1
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Krishnarjuna B, Sharma G, Hiiuk VM, Struppe J, Nagorny P, Ivanova MI, Ramamoorthy A. Nanodisc reconstitution and characterization of amyloid-β precursor protein C99. bioRxiv 2024:2024.04.21.590446. [PMID: 38659865 PMCID: PMC11042261 DOI: 10.1101/2024.04.21.590446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimers disease. Since the fragmentation of the membrane-bound APP that results in the production of amyloid-beta peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable/suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in native E. coli membrane environment is demonstrated.
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2
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Porat-Dahlerbruch G, Struppe J, Polenova T. High-efficiency low-power 13C- 15N cross polarization in MAS NMR. J Magn Reson 2024; 361:107649. [PMID: 38452523 PMCID: PMC11031345 DOI: 10.1016/j.jmr.2024.107649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 03/09/2024]
Abstract
Biomolecular solid-state magic angle spinning (MAS) NMR spectroscopy frequently relies on selective 13C-15N magnetization transfers, for various kinds of correlation experiments. Introduced in 1998, spectrally induced filtering in combination with cross polarization (SPECIFIC-CP) is a selective heteronuclear magnetization transfer experiment widely used for biological applications. At MAS frequencies below 20 kHz, commonly used for 13C-detected MAS NMR experiments, SPECIFIC-CP transfer between amide 15N and 13Cα atoms (NCA) is typically performed with radiofrequency (rf) fields set higher than the MAS frequency for both 13C and 15N channels, and high-power 1H decoupling rf field is simultaneously applied. Here, we experimentally explore a broad range of NCA zero-quantum (ZQ) SPECIFIC-CP matching conditions at the MAS frequency of 14 kHz and compare the best high- and low-power matching conditions with respect to selectivity, robustness, and sensitivity at lower 1H decoupling rf fields. We show that low-power NCA SPECIFIC-CP matching condition gives rise to 20% sensitivity enhancement compared to high-power conditions, in 2D NCA spectra of microcrystalline assemblies of HIV-1 CACTD-SP1 protein with inositol hexakis-phosphate (IP6).
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States.
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3
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Gopinath T, Shin K, Tian Y, Im W, Struppe J, Perrone B, Hassan A, Marassi FM. Solid-state NMR MAS CryoProbe enables structural studies of human blood protein vitronectin bound to hydroxyapatite. J Struct Biol 2024; 216:108061. [PMID: 38185342 PMCID: PMC10939839 DOI: 10.1016/j.jsb.2024.108061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The low sensitivity of nuclear magnetic resonance (NMR) is a major bottleneck for studying biomolecular structures of complex biomolecular assemblies. Cryogenically cooled probe technology overcomes the sensitivity limitations enabling NMR applications to challenging biomolecular systems. Here we describe solid-state NMR studies of the human blood protein vitronectin (Vn) bound to hydroxyapatite (HAP), the mineralized form of calcium phosphate, using a CryoProbe designed for magic angle spinning (MAS) experiments. Vn is a major blood protein that regulates many different physiological and pathological processes. The high sensitivity of the CryoProbe enabled us to acquire three-dimensional solid-state NMR spectra for sequential assignment and characterization of site-specific water-protein interactions that provide initial insights into the organization of the Vn-HAP complex. Vn associates with HAP in various pathological settings, including macular degeneration eyes and Alzheimer's disease brains. The ability to probe these assemblies at atomic detail paves the way for understanding their formation.
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Affiliation(s)
- T Gopinath
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kyungsoo Shin
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ye Tian
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, and Bioengineering, Lehigh University, PA 18015, USA
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | | | - Alia Hassan
- Bruker Switzerland AG, Fallanden, Switzerland
| | - Francesca M Marassi
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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4
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Chaudhary BP, Struppe J, Moktan H, Zoetewey D, Zhou DH, Mohanty S. Reconstitution and resonance assignments of yeast OST subunit Ost4 and its critical mutant Ost4V23D in liposomes by solid-state NMR. J Biomol NMR 2024:10.1007/s10858-024-00437-8. [PMID: 38421550 DOI: 10.1007/s10858-024-00437-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
N-linked glycosylation is an essential and highly conserved co- and post-translational protein modification in all domains of life. In humans, genetic defects in N-linked glycosylation pathways result in metabolic diseases collectively called Congenital Disorders of Glycosylation. In this modification reaction, a mannose rich oligosaccharide is transferred from a lipid-linked donor substrate to a specific asparagine side-chain within the -N-X-T/S- sequence (where X ≠ Proline) of the nascent protein. Oligosaccharyltransferase (OST), a multi-subunit membrane embedded enzyme catalyzes this glycosylation reaction in eukaryotes. In yeast, Ost4 is the smallest of nine subunits and bridges the interaction of the catalytic subunit, Stt3, with Ost3 (or its homolog, Ost6). Mutations of any C-terminal hydrophobic residues in Ost4 to a charged residue destabilizes the enzyme and negatively impacts its function. Specifically, the V23D mutation results in a temperature-sensitive phenotype in yeast. Here, we report the reconstitution of both purified recombinant Ost4 and Ost4V23D each in a POPC/POPE lipid bilayer and their resonance assignments using heteronuclear 2D and 3D solid-state NMR with magic-angle spinning. The chemical shifts of Ost4 changed significantly upon the V23D mutation, suggesting a dramatic change in its chemical environment.
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Affiliation(s)
- Bharat P Chaudhary
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | | | - Hem Moktan
- Department of Physics, Oklahoma State University, Stillwater, OK, 74078, USA
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David Zoetewey
- Department of Chemistry, Physics and Astronomy, Georgia College and State University, Milledgeville, GA, 31061, USA
| | - Donghua H Zhou
- Department of Physics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Smita Mohanty
- Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA.
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5
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Johann C, Wegner S, Althoff G, Struppe J. Automation in solid state NMR. J Magn Reson 2023; 355:107554. [PMID: 37717302 DOI: 10.1016/j.jmr.2023.107554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Automation in solid state NMR (ssNMR) requires appropriate hardware, from rotor loading mechanisms over highly stable rf-transmitters and probe circuitry to automatic tuning and matching capabilities including automatic magic angle adjustment for ssNMR probes. While these hardware capabilities are highly desirable and are, to various degrees, provided by manufacturers, we focus herein on automating experiment setup using radio frequency (rf) fields, which are key parameters in solid state NMR experiments. Specifically, these include spinlock fields during cross polarization (CP), or rf-fields for homo- or heteronuclear spin recoupling or decoupling. Often, these fields have specific relationships to the magic angle spinning (MAS) frequency. Relying on a well-maintained spectrometer, the experiment setup shifts from traditionally required optimization of rf-power values for each element of an experiment sequence to automatically setting all parameters correctly without any need for optimization. The proposed approach allows executing an experiment by reading its rf-amplitude requirements based on the actual MAS rotation frequency just before starting data acquisition, while all other hardware-related parameters are automatically provided through global tables and scripts. Under modest MAS frequencies, no further rf-power optimization is required while providing optimal sensitivity of better than 90% of the optimal signal to noise. Any optional parameter optimization relates only to adjusting rf-nutation frequencies to the requirements of the sample and the sample rotation frequency rather than the spectrometer hardware. Fast MAS CP experiments with MAS frequencies above 40 kHz require a semi-automated setup by optimizing Hartmann-Hahn (HH) matched rf-fields that are synchronously varied relative to the MAS-frequency. This allows for a significant reduction of setup steps by up to one order of magnitude for such experiments, avoiding the traditional grid search for optimal CPMAS conditions. The approach presented here can also be applied to decoupling or recoupling sequences, requiring rotor synchronized rf-fields, reducing the setup to a few steps addressing the spin system's properties rather than the spectrometer hardware. Our approach permits automating all basic solid state NMR experiments for high throughput analytical tasks.
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Affiliation(s)
- Christof Johann
- Buker Biospin Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | | | - Gerhard Althoff
- Buker Biospin Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States.
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6
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Zhang W, Hassan A, Struppe J, Monette M, Hung I, Gan Z, Martins V, Terskikh V, Huang Y. Overcoming challenges in 67Zn NMR: a new strategy of signal enhancement for MOF characterization. Chem Commun (Camb) 2023; 59:5205-5208. [PMID: 37042636 PMCID: PMC10155100 DOI: 10.1039/d3cc00716b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
67 Zn solid-state NMR suffers from low sensitivity, limiting its ability to probe the Zn2+ surroundings in MOFs. We report a breakthrough in overcoming challenges in 67Zn NMR. Combining new cryogenic MAS probe technology and performing NMR experiments at a high magnetic field results in remarkable signal enhancement, yielding enhanced information for MOF characterization.
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Affiliation(s)
- Wanli Zhang
- Department of Chemistry, University of Western Ontario, London, Ontario, N6A 5B7, Canada.
| | - Alia Hassan
- Bruker Switzerland AG, Fällanden, Switzerland
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - Martine Monette
- Bruker Biospin Ltd., 2800 High Point Drive, Suite 206, Milton, Ontario L9T 6P4, Canada
| | - Ivan Hung
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - Zhehong Gan
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - Vinicius Martins
- Department of Chemistry, University of Western Ontario, London, Ontario, N6A 5B7, Canada.
| | - Victor Terskikh
- Metrology, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Yining Huang
- Department of Chemistry, University of Western Ontario, London, Ontario, N6A 5B7, Canada.
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7
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Du Y, Struppe J, Perrone B, Hassan A, Codina A, Su Y. Efficient analysis of pharmaceutical drug substances and products using a solid-state NMR CryoProbe. Analyst 2023; 148:724-734. [PMID: 36722866 DOI: 10.1039/d2an01903e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) is a high-resolution and versatile spectroscopic tool for characterizing pharmaceutical solids. However, the inherent low sensitivity of NMR remains a significant challenge in the analysis of natural abundance drug substances and products. Here, we report, for the first time, the application of a CPMAS CryoProbe™ to improve the sensitivity of 13C and 15N detection by approximately 5 to 6 times for solid-state analysis of a commercial pharmaceutical drug posaconazole (POSA). The sensitivity enhancement enables two-dimensional (2D) 13C-13C and 1H-15N correlation experiments, which are otherwise time-prohibitive using regular MAS probes, for resonance assignment and structural elucidation. These polarization transfer and correlation experiments reveal drug-drug and drug-polymer interactions in amorphous POSA and its amorphous solid dispersion formulation. Our results demonstrated that the CPMAS CryoProbe™ can be widely applied for routine pharmaceutical analysis and advanced structural investigations with significantly enhanced efficiency and throughput.
