1
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Emsley L. Spiers Memorial Lecture: NMR crystallography. Faraday Discuss 2025; 255:9-45. [PMID: 39405130 PMCID: PMC11477664 DOI: 10.1039/d4fd00151f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 09/03/2024] [Indexed: 10/19/2024]
Abstract
Chemical function is directly related to the spatial arrangement of atoms. Consequently, the determination of atomic-level three-dimensional structures has transformed molecular and materials science over the past 60 years. In this context, solid-state NMR has emerged to become the method of choice for atomic-level characterization of complex materials in powder form. In the following we present an overview of current methods for chemical shift driven NMR crystallography, illustrated with applications to complex materials.
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Affiliation(s)
- Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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2
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Wei R, Rao Y, Venkatesh A, Emsley L. Solid Effect Dynamic Nuclear Polarization Enhancement of >500 at 9.4 T. J Phys Chem Lett 2024; 15:12408-12415. [PMID: 39656937 DOI: 10.1021/acs.jpclett.4c03147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Efficient polarizing agents for dynamic nuclear polarization (DNP) enhanced magic angle spinning (MAS) NMR spectroscopy are of high current interest due to the potential to significantly boost NMR sensitivity. While most efforts have centered on cross-effect (CE) or Overhauser effect (OE) mechanisms, yielding enhancement factors up to ∼300 at 9.4 T, radicals yielding solid effect (SE) DNP have seen less development. Here we model the comparative performance of OE and SE mechanisms and then measure 1H enhancement factors up to 500 from 1,3-bisdiphenylene-2-phenylallyl (BDPA) in an ortho-terphenyl (OTP) matrix at 9.4 T, 100 K, achieved via increased microwave power across the sample volume. The measured SE and OE performances are in good agreement with the predictions. We note that both the experimental and theoretical analyses indicate that SE DNP remains saturation limited, particularly at elevated temperatures, and we envisage that further improvements in microwave power will further increase SE DNP enhancement factors.
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Affiliation(s)
- Ran Wei
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Yu Rao
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Amrit Venkatesh
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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3
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Ladizhansky V, Palani RS, Mardini M, Griffin RG. Dipolar Recoupling in Rotating Solids. Chem Rev 2024; 124:12844-12917. [PMID: 39504237 DOI: 10.1021/acs.chemrev.4c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
Abstract
Magic angle spinning (MAS) nuclear magnetic resonance (NMR) has evolved significantly over the past three decades and established itself as a vital tool for the structural analysis of biological macromolecules and materials. This review delves into the development and application of dipolar recoupling techniques in MAS NMR, which are crucial for obtaining detailed structural and dynamic information. We discuss a variety of homonuclear and heteronuclear recoupling methods which are essential for measuring spatial restraints and explain in detail the spin dynamics that these sequences generate. We also explore recent developments in high spinning frequency MAS, proton detection, and dynamic nuclear polarization, underscoring their importance in advancing biomolecular NMR. Our aim is to provide a comprehensive account of contemporary dipolar recoupling methods, their principles, and their application to structural biology and materials, highlighting significant contributions to the field and emerging techniques that enhance resolution and sensitivity in MAS NMR spectroscopy.
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Affiliation(s)
- Vladimir Ladizhansky
- Biophysics Interdepartmental Group and Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ravi Shankar Palani
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael Mardini
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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Dumarieh R, Lagasca D, Krishna S, Kragelj J, Xiao Y, Frederick KK. Structural context modulates the conformational ensemble of the intrinsically disordered amino terminus of α-synuclein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.31.621304. [PMID: 39553926 PMCID: PMC11565972 DOI: 10.1101/2024.10.31.621304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Regions of intrinsic disorder play crucial roles in biological systems, yet they often elude characterization by conventional biophysical techniques. To capture conformational distributions across different timescales, we employed a freezing approach coupled with solid-state NMR analysis. Using segmentally isotopically labeled α-synuclein (α-syn), we investigated the conformational preferences of the six alanines, three glycines, and a single site (L8) in the disordered amino terminus under three distinct conditions: in 8 M urea, as a frozen monomer in buffer, and within the disordered regions flanking the amyloid core. The experimental spectra varied significantly among these conditions and deviated from those of a statistical coil. In 8 M urea, monomeric α-syn exhibited the most restricted conformational sampling, rarely accessing chemical shifts characteristic of α-helices or β-strands. In buffer, monomeric α-syn showed broader conformational sampling, favoring α-helical conformations and, to a lesser extent, random coil states. Notably, amino acids in the disordered regions flanking the amyloid core demonstrated the most extensive conformational sampling, with broad peaks encompassing the entire range of possible chemical shifts and a marked preference for highly extended β-strand conformations. Collectively, this work demonstrates that intrinsically disordered regions exhibit distinct conformational preferences, which are influenced not only by the chemical environment but also by the conformations of adjacent protein sequences. The differences in the conformational ensembles of the disordered amino terminus may explain why the monomer and the amyloid form of α-syn interact with different biomolecules inside cells.
