 3 equivalents of TEA. Further addition of TEA led to a reduction in the observed enhancement. SABRE was also employed to polarise 4-PMP.3HCl (~20% w/w) in a simulated tablet to demonstrate the forensic application of the technique (138-fold enhancement for the ortho-pyridyl protons). The amount of 4-PMP.3HCl present in the simulated tablet was quantified via NMR using D2 O as a solvent and compared well to complimentary gas chromatography-mass spectrometry data. Exchanging D2 O for CD3 OD as the solvent utilised for analysis resulted in a significantly lower amount of 4-PMP.3HCl being determined, thus highlighting safeguarding issues linked to drug abuse in relation to determining the amount of active pharmaceutical ingredient present.
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Affiliation(s)
- Thomas Tennant
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
- MANchester DRug Analysis and Knowledge Exchange, Manchester Metropolitan University, Manchester, UK
| | - Matthew C Hulme
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
- MANchester DRug Analysis and Knowledge Exchange, Manchester Metropolitan University, Manchester, UK
| | - Thomas B R Robertson
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Oliver B Sutcliffe
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
- MANchester DRug Analysis and Knowledge Exchange, Manchester Metropolitan University, Manchester, UK
| | - Ryan E Mewis
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
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12
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Di Mauro GM, Hardin NZ, Ramamoorthy A. Lipid-nanodiscs formed by paramagnetic metal chelated polymer for fast NMR data acquisition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183332. [PMID: 32360741 PMCID: PMC7340147 DOI: 10.1016/j.bbamem.2020.183332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
Lipid-nanodiscs have been shown to be an exciting innovation as a membrane-mimicking system for studies on membrane proteins by a variety of biophysical techniques, including NMR spectroscopy. Although NMR spectroscopy is unique in enabling the atomic-resolution investigation of dynamic structures of membrane-associated molecules, it, unfortunately, suffers from intrinsically low sensitivity. The long data acquisition often used to enhance the sensitivity is not desirable for sensitive membrane proteins. Instead, paramagnetic relaxation enhancement (PRE) has been used to reduce NMR data acquisition time or to reduce the amount of sample required to acquire an NMR spectra. However, the PRE approach involves the introduction of external paramagnetic probes in the system, which can induce undesired changes in the sample and on the observed NMR spectra. For example, the addition of paramagnetic ions, as frequently used, can denature the protein via direct interaction and also through sample heating. In this study, we show how the introduction of paramagnetic tags on the outer belt of polymer-nanodiscs can be used to speed-up data acquisition by significantly reducing the spin-lattice relaxation (T1) times with minimum-to-no alteration of the spectral quality. Our results also demonstrate the feasibility of using different types of paramagnetic ions (Eu3+, Gd3+, Dy3+, Er3+, Yb3+) for NMR studies on lipid-nanodiscs. Experimental results characterizing the formation of lipid-nanodiscs by the metal-chelated polymer, and their increased tolerance toward metal ions are also reported.
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Affiliation(s)
- Giacomo M Di Mauro
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Nathaniel Z Hardin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Biophysics and Chemistry Department, The University of Michigan, Ann Arbor, MI 48109-1055, USA; Macromolecular Science and Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA; Biomedical Engineering, The University of Michigan, Ann Arbor, MI 48109-1055, USA.
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13
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Bruno F, Francischello R, Bellomo G, Gigli L, Flori A, Menichetti L, Tenori L, Luchinat C, Ravera E. Multivariate Curve Resolution for 2D Solid-State NMR spectra. Anal Chem 2020; 92:4451-4458. [PMID: 32069028 PMCID: PMC7997113 DOI: 10.1021/acs.analchem.9b05420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We present a processing method, based on the multivariate curve resolution approach (MCR), to denoise 2D solid-state NMR spectra, yielding a substantial S/N ratio increase while preserving the lineshapes and relative signal intensities. These spectral features are particularly important in the quantification of silicon species, where sensitivity is limited by the low natural abundance of the 29Si nuclei and by the dilution of the intrinsic protons of silica, but can be of interest also when dealing with other intermediate-to-low receptivity nuclei. This method also offers the possibility of coprocessing multiple 2D spectra that have the signals at the same frequencies but with different intensities (e.g.: as a result of a variation in the mixing time). The processing can be carried out on the time-domain data, thus preserving the possibility of applying further processing to the data. As a demonstration, we have applied Cadzow denoising on the MCR-processed FIDs, achieving a further increase in the S/N ratio and more effective denoising also on the transients at longer indirect evolution times. We have applied the combined denoising on a set of experimental data from a lysozyme-silica composite.