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Affiliation(s)
- Yong Du
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ 07065, USA.
| | | | | | - Alia Hassan
- Bruker Switzerland AG, 8117 Faellanden, Switzerland
| | | | - Yongchao Su
- Analytical Research & Development, Merck & Co., Inc., Rahway, NJ 07065, USA.
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8
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Du Y, Frank D, Chen Z, Struppe J, Su Y. Ultrafast magic angle spinning NMR characterization of pharmaceutical solid polymorphism: A posaconazole example. J Magn Reson 2023; 346:107352. [PMID: 36535214 DOI: 10.1016/j.jmr.2022.107352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Protons represent the most NMR-sensitive nucleus in pharmaceutical compounds. Therefore, proton-detected solid-state NMR techniques under fast magic angle spinning are among the few solutions to overcome the challenge of low sensitivity to analyze natural abundant drug substances and products. In this study, we report the structural characterization of crystal polymorphs of a commercial drug molecule, posaconazole, with a relatively large molecular weight of 700.8 g·mol-1 and at the natural abundance. The enhanced sensitivity and resolution at 100 kHz MAS enables the exploration of the distinct intermolecular packing in posaconazole forms I, III, and γ. These results demonstrate that proton-detected homo- and heteronuclear correlation methods can probe the structural details of pharmaceutical polymorphism.
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Affiliation(s)
- Yong Du
- Analytical Research & Development, Merck & Co., Inc, Rahway, NJ 07065, USA
| | - Derek Frank
- Process Research & Development, Merck & Co., Inc, Rahway, NJ 07065, USA
| | - Zhenxuan Chen
- Analytical Research & Development, Merck & Co., Inc, Rahway, NJ 07065, USA
| | | | - Yongchao Su
- Analytical Research & Development, Merck & Co., Inc, Rahway, NJ 07065, USA.
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9
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Porat-Dahlerbruch G, Struppe J, Quinn CM, Gronenborn AM, Polenova T. 19F fast MAS (60-111 kHz) dipolar and scalar based correlation spectroscopy of organic molecules and pharmaceutical formulations. Solid State Nucl Magn Reson 2022; 122:101831. [PMID: 36182713 DOI: 10.1016/j.ssnmr.2022.101831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
19F magic angle spinning (MAS) NMR spectroscopy is a powerful tool for characterization of fluorinated solids. The recent development of 19F MAS NMR probes, operating at spinning frequencies of 60-111 kHz, enabled analysis of systems spanning from organic molecules to pharmaceutical formulations to biological assemblies, with unprecedented resolution. Herein, we systematically evaluate the benefits of high MAS frequencies (60-111 kHz) for 1D and 2D 19F-detected experiments in two pharmaceuticals, the antimalarial drug mefloquine and a formulation of the cholesterol-lowering drug atorvastatin calcium. We demonstrate that 1H decoupling is essential and that scalar-based, heteronuclear single quantum coherence (HSQC) and heteronuclear multiple quantum coherence (HMQC) correlation experiments become feasible and efficient at the MAS frequency of 100 kHz. This study opens doors for the applications of high frequency 19F MAS NMR to a wide range of problems in chemistry and biology.
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Angela M Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States; Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States; Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15261, United States.
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10
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Porat-Dahlerbruch G, Struppe J, Quinn CM, Gronenborn AM, Polenova T. Determination of accurate 19F chemical shift tensors with R-symmetry recoupling at high MAS frequencies (60-100 kHz). J Magn Reson 2022; 340:107227. [PMID: 35568013 DOI: 10.1016/j.jmr.2022.107227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/14/2022] [Accepted: 04/17/2022] [Indexed: 06/15/2023]
Abstract
Fluorination is a versatile and valuable modification for numerous systems, and 19F NMR spectroscopy is the premier method for their structural characterization. 19F chemical shift anisotropy is a sensitive probe of structure and dynamics, even though 19F chemical shift tensors have been reported for only a handful of systems to date. Here, we explore γ-encoded R-symmetry based recoupling sequences for the determination of 19F chemical shift tensors in fully protonated organic solids at high, 60-100 kHz MAS frequencies. We show that the performance of 19F-RNCSA experiments improves with increasing MAS frequencies, and that 1H decoupling is required to determine accurate chemical shift tensor parameters. In addition, these sequences are tolerant to B1-field inhomogeneity making them suitable for a wide range of systems and experimental conditions.
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Angela M Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States; Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States.
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11
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Ghosh Biswas R, Soong R, Ning P, Lane D, Bastawrous M, Jenne A, Schmidig D, de Castro P, Graf S, Kuehn T, Kümmerle R, Bermel W, Busse F, Struppe J, Simpson MJ, Simpson AJ. Exploring the Applications of Carbon-Detected NMR in Living and Dead Organisms Using a 13C-Optimized Comprehensive Multiphase NMR Probe. Anal Chem 2022; 94:8756-8765. [PMID: 35675504 DOI: 10.1021/acs.analchem.2c01356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Comprehensive multiphase-nuclear magnetic resonance (CMP-NMR) is a non-invasive approach designed to observe all phases (solutions, gels, and solids) in intact samples using a single NMR probe. Studies of dead and living organisms are important to understand processes ranging from biological growth to environmental stress. Historically, such studies have utilized 1H-based phase editing for the detection of soluble/swollen components and 1H-detected 2D NMR for metabolite assignments/screening. However, living organisms require slow spinning rates (∼500 Hz) to increase survivability, but at such low speeds, complications from water sidebands and spectral overlap from the modest chemical shift window (∼0-10 ppm) make 1H NMR challenging. Here, a novel 13C-optimized E-Free magic angle spinning CMP probe is applied to study all phases in ex vivo and in vivo samples. This probe consists of a two-coil design, with an inner single-tuned 13C coil providing a 113% increase in 13C sensitivity relative to a traditional multichannel single-CMP coil design. For organisms with a large biomass (∼0.1 g) like the Ganges River sprat (ex vivo), 13C-detected full spectral editing and 13C-detected heteronuclear correlation (HETCOR) can be performed at natural abundance. Unfortunately, for a single living shrimp (∼2 mg), 13C enrichment was still required, but 13C-detected HETCOR shows superior data relative to heteronuclear single-quantum coherence at low spinning speeds (due to complications from water sidebands in the latter). The probe is equipped with automatic-tuning-matching and is compatible with automated gradient shimming─a key step toward conducting multiphase screening of dead and living organisms under automation in the near future.
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Affiliation(s)
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Paris Ning
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Daniel Lane
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Monica Bastawrous
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Amy Jenne
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Daniel Schmidig
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Peter de Castro
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Stephan Graf
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Till Kuehn
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Rainer Kümmerle
- Bruker BioSpin AG, Industriestrasse 26, Fällanden 8117, Switzerland
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Falko Busse
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, 76275 Ettlingen, Germany
| | - Jochem Struppe
- Bruker Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821-3991, USA
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
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12
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Holmes JB, Liu V, Caulkins BG, Hilario E, Ghosh RK, Drago VN, Young RP, Romero JA, Gill AD, Bogie PM, Paulino J, Wang X, Riviere G, Bosken YK, Struppe J, Hassan A, Guidoulianov J, Perrone B, Mentink-Vigier F, Chang CEA, Long JR, Hooley RJ, Mueser TC, Dunn MF, Mueller LJ. Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate. Proc Natl Acad Sci U S A 2022; 119:e2109235119. [PMID: 34996869 PMCID: PMC8764694 DOI: 10.1073/pnas.2109235119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 02/07/2023] Open
Abstract
NMR-assisted crystallography-the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry-holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5'-phosphate-dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid-base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate Cβ and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.
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Affiliation(s)
- Jacob B Holmes
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Viktoriia Liu
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Bethany G Caulkins
- Department of Chemistry, University of California, Riverside, CA 92521
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711
| | - Eduardo Hilario
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Rittik K Ghosh
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Victoria N Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606
| | - Robert P Young
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Jennifer A Romero
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Adam D Gill
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Paul M Bogie
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Joana Paulino
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310
| | - Xiaoling Wang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310
| | - Gwladys Riviere
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, National High Magnetic Field Laboratory, University of Florida, Gainesville, FL 32610
| | - Yuliana K Bosken
- Department of Biochemistry, University of California, Riverside, CA 92521
| | | | - Alia Hassan
- Bruker Switzerland AG 8117 Fällanden, Switzerland
| | | | | | | | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Joanna R Long
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, National High Magnetic Field Laboratory, University of Florida, Gainesville, FL 32610
| | - Richard J Hooley
- Department of Chemistry, University of California, Riverside, CA 92521
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Timothy C Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606
| | - Michael F Dunn
- Department of Biochemistry, University of California, Riverside, CA 92521;
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, CA 92521;
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13
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Shen J, Terskikh V, Struppe J, Hassan A, Monette M, Hung I, Gan Z, Brinkmann A, Wu G. Solid-state 17O NMR study of α-d-glucose: exploring new frontiers in isotopic labeling, sensitivity enhancement, and NMR crystallography. Chem Sci 2022; 13:2591-2603. [PMID: 35340864 PMCID: PMC8890099 DOI: 10.1039/d1sc06060k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/31/2021] [Indexed: 01/03/2023] Open
Abstract
We report the first “total synthesis” of 17O-labeled d-glucose and its solid-state 17O NMR characterization with unprecedented sensitivity and resolution.
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Affiliation(s)
- Jiahui Shen
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Victor Terskikh
- Metrology, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, USA
| | - Alia Hassan
- Bruker Switzerland AG, Fällanden, Switzerland
| | - Martine Monette
- Bruker Biospin Ltd., 2800 High Point Drive, Suite 206, Milton, Ontario L9T 6P4, Canada
| | - Ivan Hung
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - Zhehong Gan
- National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, USA
| | - Andreas Brinkmann
- Metrology, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
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14
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Ha M, Nader S, Pawsey S, Struppe J, Monette M, Mansy SS, Boekhoven J, Michaelis VK. Racing toward Fast and Effective 17O Isotopic Labeling and Nuclear Magnetic Resonance Spectroscopy of N-Formyl-MLF-OH and Associated Building Blocks. J Phys Chem B 2021; 125:11916-11926. [PMID: 34694819 DOI: 10.1021/acs.jpcb.1c07397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solid-state 1H, 13C, and 15N nuclear magnetic resonance (NMR) spectroscopy has been an essential analytical method in studying complex molecules and biomolecules for decades. While oxygen-17 (17O) NMR is an ideal and robust candidate to study hydrogen bonding within secondary and tertiary protein structures for example, it continues to elude many. We discuss an improved multiple-turnover labeling procedure to develop a fast and cost-effective method to 17O label fluoroenylmethyloxycarbonyl (Fmoc)-protected amino acid building blocks. This approach allows for inexpensive ($0.25 USD/mg) insertion of 17O labels, an important barrier to overcome for future biomolecular studies. The 17O NMR results of these building blocks and a site-specific strategy for labeled N-acetyl-MLF-OH and N-formyl-MLF-OH tripeptides are presented. We showcase growth in NMR development for maximizing sensitivity gains using emerging sensitivity enhancement techniques including population transfer, high-field dynamic nuclear polarization, and cross-polarization magic-angle spinning cryoprobes.
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Affiliation(s)
- Michelle Ha
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Serge Nader
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Shane Pawsey
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Martine Monette
- Bruker BioSpin Ltd., Bruker Corporation, 555 Steeles Avenue E, Milton, Ontario L9T 1Y6, Canada
| | - Sheref S Mansy
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, Garching 85748, Germany.,Institute for Advanced Study, Technical University of Munich, Lichtenbergstraße 2a, Garching 85748, Germany
| | - Vladimir K Michaelis
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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15
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Quinn CM, Zadorozhnyi R, Struppe J, Sergeyev IV, Gronenborn AM, Polenova T. Fast 19F Magic-Angle Spinning Nuclear Magnetic Resonance for the Structural Characterization of Active Pharmaceutical Ingredients in Blockbuster Drugs. Anal Chem 2021; 93:13029-13037. [PMID: 34517697 DOI: 10.1021/acs.analchem.1c02917] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fluorinated drugs occupy a large and growing share of the pharmaceutical market. Here, we explore high-frequency, 60 to 111 kHz, 19F magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy for the structural characterization of fluorinated active pharmaceutical ingredients in commercial formulations of seven blockbuster drugs: Celebrex, Cipro, Crestor, Levaquin, Lipitor, Prozac, and Zyvox. 19F signals can be observed in a single scan, and spectra with high signal-to-noise ratios can be acquired in minutes. 19F spectral parameters, such as chemical shifts and line widths, are sensitive to both the nature of the fluorine moiety and the formulation. We anticipate that the fast 19F MAS NMR-based approach presented here will be valuable for the rapid analysis of fluorine-containing drugs in a wide variety of formulations.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Roman Zadorozhnyi
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
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16
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Ning P, Lane D, Ghosh Biswas R, Soong R, Schmidig D, Frei T, De Castro P, Kovacevic I, Graf S, Wegner S, Busse F, Kuehn T, Struppe J, Fey M, Stronks HJ, Monette M, Simpson MJ, Simpson AJ. Comprehensive Multiphase NMR Probehead with Reduced Radiofrequency Heating Improves the Analysis of Living Organisms and Heat-Sensitive Samples. Anal Chem 2021; 93:10326-10333. [PMID: 34259008 DOI: 10.1021/acs.analchem.1c01932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Comprehensive multiphase (CMP) NMR, first described in 2012, combines all of the hardware components necessary to analyze all phases (solid, gel, and solution) in samples in their natural state. In combination with spectral editing experiments, it can fully differentiate phases and study the transfer of chemical species across and between phases, providing unprecedented molecular-level information in unaltered natural systems. However, many natural samples, such as swollen soils, plants, and small organisms, contain water, salts, and ionic compounds, making them electrically lossy and susceptible to RF heating, especially when using high-strength RF fields required to select the solid domains. While dedicated reduced-heating probes have been developed for solid-state NMR, to date, all CMP-NMR probes have been based on solenoid designs, which can lead to problematic sample heating. Here, a new prototype CMP probe was developed, incorporating a loop gap resonator (LGR) for decoupling. Temperature increases are monitored in salt solutions analogous to those in small aquatic organisms and then tested in vivo on Hyalella azteca (freshwater shrimp). In the standard CMP probe (solenoid), 80% of organisms died within 4 h under high-power decoupling, while in the LGR design, all organisms survived the entire test period of 12 h. The LGR design reduced heating by a factor of ∼3, which allowed 100 kHz decoupling to be applied to salty samples with generally ≤10 °C sample heating. In addition to expanding the potential for in vivo research, the ability to apply uncompromised high-power decoupling could be beneficial for multiphase samples containing true crystalline solids that require the strongest possible decoupling fields for optimal detection.
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Affiliation(s)
- Paris Ning
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Daniel Lane
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | | | - Ronald Soong
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - Daniel Schmidig
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Thomas Frei
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Peter De Castro
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Ivan Kovacevic
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Stephan Graf
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Sebastian Wegner
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Falko Busse
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Till Kuehn
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Jochem Struppe
- Bruker BioSpin Corp., 15 Fortune Drive, Billerica, Massachusetts 01821-3991, United States
| | - Michael Fey
- Bruker BioSpin Corp., 15 Fortune Drive, Billerica, Massachusetts 01821-3991, United States
| | - Henry J Stronks
- Bruker Ltd., 2800 High Point Drive, Milton, Ontario L9T 6P4, Canada
| | - Martine Monette
- Bruker Ltd., 2800 High Point Drive, Milton, Ontario L9T 6P4, Canada
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
| | - André J Simpson
- Environmental NMR Centre, University of Toronto, Toronto, Ontario M1C 1A4, Canada
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17
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Ning P, Lane D, Ghosh Biswas R, Jenne A, Bastawrous M, Soong R, Schmidig D, Frei T, De Castro P, Kovacevic I, Graf S, Wegner S, Bermel W, Busse F, Kuehn T, Kuemmerle R, Struppe J, Fey M, Stronks HJ, Monette M, Simpson MJ, Simpson AJ. Expanding current applications and permitting the analysis of larger intact samples by means of a 7 mm CMP-NMR probe. Analyst 2021; 146:4461-4472. [PMID: 34136891 DOI: 10.1039/d1an00809a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Comprehensive multiphase NMR combines the ability to study and differentiate all phases (solids, gels, and liquids) using a single NMR probe. The general goal of CMP-NMR is to study intact environmental and biological samples to better understand conformation, organization, association, and transfer between and across phases/interfaces that may be lost with conventional sample preparation such as drying or solubilization. To date, all CMP-NMR studies have used 4 mm probes and rotors. Here, a larger 7 mm probehead is introduced which provides ∼3 times the volume and ∼2.4 times the signal over a 4 mm version. This offers two main advantages: (1) the additional biomass reduces experiment time, making 13C detection at natural abundance more feasible; (2) it allows the analysis of larger samples that cannot fit within a 4 mm rotor. Chicken heart tissue and Hyalella azteca (freshwater shrimp) are used to demonstrate that phase-based spectral editing works with 7 mm rotors and that the additional biomass from the larger volumes allows detection with 13C at natural abundance. Additionally, a whole pomegranate seed berry (aril) and an intact softgel capsule of hydroxyzine hydrochloride are used to demonstrate the analysis of samples too large to fit inside a conventional 4 mm CMP probe. The 7 mm version introduced here extends the range of applications and sample types that can be studied and is recommended when 4 mm CMP probes cannot provide adequate signal-to-noise (S/N), or intact samples are simply too big for 4 mm rotors.
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Affiliation(s)
- Paris Ning
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Daniel Lane
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Rajshree Ghosh Biswas
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Amy Jenne
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Monica Bastawrous
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Ronald Soong
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - Daniel Schmidig
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Thomas Frei
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Peter De Castro
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Ivan Kovacevic
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Stephan Graf
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Sebastian Wegner
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Falko Busse
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Till Kuehn
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Rainer Kuemmerle
- Bruker BioSpin AG, Industriestrasse 26, 8117 Fällanden, Switzerland
| | - Jochem Struppe
- Bruker BioSpin Corp., 15 Fortune Drive, Billerica, Massachusetts 01821-3991, USA
| | - Michael Fey
- Bruker BioSpin Corp., 15 Fortune Drive, Billerica, Massachusetts 01821-3991, USA
| | - Henry J Stronks
- Bruker Ltd., 2800 High Point Drive, Milton, ON, L9T 6P4Canada
| | - Martine Monette
- Bruker Ltd., 2800 High Point Drive, Milton, ON, L9T 6P4Canada
| | - Myrna J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
| | - André J Simpson
- Environmental NMR Centre, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada.
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18
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Guo C, Fritz MP, Struppe J, Wegner S, Stringer J, Sergeyev IV, Quinn CM, Gronenborn AM, Polenova T. Fast 19F Magic Angle Spinning NMR Crystallography for Structural Characterization of Fluorine-Containing Pharmaceutical Compounds. Anal Chem 2021; 93:8210-8218. [PMID: 34080855 DOI: 10.1021/acs.analchem.1c00784] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fluorine-containing compounds comprise 20 to 30 percent of all commercial drugs, and the proportion of fluorinated pharmaceuticals is rapidly growing. While magic angle spinning (MAS) NMR spectroscopy is a popular technique for analysis of solid pharmaceutical compounds, fluorine has been underutilized as a structural probe so far. Here, we report a fast (40-60 kHz) MAS 19F NMR approach for structural characterization of fluorine-containing crystalline pharmaceutical compounds at natural abundance, using the antimalarial fluorine-containing drug mefloquine as an example. We demonstrate the utility of 2D 19F-13C and 19F-19F dipolar-coupling-based correlation experiments for 19F and 13C resonance frequency assignment, which permit identification of crystallographically inequivalent sites. The efficiency of 19F-13C cross-polarization and the effect of 1H and 19F decoupling on spectral resolution and sensitivity were evaluated in a broad range of experimental conditions. We further demonstrate a protocol for measuring accurate interfluorine distances based on 1D DANTE-RFDR experiments combined with multispin numerical simulations.
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Affiliation(s)
- Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Matthew P Fritz
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | | | - John Stringer
- PhoenixNMR, 510 E. 5th Street, Loveland, Colorado 80537, United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
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19
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Sergeyev IV, Quinn CM, Struppe J, Gronenborn A, Polenova T. Competing Transfer Pathways in Direct and Indirect Dynamic Nuclear Polarization MAS NMR Experiments on HIV-1 Capsid Assemblies: Implications for Sensitivity and Resolution. Magn Reson (Gott) 2021; 2:239-249. [PMID: 34136885 PMCID: PMC8203495 DOI: 10.5194/mr-2-239-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/23/2021] [Indexed: 04/25/2023]
Abstract
Dynamic nuclear polarization-enhanced (DNP) magic angle spinning (MAS) NMR of biological systems is a rapidly growing field. Large signal enhancements make the technique particularly attractive for signal-limited cases, such as studies of complex biological assemblies or at natural isotopic abundance. However, spectral resolution is considerably reduced compared to ambient-temperature non-DNP spectra. Herein, we report a systematic investigation into sensitivity and resolution of 1D and 2D 13C-detected DNP MAS NMR experiments on HIV-1 CA tubular assemblies. We show that the magnitude and sign of signal enhancement as well as the homogeneous line width are strongly dependent on the biradical concentration, the dominant polarization transfer pathway, and the enhancement buildup time. Our findings provide guidance for optimal choice of sample preparation and experimental conditions in DNP experiments.