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Affiliation(s)
- Francesco Bruno
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Roberto Francischello
- Institute of Clinical Physiology, National Research Council, Via G. Moruzzi, 1 56124 Pisa, Italy.,Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giovanni Bellomo
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Alessandra Flori
- Fondazione Regione Toscana G. Monasterio, Via G. Moruzzi 1, Pisa 56124, Italy
| | - Luca Menichetti
- Institute of Clinical Physiology, National Research Council, Via G. Moruzzi, 1 56124 Pisa, Italy.,Fondazione Regione Toscana G. Monasterio, Via G. Moruzzi 1, Pisa 56124, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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14
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Lu X, Tsutsumi Y, Huang C, Xu W, Byrn SR, Templeton AC, Buevich AV, Amoureux JP, Su Y. Molecular packing of pharmaceuticals analyzed with paramagnetic relaxation enhancement and ultrafast magic angle pinning NMR. Phys Chem Chem Phys 2020; 22:13160-13170. [DOI: 10.1039/d0cp02049d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Probing molecular details of fluorinated pharmaceutical compounds at a faster acquisition utilizing paramagnetic relaxation enhancement and better resolution from ultrafast magic angle spinning (νrot = 110 kHz) and high magnetic field (B0 = 18.8 T).
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Affiliation(s)
| | | | | | - Wei Xu
- MRL, Merck & Co., Inc
- Kenilworth
- USA
| | - Stephen R. Byrn
- Department of Industrial and Physical Pharmacy
- College of Pharmacy
- Purdue University
- Indiana 47907
- USA
| | | | | | | | - Yongchao Su
- MRL, Merck & Co., Inc
- Kenilworth
- USA
- Department of Industrial and Physical Pharmacy
- College of Pharmacy
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15
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Hardin NZ, Kocman V, Di Mauro GM, Ravula T, Ramamoorthy A. Metal‐Chelated Polymer Nanodiscs for NMR Studies. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Nathaniel Z. Hardin
- Biophysics Program and Department of ChemistryUniversity of Michigan Ann Arbor MI 48109-1055 USA
| | - Vojč Kocman
- Biophysics Program and Department of ChemistryUniversity of Michigan Ann Arbor MI 48109-1055 USA
| | - Giacomo M. Di Mauro
- Biophysics Program and Department of ChemistryUniversity of Michigan Ann Arbor MI 48109-1055 USA
| | - Thirupathi Ravula
- Biophysics Program and Department of ChemistryUniversity of Michigan Ann Arbor MI 48109-1055 USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of ChemistryUniversity of Michigan Ann Arbor MI 48109-1055 USA
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16
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Hardin NZ, Kocman V, Di Mauro GM, Ravula T, Ramamoorthy A. Metal-Chelated Polymer Nanodiscs for NMR Studies. Angew Chem Int Ed Engl 2019; 58:17246-17250. [PMID: 31529579 PMCID: PMC6861636 DOI: 10.1002/anie.201910118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/11/2019] [Indexed: 01/20/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) is commonly used to speed up spin lattice relaxation time (T1 ) for rapid data acquisition in NMR structural studies. Consequently, there is significant interest in novel paramagnetic labels for enhanced NMR studies on biomolecules. Herein, we report the synthesis and characterization of a modified poly(styrene-co-maleic acid) polymer which forms nanodiscs while showing the ability to chelate metal ions. Cu2+ -chelated nanodiscs are demonstrated to reduce the T1 of protons for both polymer and lipid-nanodisc components. The chelated nanodiscs also decrease the proton T1 values for a water-soluble DNA G-quadruplex. These results suggest that polymer nanodiscs functionalized with paramagnetic tags can be used to speed-up data acquisition from lipid bilayer samples and also to provide structural information from water-soluble biomolecules.
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Affiliation(s)
- Nathaniel Z Hardin
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Vojč Kocman
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Giacomo M Di Mauro
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Thirupathi Ravula
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109-1055, USA
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17
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Bondarenko V, Wells MM, Chen Q, Singewald KC, Saxena S, Xu Y, Tang P. 19F Paramagnetic Relaxation-Based NMR for Quaternary Structural Restraints of Ion Channels. ACS Chem Biol 2019; 14:2160-2165. [PMID: 31525026 DOI: 10.1021/acschembio.9b00692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quaternary distance restraints are essential to define the three-dimensional structures of protein assemblies. These distances often fall within a range of 10-18 Å, which challenges the high and low measurement limits of conventional nuclear magnetic resonance (NMR) and double electron-electron resonance electron spin resonance spectroscopies. Here, we report the use of 19F paramagnetic relaxation enhancement (PRE) NMR in combination with 19F/paramagnetic labeling to equivalent sites in different subunits of a protein complex in micelles to determine intersubunit distances. The feasibility of this strategy was evaluated on a pentameric ligand-gated ion channel, for which we found excellent agreement of the 19F PRE NMR results with previous structural information. The study suggests that 19F PRE NMR is a viable tool in extracting distance restraints to define quaternary structures.
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Affiliation(s)
- Vasyl Bondarenko
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Marta M. Wells
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qiang Chen
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kevin C. Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yan Xu
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Pei Tang
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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