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Affiliation(s)
- Ivan V. Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
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20
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Ghosh Biswas R, Fortier-McGill B, Akhter M, Soong R, Ning P, Bastawrous M, Jenne A, Schmidig D, De Castro P, Graf S, Kuehn T, Busse F, Struppe J, Fey M, Heumann H, Boenisch H, Gundy M, Simpson MJ, Simpson AJ. Ex vivo Comprehensive Multiphase NMR of whole organisms: A complementary tool to in vivo NMR. Anal Chim Acta X 2020; 6:100051. [PMID: 33392494 PMCID: PMC7772632 DOI: 10.1016/j.acax.2020.100051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/29/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a non-invasive analytical technique which allows for the study of intact samples. Comprehensive Multiphase NMR (CMP-NMR) combines techniques and hardware from solution state and solid state NMR to allow for the holistic analysis of all phases (i.e. solutions, gels and solids) in unaltered samples. This study is the first to apply CMP-NMR to deceased, intact organisms and uses 13C enriched Daphnia magna (water fleas) as an example. D. magna are commonly used model organisms for environmental toxicology studies. As primary consumers, they are responsible for the transfer of nutrients across trophic levels, and a decline in their population can potentially impact the entire freshwater aquatic ecosystem. Though in vivo research is the ultimate tool to understand an organism’s most biologically relevant state, studies are limited by conditions (i.e. oxygen requirements, limited experiment time and reduced spinning speed) required to keep the organisms alive, which can negatively impact the quality of the data collected. In comparison, ex vivo CMP-NMR is beneficial in that; organisms do not need oxygen (eliminating air holes in rotor caps and subsequent evaporation); samples can be spun faster, leading to improved spectral resolution; more biomass per sample can be analyzed; and experiments can be run for longer. In turn, higher quality ex vivo NMR, can provide more comprehensive NMR assignments, which in many cases could be transferred to better understand less resolved in vivo signals. This manuscript is divided into three sections: 1) multiphase spectral editing techniques, 2) detailed metabolic assignments of 2D NMR of 13C enriched D. magna and 3) multiphase biological changes over different life stages, ages and generations of D. magna. In summary, ex vivo CMP-NMR proves to be a very powerful approach to study whole organisms in a comprehensive manner and should provide very complementary information to in vivo based research. Comprehensive Multiphase NMR detects all phases (solid/liquid/gel) in whole samples. Deceased organisms are not subjected to the limitations of in vivo NMR studies. 2D ex vivo NMR offer increased spectral resolution, improving metabolite assignment. Holistic analysis shows biological changes in D. magna over different life stages. Ex vivo NMR can be a complementary tool for in vivo NMR metabolomic studies.
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Affiliation(s)
- Rajshree Ghosh Biswas
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Blythe Fortier-McGill
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Mohammad Akhter
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Ronald Soong
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Paris Ning
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Monica Bastawrous
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Amy Jenne
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - Daniel Schmidig
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Peter De Castro
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Stephan Graf
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Till Kuehn
- Bruker Switzerland AG, Industriestrasse 26, 8117, Fällanden, Switzerland
| | - Falko Busse
- Bruker Biospin GmbH, Silberstreifen 4, 76287, Rheinstetten, Germany
| | - Jochem Struppe
- Bruker Corporation, 15 Fortune Drive, Billerica, MA, 01821-3991, USA
| | - Michael Fey
- Bruker Corporation, 15 Fortune Drive, Billerica, MA, 01821-3991, USA
| | - Hermann Heumann
- Silantes GmbH, Gollierstrasse 70c, D-80339, München, Germany
| | - Holger Boenisch
- Silantes GmbH, Gollierstrasse 70c, D-80339, München, Germany
| | - Marcel Gundy
- Silantes GmbH, Gollierstrasse 70c, D-80339, München, Germany
| | - Myrna J Simpson
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
| | - André J Simpson
- University of Toronto Scarborough, Department of Physical & Environmental Sciences, 1265, Military Trail, M1C 1A4, ON, Canada
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21
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Hassan A, Quinn CM, Struppe J, Sergeyev IV, Zhang C, Guo C, Runge B, Theint T, Dao HH, Jaroniec CP, Berbon M, Lends A, Habenstein B, Loquet A, Kuemmerle R, Perrone B, Gronenborn AM, Polenova T. Sensitivity boosts by the CPMAS CryoProbe for challenging biological assemblies. J Magn Reson 2020; 311:106680. [PMID: 31951864 PMCID: PMC7060763 DOI: 10.1016/j.jmr.2019.106680] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 06/09/2023]
Abstract
Despite breakthroughs in MAS NMR hardware and experimental methodologies, sensitivity remains a major challenge for large and complex biological systems. Here, we report that 3-4 fold higher sensitivities can be obtained in heteronuclear-detected experiments, using a novel HCN CPMAS probe, where the sample coil and the electronics operate at cryogenic temperatures, while the sample is maintained at ambient temperatures (BioSolids CryoProbe™). Such intensity enhancements permit recording 2D and 3D experiments that are otherwise time-prohibitive, such as 2D 15N-15N proton-driven spin diffusion and 15N-13C double cross polarization to natural abundance carbon experiments. The benefits of CPMAS CryoProbe-based experiments are illustrated for assemblies of kinesin Kif5b with microtubules, HIV-1 capsid protein assemblies, and fibrils of human Y145Stop and fungal HET-s prion proteins - demanding systems for conventional MAS solid-state NMR and excellent reference systems in terms of spectral quality. We envision that this probe technology will be beneficial for a wide range of applications, especially for biological systems suffering from low intrinsic sensitivity and at physiological temperatures.
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Affiliation(s)
- Alia Hassan
- Bruker Biospin Corporation, Fällanden, Switzerland.
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Chunting Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Brent Runge
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Theint Theint
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Hanh H Dao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Mélanie Berbon
- CNRS, CBMN, UMR5248, University of Bordeaux, F-33600 Pessac, France
| | - Alons Lends
- CNRS, CBMN, UMR5248, University of Bordeaux, F-33600 Pessac, France
| | | | - Antoine Loquet
- CNRS, CBMN, UMR5248, University of Bordeaux, F-33600 Pessac, France
| | | | | | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, United States.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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22
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Abstract
Magic angle spinning (MAS) NMR is a powerful method for the study of pharmaceutical compounds, and probes with spinning frequencies above 100 kHz enable an atomic-resolution analysis of sub-micromole quantities of fully protonated solids. Here, we present an ultrafast NMR crystallography approach for structural characterization of organic solids at MAS frequencies of 100-111 kHz. We assess the efficiency of 1H-detected experiments in the solid state and demonstrate the utility of 2D and 3D homo- and heteronuclear correlation spectra for resonance assignments. These experiments are demonstrated for an amino acid, U-13C,15N-histidine, and also for the significantly larger, natural product Posaconazole, an antifungal compound investigated at natural abundance. Our results illustrate the power for characterizing organic molecules, enabled by exploiting the increased 1H resolution and sensitivity at MAS frequencies above 100 kHz.
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Affiliation(s)
- Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sucharita Sarkar
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Angela M Gronenborn
- Department of Structural Biology , University of Pittsburgh School of Medicine , Pittsburgh , Pennsylvania 15260 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , Pittsburgh , Pennsylvania 15260 , United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , Pittsburgh , Pennsylvania 15260 , United States
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23
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Fritz M, Kraus J, Quinn CM, Yap GPA, Struppe J, Sergeyev IV, Gronenborn AM, Polenova T. Measurement of Accurate Interfluorine Distances in Crystalline Organic Solids: A High-Frequency Magic Angle Spinning NMR Approach. J Phys Chem B 2019; 123:10680-10690. [PMID: 31682453 DOI: 10.1021/acs.jpcb.9b08919] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Long-range interatomic distance restraints are critical for the determination of molecular structures by NMR spectroscopy, both in solution and in the solid state. Fluorine is a powerful NMR probe in a wide variety of contexts, owing to its favorable magnetic properties, ease of incorporation into biological molecules, and ubiquitous use in synthetic organic molecules designed for diverse applications. Because of the large gyromagnetic ratio of the 100% naturally abundant 19F isotope, interfluorine distances as long as 20 Å are accessible in magic-angle spinning (MAS) dipolar recoupling experiments. Herein, we present an approach for the determination of accurate interfluorine distances in multispin systems, using the finite pulse radio frequency driven recoupling (fpRFDR) at high MAS frequencies of 40-60 kHz. We use a series of crystalline "molecular ruler" solids, difluorobenzoic acids and 7F-L-tryptophan, for which the intra- and intermolecular interfluorine distances are known. We describe the optimal experimental conditions for accurate distance determinations, including the choice of a phase cycle, the relative advantages of selective inversion one-dimensional versus two-dimensional correlation experiments, and the appropriate numerical simulation protocols. An optimal strategy for the analysis of RFDR exchange curves in organic solids with extended spin interaction networks is presented, which, even in the absence of crystal structures, can be potentially incorporated into NMR structure determination.
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Affiliation(s)
- Matthew Fritz
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Jodi Kraus
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States.,Department of Structural Biology , University of Pittsburgh School of Medicine , 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
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24
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Gupta R, Zhang H, Lu M, Hou G, Caporini M, Rosay M, Maas W, Struppe J, Ahn J, Byeon IJL, Oschkinat H, Jaudzems K, Barbet-Massin E, Emsley L, Pintacuda G, Lesage A, Gronenborn AM, Polenova T. Dynamic Nuclear Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Combined with Molecular Dynamics Simulations Permits Detection of Order and Disorder in Viral Assemblies. J Phys Chem B 2019; 123:5048-5058. [PMID: 31125232 DOI: 10.1021/acs.jpcb.9b02293] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR spectroscopy in viral capsids from HIV-1 and bacteriophage AP205. Viruses regulate their life cycles and infectivity through modulation of their structures and dynamics. While static structures of capsids from several viruses are now accessible with near-atomic-level resolution, atomic-level understanding of functionally important motions in assembled capsids is lacking. We observed up to 64-fold signal enhancements by DNP, which permitted in-depth analysis of these assemblies. For the HIV-1 CA assemblies, a remarkably high spectral resolution in the 3D and 2D heteronuclear data sets permitted the assignment of a significant fraction of backbone and side-chain resonances. Using an integrated DNP MAS NMR and molecular dynamics (MD) simulation approach, the conformational space sampled by the assembled capsid at cryogenic temperatures was mapped. Qualitatively, a remarkable agreement was observed for the experimental 13C/15N chemical shift distributions and those calculated from substructures along the MD trajectory. Residues that are mobile at physiological temperatures are frozen out in multiple conformers at cryogenic conditions, resulting in broad experimental and calculated chemical shift distributions. Overall, our results suggest that DNP MAS NMR measurements in combination with MD simulations facilitate a thorough understanding of the dynamic signatures of viral capsids.
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Affiliation(s)
- Rupal Gupta
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Huilan Zhang
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Manman Lu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Marc Caporini
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Melanie Rosay
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Werner Maas
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | | | | | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie , Robert-Roessle-Str. 10 , 13125 Berlin , Germany
| | - Kristaps Jaudzems
- Centre de RMN à Très Hauts Champs , Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon , 5 Rue de la Doua , Villeurbanne, 69100 Lyon , France
| | - Emeline Barbet-Massin
- Centre de RMN à Très Hauts Champs , Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon , 5 Rue de la Doua , Villeurbanne, 69100 Lyon , France
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimques , Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne , Switzerland
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs , Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon , 5 Rue de la Doua , Villeurbanne, 69100 Lyon , France
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs , Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon , 5 Rue de la Doua , Villeurbanne, 69100 Lyon , France
| | | | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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25
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Lu M, Wang M, Sergeyev IV, Quinn CM, Struppe J, Rosay M, Maas W, Gronenborn AM, Polenova T. 19F Dynamic Nuclear Polarization at Fast Magic Angle Spinning for NMR of HIV-1 Capsid Protein Assemblies. J Am Chem Soc 2019; 141:5681-5691. [PMID: 30871317 PMCID: PMC6521953 DOI: 10.1021/jacs.8b09216] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report remarkably high, up to 100-fold, signal enhancements in 19F dynamic nuclear polarization (DNP) magic angle spinning (MAS) spectra at 14.1 T on HIV-1 capsid protein (CA) assemblies. These enhancements correspond to absolute sensitivity ratios of 12-29 and are of similar magnitude to those seen for 1H signals in the same samples. At MAS frequencies above 20 kHz, it was possible to record 2D 19F-13C HETCOR spectra, which contain long-range intra- and intermolecular correlations. Such correlations provide unique distance restraints, inaccessible in conventional experiments without DNP, for protein structure determination. Furthermore, systematic quantification of the DNP enhancements as a function of biradical concentration, MAS frequency, temperature, and microwave power is reported. Our work establishes the power of DNP-enhanced 19F MAS NMR spectroscopy for structural characterization of HIV-1 CA assemblies, and this approach is anticipated to be applicable to a wide range of large biomolecular systems.
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Affiliation(s)
- Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Ivan V. Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Melanie Rosay
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Werner Maas
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
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26
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Lu M, Wang M, Struppe J, Maas W, Gronenborn A, Polenova T. Towards Atomic-Resolution Structure Determination of HIV-1 Capsid Assemblies using Magic Angle Spinning NMR. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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27
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Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin L, Struppe J, Case DA, Gronenborn AM. Accurate Measurement and Prediction of 15NH and 13Cα Chemical Shift Tensors in Proteins. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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28
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Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Struppe J, Case DA, Polenova T, Gronenborn AM. Determination of accurate backbone chemical shift tensors in microcrystalline proteins by integrating MAS NMR and QM/MM. Phys Chem Chem Phys 2019; 20:9543-9553. [PMID: 29577158 DOI: 10.1039/c8cp00647d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical shifts are highly sensitive probes of local conformation and overall structure. Both isotropic shifts and chemical shift tensors are readily accessible from NMR experiments but their quantum mechanical calculations remain challenging. In this work, we report and compare accurately measured and calculated 15NH and 13Cα chemical shift tensors in proteins, using the microcrystalline agglutinin from Oscillatoria agardhii (OAA). Experimental 13Cα and 15NH chemical tensors were obtained by solid-state NMR spectroscopy, employing tailored recoupling sequences, and for their quantum mechanics/molecular mechanics (QM/MM) calculations different sets of functionals were evaluated. We show that 13Cα chemical shift tensors are primarily determined by backbone dihedral angles and dynamics, while 15NH tensors mainly depend on local electrostatic contributions from solvation and hydrogen bonding. In addition, the influence of including crystallographic waters, the molecular mechanics geometry optimization protocol, and the level of theory on the accuracy of the calculated chemical shift tensors is discussed. Specifically, the power of QM/MM calculations in accurately predicting the unusually upfield shifted 1HN G26 and G93 resonances is highlighted. Our integrated approach is expected to benefit structure refinement of proteins and protein assemblies.
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Affiliation(s)
- Matthew Fritz
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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29
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Wang M, Lu M, Fritz MP, Quinn CM, Byeon IJL, Byeon CH, Struppe J, Maas W, Gronenborn AM, Polenova T. Fast Magic-Angle Spinning 19 F NMR Spectroscopy of HIV-1 Capsid Protein Assemblies. Angew Chem Int Ed Engl 2018; 57:16375-16379. [PMID: 30225969 PMCID: PMC6279522 DOI: 10.1002/anie.201809060] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Indexed: 01/18/2023]
Abstract
19 F NMR spectroscopy is an attractive and growing area of research with broad applications in biochemistry, chemical biology, medicinal chemistry, and materials science. We have explored fast magic angle spinning (MAS) 19 F solid-state NMR spectroscopy in assemblies of HIV-1 capsid protein. Tryptophan residues with fluorine substitution at the 5-position of the indole ring were used as the reporters. The 19 F chemical shifts for the five tryptophan residues are distinct, reflecting differences in their local environment. Spin-diffusion and radio-frequency-driven-recoupling experiments were performed at MAS frequencies of 35 kHz and 40-60 kHz, respectively. Fast MAS frequencies of 40-60 kHz are essential for consistently establishing 19 F-19 F correlations, yielding interatomic distances of the order of 20 Å. Our results demonstrate the potential of fast MAS 19 F NMR spectroscopy for structural analysis in large biological assemblies.
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Affiliation(s)
- Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Brown Laboratories; Newark, DE 19716, United States,
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States,
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Brown Laboratories; Newark, DE 19716, United States,
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States,
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Matthew P. Fritz
- Department of Chemistry and Biochemistry, University of Delaware, Brown Laboratories; Newark, DE 19716, United States,
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States,
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Brown Laboratories; Newark, DE 19716, United States,
| | - In-Ja L. Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States,
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Chang-Hyeock Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States,
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Werner Maas
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States,
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Brown Laboratories; Newark, DE 19716, United States,
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States,
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30
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Wang M, Lu M, Fritz MP, Quinn CM, Byeon IL, Byeon C, Struppe J, Maas W, Gronenborn AM, Polenova T. Fast Magic‐Angle Spinning
19
F NMR Spectroscopy of HIV‐1 Capsid Protein Assemblies. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mingzhang Wang
- Department of Chemistry and Biochemistry University of Delaware Brown Laboratories Newark DE 19716 USA
- Pittsburgh Center for HIV Protein Interactions University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
| | - Manman Lu
- Department of Chemistry and Biochemistry University of Delaware Brown Laboratories Newark DE 19716 USA
- Pittsburgh Center for HIV Protein Interactions University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
- Department of Structural Biology University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
| | - Matthew P. Fritz
- Department of Chemistry and Biochemistry University of Delaware Brown Laboratories Newark DE 19716 USA
- Pittsburgh Center for HIV Protein Interactions University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry University of Delaware Brown Laboratories Newark DE 19716 USA
| | - In‐Ja L. Byeon
- Pittsburgh Center for HIV Protein Interactions University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
- Department of Structural Biology University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
| | - Chang‐Hyeock Byeon
- Pittsburgh Center for HIV Protein Interactions University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
- Department of Structural Biology University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
| | - Jochem Struppe
- Bruker Biospin Corporation 15 Fortune Drive Billerica MA USA
| | - Werner Maas
- Bruker Biospin Corporation 15 Fortune Drive Billerica MA USA
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
- Department of Structural Biology University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry University of Delaware Brown Laboratories Newark DE 19716 USA
- Pittsburgh Center for HIV Protein Interactions University of Pittsburgh School of Medicine 1051 Biomedical Science Tower 3, 3501 Fifth Avenue Pittsburgh PA 15261 USA
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31
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Gupta R, Stringer J, Struppe J, Rehder D, Polenova T. Direct detection and characterization of bioinorganic peroxo moieties in a vanadium complex by 17O solid-state NMR and density functional theory. Solid State Nucl Magn Reson 2018; 91:15-20. [PMID: 29506770 PMCID: PMC6267778 DOI: 10.1016/j.ssnmr.2018.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Electronic and structural properties of short-lived metal-peroxido complexes, which are key intermediates in many enzymatic reactions, are not fully understood. While detected in various enzymes, their catalytic properties remain elusive because of their transient nature, making them difficult to study spectroscopically. We integrated 17O solid-state NMR and density functional theory (DFT) to directly detect and characterize the peroxido ligand in a bioinorganic V(V) complex mimicking intermediates non-heme vanadium haloperoxidases. 17O chemical shift and quadrupolar tensors, measured by solid-state NMR spectroscopy, probe the electronic structure of the peroxido ligand and its interaction with the metal. DFT analysis reveals the unusually large chemical shift anisotropy arising from the metal orbitals contributing towards the magnetic shielding of the ligand. The results illustrate the power of an integrated approach for studies of oxygen centers in enzyme reaction intermediates.
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Affiliation(s)
- Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
| | - John Stringer
- PhoenixNMR, 4921 Eagle Lake Drive, Fort Collins, CO, USA
| | | | - Dieter Rehder
- Department of Chemistry, University of Hamburg, D-20146, Hamburg, Germany
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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32
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Lu M, Sarkar S, Wang M, Kraus J, Fritz M, Quinn CM, Bai S, Holmes ST, Dybowski C, Yap GPA, Struppe J, Sergeyev IV, Maas W, Gronenborn AM, Polenova T. 19F Magic Angle Spinning NMR Spectroscopy and Density Functional Theory Calculations of Fluorosubstituted Tryptophans: Integrating Experiment and Theory for Accurate Determination of Chemical Shift Tensors. J Phys Chem B 2018. [PMID: 29756776 DOI: 10.1021/acs.jpcb.1028b00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
The 19F chemical shift is a sensitive NMR probe of structure and electronic environment in organic and biological molecules. In this report, we examine chemical shift parameters of 4F-, 5F-, 6F-, and 7F-substituted crystalline tryptophan by magic angle spinning (MAS) solid-state NMR spectroscopy and density functional theory. Significant narrowing of the 19F lines was observed under fast MAS conditions, at spinning frequencies above 50 kHz. The parameters characterizing the 19F chemical shift tensor are sensitive to the position of the fluorine in the aromatic ring and, to a lesser extent, the chirality of the molecule. Accurate calculations of 19F magnetic shielding tensors require the PBE0 functional with a 50% admixture of a Hartree-Fock exchange term, as well as taking account of the local crystal symmetry. The methodology developed will be beneficial for 19F-based MAS NMR structural analysis of proteins and protein assemblies.
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Affiliation(s)
- Manman Lu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Sucharita Sarkar
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Jodi Kraus
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Matthew Fritz
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Shi Bai
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sean T Holmes
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Werner Maas
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
- Department of Structural Biology , University of Pittsburgh School of Medicine , 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
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Cao W, Wang WD, Xu HS, Sergeyev IV, Struppe J, Wang X, Mentink-Vigier F, Gan Z, Xiao MX, Wang LY, Chen GP, Ding SY, Bai S, Wang W. Exploring Applications of Covalent Organic Frameworks: Homogeneous Reticulation of Radicals for Dynamic Nuclear Polarization. J Am Chem Soc 2018; 140:6969-6977. [PMID: 29799739 PMCID: PMC6045815 DOI: 10.1021/jacs.8b02839] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid progress has been witnessed in the past decade in the fields of covalent organic frameworks (COFs) and dynamic nuclear polarization (DNP). In this contribution, we bridge these two fields by constructing radical-embedded COFs as promising DNP agents. Via polarization transfer from unpaired electrons to nuclei, DNP realizes significant enhancement of NMR signal intensities. One of the crucial issues in DNP is to screen for suitable radicals to act as efficient polarizing agents, the basic criteria for which are homogeneous distribution and fixed orientation of unpaired electrons. We therefore envisioned that the crystalline and porous structures of COFs, if evenly embedded with radicals, may work as a new "crystalline sponge" for DNP experiments. As a proof of concept, we constructed a series of proxyl-radical-embedded COFs (denoted as PR( x)-COFs) and successfully applied them to achieve substantial DNP enhancement. Benefiting from the bottom-up and multivariate synthetic strategies, proxyl radicals have been covalently reticulated, homogeneously distributed, and rigidly embedded into the crystalline and mesoporous frameworks with adjustable concentration ( x%). Excellent performance of PR( x)-COFs has been observed for DNP 1H, 13C, and 15N solid-state NMR enhancements. This contribution not only realizes the direct construction of radical COFs from radical monomers, but also explores the new application of COFs as DNP polarizing agents. Given that many radical COFs can therefore be rationally designed and facilely constructed with well-defined composition, distribution, and pore size, we expect that our effort will pave the way for utilizing radical COFs as standard polarizing agents in DNP NMR experiments.
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Affiliation(s)
- Wei Cao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Wei David Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Hai-Sen Xu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Ivan V Sergeyev
- Bruker BioSpin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Jochem Struppe
- Bruker BioSpin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Xiaoling Wang
- National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Zhehong Gan
- National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Ming-Xing Xiao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Lu-Yao Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Guo-Peng Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - San-Yuan Ding
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Shi Bai
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Wei Wang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering , Lanzhou University , Lanzhou , Gansu 730000 , China
- Collaborative Innovation Center of Chemical Science and Engineering , Tianjin 300071 , China
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34
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Lu M, Sarkar S, Wang M, Kraus J, Fritz M, Quinn CM, Bai S, Holmes ST, Dybowski C, Yap GPA, Struppe J, Sergeyev IV, Maas W, Gronenborn AM, Polenova T. 19F Magic Angle Spinning NMR Spectroscopy and Density Functional Theory Calculations of Fluorosubstituted Tryptophans: Integrating Experiment and Theory for Accurate Determination of Chemical Shift Tensors. J Phys Chem B 2018; 122:6148-6155. [PMID: 29756776 DOI: 10.1021/acs.jpcb.8b00377] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 19F chemical shift is a sensitive NMR probe of structure and electronic environment in organic and biological molecules. In this report, we examine chemical shift parameters of 4F-, 5F-, 6F-, and 7F-substituted crystalline tryptophan by magic angle spinning (MAS) solid-state NMR spectroscopy and density functional theory. Significant narrowing of the 19F lines was observed under fast MAS conditions, at spinning frequencies above 50 kHz. The parameters characterizing the 19F chemical shift tensor are sensitive to the position of the fluorine in the aromatic ring and, to a lesser extent, the chirality of the molecule. Accurate calculations of 19F magnetic shielding tensors require the PBE0 functional with a 50% admixture of a Hartree-Fock exchange term, as well as taking account of the local crystal symmetry. The methodology developed will be beneficial for 19F-based MAS NMR structural analysis of proteins and protein assemblies.
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Affiliation(s)
- Manman Lu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Sucharita Sarkar
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Jodi Kraus
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Matthew Fritz
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Shi Bai
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sean T Holmes
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Cecil Dybowski
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Werner Maas
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States.,Department of Structural Biology , University of Pittsburgh School of Medicine , 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
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35
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Struppe J, Quinn CM, Lu M, Wang M, Hou G, Lu X, Kraus J, Andreas LB, Stanek J, Lalli D, Lesage A, Pintacuda G, Maas W, Gronenborn AM, Polenova T. Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz. Solid State Nucl Magn Reson 2017; 87:117-125. [PMID: 28732673 PMCID: PMC5824719 DOI: 10.1016/j.ssnmr.2017.07.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/28/2017] [Accepted: 07/02/2017] [Indexed: 05/20/2023]
Abstract
The recent breakthroughs in NMR probe technologies resulted in the development of MAS NMR probes with rotation frequencies exceeding 100 kHz. Herein, we explore dramatic increases in sensitivity and resolution observed at MAS frequencies of 110-111 kHz in a novel 0.7 mm HCND probe that enable structural analysis of fully protonated biological systems. Proton- detected 2D and 3D correlation spectroscopy under such conditions requires only 0.1-0.5 mg of sample and a fraction of time compared to conventional 13C-detected experiments. We discuss the performance of several proton- and heteronuclear- (13C-,15N-) based correlation experiments in terms of sensitivity and resolution, using a model microcrystalline fMLF tripeptide. We demonstrate the applications of ultrafast MAS to a large, fully protonated protein assembly of the 231-residue HIV-1 CA capsid protein. Resonance assignments of protons and heteronuclei, as well as 1H-15N dipolar and 1HN CSA tensors are readily obtained from the high sensitivity and resolution proton-detected 3D experiments. The approach demonstrated here is expected to enable the determination of atomic-resolution structures of large protein assemblies, inaccessible by current methodologies.
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Affiliation(s)
- Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States.
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Jodi Kraus
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Jan Stanek
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Daniela Lalli
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Werner Maas
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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36
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Gupta R, Lu M, Hou G, Caporini MA, Rosay M, Maas W, Struppe J, Suiter C, Ahn J, Byeon IJL, Franks WT, Orwick-Rydmark M, Bertarello A, Oschkinat H, Lesage A, Pintacuda G, Gronenborn AM, Polenova T. Dynamic Nuclear Polarization Enhanced MAS NMR Spectroscopy for Structural Analysis of HIV-1 Protein Assemblies. J Phys Chem B 2016; 120:329-39. [PMID: 26709853 DOI: 10.1021/acs.jpcb.5b12134] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mature infectious HIV-1 virions contain conical capsids composed of CA protein, generated by the proteolytic cleavage cascade of the Gag polyprotein, termed maturation. The mechanism of capsid core formation through the maturation process remains poorly understood. We present DNP-enhanced MAS NMR studies of tubular assemblies of CA and Gag CA-SP1 maturation intermediate and report 20-64-fold sensitivity enhancements due to DNP at 14.1 T. These sensitivity enhancements enabled direct observation of spacer peptide 1 (SP1) resonances in CA-SP1 by dipolar-based correlation experiments, unequivocally indicating that the SP1 peptide is unstructured in assembled CA-SP1 at cryogenic temperatures, corroborating our earlier results. Furthermore, the dependence of DNP enhancements and spectral resolution on magnetic field strength (9.4-18.8 T) and temperature (109-180 K) was investigated. Our results suggest that DNP-based measurements could potentially provide residue-specific dynamics information by allowing for the extraction of the temperature dependence of the anisotropic tensorial or relaxation parameters. With DNP, we were able to detect multiple well-resolved isoleucine side-chain conformers; unique intermolecular correlations across two CA molecules; and functionally relevant conformationally disordered states such as the 14-residue SP1 peptide, none of which are visible at ambient temperatures. The detection of isolated conformers and intermolecular correlations can provide crucial constraints for structure determination of these assemblies. Overall, our results establish DNP-based MAS NMR spectroscopy as an excellent tool for the characterization of HIV-1 assemblies.
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Affiliation(s)
- Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | - Marc A Caporini
- Bruker Biospin Corporation , 15 Fortune Drive, Billerica, Massachusetts United States
| | - Melanie Rosay
- Bruker Biospin Corporation , 15 Fortune Drive, Billerica, Massachusetts United States
| | - Werner Maas
- Bruker Biospin Corporation , 15 Fortune Drive, Billerica, Massachusetts United States
| | - Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive, Billerica, Massachusetts United States
| | - Christopher Suiter
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
| | | | | | - W Trent Franks
- Leibniz-Institut für Molekulare Pharmakologie , Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Marcella Orwick-Rydmark
- Leibniz-Institut für Molekulare Pharmakologie , Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Andrea Bertarello
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS/Ecole Normale Supérieure de Lyon , 5 rue de la Doua, 69100 Villeurbanne (Lyon), France
| | - Hartmut Oschkinat
- Leibniz-Institut für Molekulare Pharmakologie , Robert-Roessle-Straße 10, 13125 Berlin, Germany
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS/Ecole Normale Supérieure de Lyon , 5 rue de la Doua, 69100 Villeurbanne (Lyon), France
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS/Ecole Normale Supérieure de Lyon , 5 rue de la Doua, 69100 Villeurbanne (Lyon), France
| | | | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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Wang Z, Randazzo K, Hou X, Simpson J, Struppe J, Ugrinov A, Kastern B, Wysocki E, Chu QR. Stereoregular Two-Dimensional Polymers Constructed by Topochemical Polymerization. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00109] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Zhihan Wang
- Department
of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Katelyn Randazzo
- Department
of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Xiaodong Hou
- Department
of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Jeffrey Simpson
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jochem Struppe
- Bruker Biospin Ltd., Billerica, Massachusetts 01821, United States
| | - Angel Ugrinov
- Department
of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Brent Kastern
- Department
of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Erin Wysocki
- Department
of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Qianli R. Chu
- Department
of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
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Struppe J, Zhang Y, Rozovsky S. (77)Se chemical shift tensor of L-selenocystine: experimental NMR measurements and quantum chemical investigations of structural effects. J Phys Chem B 2015; 119:3643-50. [PMID: 25654666 DOI: 10.1021/jp510857s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The genetically encoded amino acid selenocysteine and its dimeric form, selenocystine, are both utilized by nature. They are found in active sites of selenoproteins, enzymes that facilitate a diverse range of reactions, including the detoxification of reactive oxygen species and regulation of redox pathways. Due to selenocysteine and selenocystine's specialized biological roles, it is of interest to examine their (77)Se NMR properties and how those can in turn be employed to study biological systems. We report the solid-state (77)Se NMR measurements of the L-selenocystine chemical shift tensor, which provides the first experimental chemical shift tensor information on selenocysteine-containing systems. Quantum chemical calculations of L-selenocystine models were performed to help understand various structural effects on (77)Se L-selenocystine's chemical shift tensor. The effects of protonation state, protein environment, and substituent of selenium-bonded carbon on the isotropic chemical shift were found to be in a range of ca. 10-20 ppm. However, the conformational effect was found to be much larger, spanning ca. 600 ppm for the C-Se-Se-C dihedral angle range of -180° to +180°. Our calculations show that around the minimum energy structure with a C-Se-Se-C dihedral angle of ca. -90°, the energy costs to alter the dihedral angle in the range from -120° to -60° are within only 2.5 kcal/mol. This makes it possible to realize these conformations in a protein or crystal environment. (77)Se NMR was found to be a sensitive probe to such changes and has an isotropic chemical shift range of 272 ± 30 ppm for this energetically favorable conformation range. The energy-minimized structures exhibited calculated isotropic shifts that lay within 3-9% of those reported in previous solution NMR studies. The experimental solid-state NMR isotropic chemical shift is near the lower bound of this calculated range for these readily accessible conformations. These results suggest that the dihedral information may be deduced for a protein with appropriate structural models. These first-time experimental and theoretical results will facilitate future NMR studies of selenium-containing compounds and proteins.
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Affiliation(s)
- Jochem Struppe
- Bruker BioSpin Corporation, 15 Fortune Drive, Manning Park, Billerica, Massachusetts 01821, United States
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39
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Guo C, Hou G, Lu X, O’Hare B, Struppe J, Polenova T. Fast magic angle spinning NMR with heteronucleus detection for resonance assignments and structural characterization of fully protonated proteins. J Biomol NMR 2014; 60:219-229. [PMID: 25381566 PMCID: PMC4282927 DOI: 10.1007/s10858-014-9870-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 10/25/2014] [Indexed: 06/04/2023]
Abstract
Heteronucleus-detected dipolar based correlation spectroscopy is established for assignments of ¹H, ¹³C, and ¹⁵N resonances and structural analysis in fully protonated proteins. We demonstrate that ¹³C detected 3D experiments are highly efficient and permit assignments of the majority of backbone resonances, as shown in an 89-residue dynein light chain 8, LC8 protein. With these experiments, we have resolved many ambiguities that were persistent in our previous studies using moderate MAS frequencies and lacking the ¹H dimension. The availability of ¹H isotropic chemical shifts measured with the heteronucleus-detected fast-MAS experiments presented here is essential for the accurate determination of the ¹H CSA tensors, which provide very useful structural probe. Finally, our results indicate that ¹³C detection in fast-MAS HETCOR experiments may be advantageous compared with ¹H detection as it yields datasets of significantly higher resolution in the ¹³C dimension than the ¹H detected HETCOR versions.
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Affiliation(s)
- Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Bernie O’Hare
- Bruker Biospin Corp., Billerica, MA 01821, United States
| | - Jochem Struppe
- Bruker Biospin Corp., Billerica, MA 01821, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
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Struppe J, Noack F, Klose G. NMR Study of Collective Motions and Bending Rigidity in Multilamellar System of Lipid and Surfactant Bilayers. ACTA ACUST UNITED AC 2014. [DOI: 10.1515/zna-1997-1001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The frequency dependence of the longitudinal proton spin relaxation time T1 was measured by field-cycling and standard NMR techniques at different temperatures in the liquid crystalline lamellar phases of bilayer systems, composed of lipids, nonionic surfactants, and lipid-surfactant mixtures. We show by our data analysis, comparing various motional models such as layer undulations (LUs) and relaxation by translational diffusion mediated reorientations (TR), that collective layer undulations with their typical T1~ν behaviour determine the low frequency T1 dispersion in both unoriented and glass plate-oriented bilayer systems. The angular dependence of the T1 dispersion for the oriented bilayer system supports these findings and provides a more critical analysis of the two dimensional self-diffusion than in unoriented samples. The evaluated fitting parameters of the LU model allows, together with the measured second moment of the proton NMR signal for the lipid, calculation of the bending rigidity ϰc for these bilayers at different levels of hydration. The obtained values of ϰc turn out to be too large compared with the literature. However, using recent LU models (B. Halle) which include the obvious couplings between neighbouring bilayers at low Larmor frequencies, the corrected ϰc of the fully hydrated membrane systems are comparable to those obtained from the standard videooptical experiments. Therefore proton spin relaxation measure-ments at low Larmor frequencies with the field-cycling technique are a suitable means to determine the bending rigidity ϰc of model membrane systems at low hydrations and of systems containing surfactants.
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Affiliation(s)
- J. Struppe
- Universität Stuttgart, Physikalisches Institut Teil 4, Pfaffenwaldring 57, D-70550 Stuttgart
| | - F. Noack
- Universität Stuttgart, Physikalisches Institut Teil 4, Pfaffenwaldring 57, D-70550 Stuttgart
| | - G. Klose
- Universität Leipzig, Physikalisches Institut Abteilung BIM, Linnestr. 5, D-04103 Leipzig
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Good DB, Wang S, Ward ME, Struppe J, Brown LS, Lewandowski JR, Ladizhansky V. Conformational Dynamics of a Seven Transmembrane Helical Protein Anabaena Sensory Rhodopsin Probed by Solid-State NMR. J Am Chem Soc 2014; 136:2833-42. [DOI: 10.1021/ja411633w] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | | | | | - Jochem Struppe
- Bruker Biospin Ltd., Billerica, Massachusetts 01821, United States
| | | | - Józef R. Lewandowski
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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42
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Lam L, Soong R, Sutrisno A, de Visser R, Simpson MJ, Wheeler HL, Campbell M, Maas WE, Fey M, Gorissen A, Hutchins H, Andrew B, Struppe J, Krishnamurthy S, Kumar R, Monette M, Stronks HJ, Hume A, Simpson AJ. Comprehensive multiphase NMR spectroscopy of intact ¹³C-labeled seeds. J Agric Food Chem 2014; 62:107-115. [PMID: 24354469 DOI: 10.1021/jf4045638] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Seeds are complex entities composed of liquids, gels, and solids. NMR spectroscopy is a powerful tool for studying molecular structure but has evolved into two fields, solution and solid state. Comprehensive multiphase (CMP) NMR spectroscopy is capable of liquid-, gel-, and solid-state experiments for studying intact samples where all organic components are studied and differentiated in situ. Herein, intact (13)C-labeled seeds were studied by a variety of 1D/2D (1)H/(13)C experiments. In the mobile phase, an assortment of metabolites in a single (13)C-labeled wheat seed were identified; the gel phase was dominated by triacylglycerides; the semisolid phase was composed largely of carbohydrate biopolymers, and the solid phase was greatly influenced by starchy endosperm signals. Subsequently, the seeds were compared and relative similarities and differences between seed types discussed. This study represents the first application of CMP-NMR to food chemistry and demonstrates its general utility and feasibility for studying intact heterogeneous samples.
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Affiliation(s)
- Leayen Lam
- Department of Physical and Environment Sciences, University of Toronto Scarborough , 1265 Military Trail, Toronto, Ontario, Canada M1C 1A4
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43
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Longstaffe JG, Courtier-Murias D, Soong R, Simpson MJ, Maas WE, Fey M, Hutchins H, Krishnamurthy S, Struppe J, Alaee M, Kumar R, Monette M, Stronks HJ, Simpson AJ. In-situ molecular-level elucidation of organofluorine binding sites in a whole peat soil. Environ Sci Technol 2012; 46:10508-10513. [PMID: 22946434 DOI: 10.1021/es3026769] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The chemical nature of xenobiotic binding sites in soils is of vital importance to environmental biogeochemistry. Interactions between xenobiotics and the naturally occurring organic constituents of soils are strongly correlated to environmental persistence, bioaccessibility, and ecotoxicity. Nevertheless, because of the complex structural and chemical heterogeneity of soils, studies of these interactions are most commonly performed indirectly, using correlative methods, fractionation, or chemical modification. Here we identify the organic components of an unmodified peat soil where some organofluorine xenobiotic compounds interact using direct molecular-level methods. Using (19)F→(1)H cross-polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, the (19)F nuclei of organofluorine compounds are used to induce observable transverse magnetization in the (1)H nuclei of organic components of the soil with which they interact after sorption. The observed (19)F→(1)H CP-MAS spectra and dynamics are compared to those produced using model soil organic compounds, lignin and albumin. It is found that lignin-like components can account for the interactions observed in this soil for heptafluoronaphthol (HFNap) while protein structures can account for the interactions observed for perfluorooctanoic acid (PFOA). This study employs novel comprehensive multi-phase (CMP) NMR technology that permits the application of solution-, gel-, and solid-state NMR experiments on intact soil samples in their swollen state.
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Affiliation(s)
- James G Longstaffe
- Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, Ontario, Canada, M1C 1A4
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Courtier-Murias D, Farooq H, Masoom H, Botana A, Soong R, Longstaffe JG, Simpson MJ, Maas WE, Fey M, Andrew B, Struppe J, Hutchins H, Krishnamurthy S, Kumar R, Monette M, Stronks HJ, Hume A, Simpson AJ. Comprehensive multiphase NMR spectroscopy: basic experimental approaches to differentiate phases in heterogeneous samples. J Magn Reson 2012; 217:61-76. [PMID: 22425441 DOI: 10.1016/j.jmr.2012.02.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 02/15/2012] [Indexed: 05/16/2023]
Abstract
Heterogeneous samples, such as soils, sediments, plants, tissues, foods and organisms, often contain liquid-, gel- and solid-like phases and it is the synergism between these phases that determine their environmental and biological properties. Studying each phase separately can perturb the sample, removing important structural information such as chemical interactions at the gel-solid interface, kinetics across boundaries and conformation in the natural state. In order to overcome these limitations a Comprehensive Multiphase-Nuclear Magnetic Resonance (CMP-NMR) probe has been developed, and is introduced here, that permits all bonds in all phases to be studied and differentiated in whole unaltered natural samples. The CMP-NMR probe is built with high power circuitry, Magic Angle Spinning (MAS), is fitted with a lock channel, pulse field gradients, and is fully susceptibility matched. Consequently, this novel NMR probe has to cover all HR-MAS aspects without compromising power handling to permit the full range of solution-, gel- and solid-state experiments available today. Using this technology, both structures and interactions can be studied independently in each phase as well as transfer/interactions between phases within a heterogeneous sample. This paper outlines some basic experimental approaches using a model heterogeneous multiphase sample containing liquid-, gel- and solid-like components in water, yielding separate (1)H and (13)C spectra for the different phases. In addition, (19)F performance is also addressed. To illustrate the capability of (19)F NMR soil samples, containing two different contaminants, are used, demonstrating a preliminary, but real-world application of this technology. This novel NMR approach possesses a great potential for the in situ study of natural samples in their native state.
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Affiliation(s)
- Denis Courtier-Murias
- Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, ON, Canada M1C 1A4
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45
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Tiburu EK, Tyukhtenko S, Zhou H, Janero DR, Struppe J, Makriyannis A. Human cannabinoid 1 GPCR C-terminal domain interacts with bilayer phospholipids to modulate the structure of its membrane environment. AAPS J 2011; 13:92-8. [PMID: 21234731 DOI: 10.1208/s12248-010-9244-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 11/21/2010] [Indexed: 02/08/2023]
Abstract
G protein-coupled receptors (GPCRs) play critical physiological and therapeutic roles. The human cannabinoid 1 GPCR (hCB1) is a prime pharmacotherapeutic target for addiction and cardiometabolic disease. Our prior biophysical studies on the structural biology of a synthetic peptide representing the functionally significant hCB1 transmembrane helix 7 (TMH7) and its cytoplasmic extension, helix 8 (H8), [hCB1(TMH7/H8)] demonstrated that the helices are oriented virtually perpendicular to each other in membrane-mimetic environments. We identified several hCB1(TMH7/H8) structure-function determinants, including multiple electrostatic amino-acid interactions and a proline kink involving the highly conserved NPXXY motif. In phospholipid bicelles, TMH7 structure, orientation, and topology relative to H8 are dynamically modulated by the surrounding membrane phospholipid bilayer. These data provide a contextual basis for the present solid-state NMR study to investigate whether intermolecular interactions between hCB1(TMH7/H8) and its phospholipid environment may affect membrane-bilayer structure. For this purpose, we measured (1)H-(13)C heteronuclear dipolar couplings for the choline, glycerol, and acyl-chain regions of dimyristoylphosphocholine in a magnetically aligned hCB1(TMH7/H8) bicelle sample. The results identify discrete regional interactions between hCB1(TMH7/H8) and membrane lipid molecules that increase phospholipid motion and decrease phospholipid order, indicating that the peptide's partial traversal of the bilayer alters membrane structure. These data offer new insight into hCB1(TMH7/H8) properties and support the concept that the membrane bilayer itself may serve as a mechanochemical mediator of hCB1/GPCR signal transduction. Since interaction with its membrane environment has been implicated in hCB1 function and its modulation by small-molecule therapeutics, our work should help inform hCB1 pharmacology and the design of hCB1-targeted drugs.
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Affiliation(s)
- Elvis K Tiburu
- Center for Drug Discovery and Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 116 Mugar Hall, Boston, Massachusetts 02115-5000, United States of America
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46
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Abstract
We demonstrate the successful application of (13)C-(13)C proton assisted recoupling (PAR) on [U-(13)C,(15)N] N-f-MLF-OH and [U-(13)C,(15)N] protein GB1 at high magic angle spinning (MAS) frequencies (omega(r)/2pi = 65 kHz). Specifically, by combining PAR mixing with low power heteronuclear decoupling (omega(1H)/2pi approximately 16 kHz) and high spinning frequencies, we obtain high resolution 2D spectra displaying long-range (13)C-(13)C contacts from which distance estimates can be extracted. These experiments therefore demonstrate the possibility of performing high resolution structural studies in the limit of high spinning frequency and low power (1)H decoupling, a regime which optimizes the resolution of protein samples and preserves their integrity.
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Affiliation(s)
- Józef R. Lewandowski
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Gaël De Paëpe
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Matthew T. Eddy
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jochem Struppe
- Bruker BioSpin Corporation, Billerica, Massachusetts 01821
| | - Werner Maas
- Bruker BioSpin Corporation, Billerica, Massachusetts 01821
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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47
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Lee D, Struppe J, Elliott DW, Mueller LJ, Titman JJ. Sensitive absorptive refocused scalar correlation NMR spectroscopy in solids. Phys Chem Chem Phys 2009; 11:3547-53. [PMID: 19421560 DOI: 10.1039/b818867j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new two-dimensional NMR experiment is described which is suitable for obtaining magic angle spinning (MAS) scalar correlation spectra in solids. The new experiment has several advantages, including increased cross peak intensities, coupled with good suppression of the diagonal. Its utility is demonstrated via assignments of the carbon-13 MAS spectra of progesterone at natural abundance and of the polymer phase of 50%-U-13C-CsC60.
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Affiliation(s)
- Daniel Lee
- School of Chemistry, University of Nottingham, University Park, Nottingham, UK NG7 2RD
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48
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Andronesi OC, Mintzopoulos D, Struppe J, Black PM, Tzika AA. Solid-state NMR adiabatic TOBSY sequences provide enhanced sensitivity for multidimensional high-resolution magic-angle-spinning 1H MR spectroscopy. J Magn Reson 2008; 193:251-258. [PMID: 18556227 DOI: 10.1016/j.jmr.2008.05.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 05/12/2008] [Accepted: 05/12/2008] [Indexed: 05/26/2023]
Abstract
We propose a solid-state NMR method that maximizes the advantages of high-resolution magic-angle-spinning (HRMAS) applied to intact biopsies when compared to more conventional liquid-state NMR approaches. Theoretical treatment, numerical simulations and experimental results on intact human brain biopsies are presented. Experimentally, it is proven that an optimized adiabatic TOBSY (TOtal through Bond correlation SpectroscopY) solid-state NMR pulse sequence for two-dimensional 1H-1H homonuclear scalar-coupling longitudinal isotropic mixing provides a 20%-50% improvement in signal-to-noise ratio relative to its liquid-state analogue TOCSY (TOtal Correlation SpectroscopY). For this purpose we have refined the C9(15)1 symmetry-based 13C TOBSY pulse sequence for 1H MRS use and compared it to MLEV-16 TOCSY sequence. Both sequences were rotor-synchronized and implemented using WURST-8 adiabatic inversion pulses. As discussed theoretically and shown in simulations, the improved magnetization-transfer comes from actively removing residual dipolar couplings from the average Hamiltonian. Importantly, the solid-state NMR techniques are tailored to perform measurements at low temperatures where sample degradation is reduced. This is the first demonstration of such a concept for HRMAS metabolic profiling of disease processes, including cancer, from biopsies requiring reduced sample degradation for further genomic analysis.
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Affiliation(s)
- Ovidiu C Andronesi
- NMR Surgical Laboratory, Department of Surgery, Massachusetts General Hospital and Shriner's Burn Institute, Harvard Medical School, 51 Blossom Street, Room 261, Boston, MA 02114, USA.
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49
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Xu J, Struppe J, Ramamoorthy A. Two-dimensional homonuclear chemical shift correlation established by the cross-relaxation driven spin diffusion in solids. J Chem Phys 2008; 128:052308. [PMID: 18266425 DOI: 10.1063/1.2826323] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A new type of spin diffusion, cross-relaxation driven spin diffusion (CRDSD), is investigated using (15)N NMR on a N-acetyl-L-valyl-L-leucine (NAVL) single crystal under stationary condition. A two-dimensional (2D) pulse sequence that correlates the chemical shifts of (15)N nuclei, with a radio-frequency spin lock on the (15)N channel during the mixing time, is used to observe CRDSD. Experimental results obtained using CRDSD, rf-driven spin diffusion, and proton driven spin diffusion approaches on the NAVL single crystal are compared. Our experimental results suggest that the (15)N spin diffusion rate can be enhanced by about 1000 times using CRDSD than by the normal proton driven spin diffusion. Interestingly, the required spin-locking rf field strength for CRDSD is much lower than that used for the rf-driven spin diffusion experiments. The cross-peak patterns observed in 2D (15)N-(15)N correlation spectra using CRDSD and RFDSD are very different as they arise from different spin-spin interactions. A detailed theory describing CRDSD and RFDSD processes is also presented using a thermodynamic model. The speedy spin diffusion process rendered by the CRDSD approach will be useful to assign resonances from a uniformly (15)N or (13)C labeled proteins and peptides, particularly in aligned samples.
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Affiliation(s)
- Jiadi Xu
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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50
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McNeill SA, Gor'kov PL, Struppe J, Brey WW, Long JR. Optimizing ssNMR experiments for dilute proteins in heterogeneous mixtures at high magnetic fields. Magn Reson Chem 2007; 45 Suppl 1:S209-20. [PMID: 18157844 DOI: 10.1002/mrc.2146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Solid-state NMR spectroscopy at high magnetic fields is proving to be an effective technique in structural biology, particularly for proteins which are not amenable to traditional X-ray and solution NMR approaches. Several parameters can be selected to provide optimal sensitivity, improve sample stability, and ensure biological relevance for ssNMR measurements on protein samples. These include selection of sample conditions, NMR probe design, and design of pulse experiments. Here, we demonstrate and evaluate several engineering and experimental approaches for pursuing measurements on dilute proteins in heterogeneous mixtures.
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Affiliation(s)
- Seth A McNeill
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
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