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Affiliation(s)
- Rania Dumarieh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Dominique Lagasca
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Sakshi Krishna
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Jaka Kragelj
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Kendra K. Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
- Center for Alzheimer’s and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX 75390
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5
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Ansari S, Lagasca D, Dumarieh R, Xiao Y, Krishna S, Li Y, Frederick KK. In cell NMR reveals cells selectively amplify and structurally remodel amyloid fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612142. [PMID: 39314304 PMCID: PMC11419106 DOI: 10.1101/2024.09.09.612142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Amyloid forms of α-synuclein adopt different conformations depending on environmental conditions. Advances in structural biology have accelerated fibril characterization. However, it remains unclear which conformations predominate in biological settings because current methods typically not only require isolating fibrils from their native environments, but they also do not provide insight about flexible regions. To address this, we characterized α-syn amyloid seeds and used sensitivity enhanced nuclear magnetic resonance to investigate the amyloid fibrils resulting from seeded amyloid propagation in different settings. We found that the amyloid fold and conformational preferences of flexible regions are faithfully propagated in vitro and in cellular lysates. However, seeded propagation of amyloids inside cells led to the minority conformation in the seeding population becoming predominant and more ordered, and altered the conformational preferences of flexible regions. The examination of the entire ensemble of protein conformations in biological settings that is made possible with this approach may advance our understanding of protein misfolding disorders and facilitate structure-based drug design efforts.
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Affiliation(s)
- Shoyab Ansari
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Dominique Lagasca
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Rania Dumarieh
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Yiling Xiao
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Sakshi Krishna
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Yang Li
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
| | - Kendra K. Frederick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390-8816
- Center for Alzheimer’s and Neurodegenerative Disease, UT Southwestern Medical Center, Dallas, TX 75390
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6
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Scott FJ, Dubroca T, Schurko RW, Hill S, Long JR, Mentink-Vigier F. Characterization of dielectric properties and their impact on MAS-DNP NMR applications. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 365:107742. [PMID: 39116460 DOI: 10.1016/j.jmr.2024.107742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/17/2024] [Accepted: 07/13/2024] [Indexed: 08/10/2024]
Abstract
The dielectric properties of materials play a crucial role in the propagation and absorption of microwave beams employed in Magic Angle Spinning - Dynamic Nuclear Polarization (MAS-DNP) NMR experiments. Despite ongoing optimization efforts in sample preparation, routine MAS-DNP NMR applications often fall short of theoretical sensitivity limits. Offering a different perspective, we report the refractive indices and extinction coefficients of diverse materials used in MAS-DNP NMR experiments, spanning a frequency range from 70 to 960 GHz. Knowledge of their dielectric properties enables the accurate simulation of electron nutation frequencies, thereby guiding the design of more efficient hardware and sample preparation of biological or material samples. This is illustrated experimentally for four different rotor materials (sapphire, yttria-stabilized zirconia (YSZ), aluminum nitride (AlN), and SiAlON ceramics) used for DNP at 395 GHz/1H 600 MHz. Finally, electromagnetic simulations and state-of-the-art MAS-DNP numerical simulations provide a rational explanation for the observed magnetic field dependence of the enhancement when using nitroxide biradicals, offering insights that will improve MAS-DNP NMR at high magnetic fields.
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Affiliation(s)
- Faith J Scott
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Thierry Dubroca
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Robert W Schurko
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Stephen Hill
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Joanna R Long
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA; Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA.
| | - Frédéric Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, 1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA.
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7
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Golota NC, Michael B, Saliba EP, Linse S, Griffin RG. Structural characterization of E22G Aβ 1-42 fibrils via1H detected MAS NMR. Phys Chem Chem Phys 2024; 26:14664-14674. [PMID: 38715538 PMCID: PMC11110645 DOI: 10.1039/d4cp00553h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Amyloid fibrils have been implicated in the pathogenesis of several neurodegenerative diseases, the most prevalent example being Alzheimer's disease (AD). Despite the prevalence of AD, relatively little is known about the structure of the associated amyloid fibrils. This has motivated our studies of fibril structures, extended here to the familial Arctic mutant of Aβ1-42, E22G-Aβ1-42. We found E22G-AβM0,1-42 is toxic to Escherichia coli, thus we expressed E22G-Aβ1-42 fused to the self-cleavable tag NPro in the form of its EDDIE mutant. Since the high surface activity of E22G-Aβ1-42 makes it difficult to obtain more than sparse quantities of fibrils, we employed 1H detected magic angle spinning (MAS) nuclear magnetic resonance (NMR) experiments to characterize the protein. The 1H detected 13C-13C methods were first validated by application to fully protonated amyloidogenic nanocrystals of GNNQQNY, and then applied to fibrils of the Arctic mutant of Aβ, E22G-Aβ1-42. The MAS NMR spectra indicate that the biosynthetic samples of E22G-Aβ1-42 fibrils comprise a single conformation with 13C chemical shifts extracted from hCH, hNH, and hCCH spectra that are very similar to those of wild type Aβ1-42 fibrils. These results suggest that E22G-Aβ1-42 fibrils have a structure similar to that of wild type Aβ1-42.
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Affiliation(s)
- Natalie C Golota
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Brian Michael
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Edward P Saliba
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sara Linse
- Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, SE 22100, Sweden
| | - Robert G Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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8
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Pujahari SR, Purusottam RN, Mali PS, Sarkar S, Khaneja N, Vajpai N, Kumar A. Exploring the Higher Order Structure and Conformational Transitions in Insulin Microcrystalline Biopharmaceuticals by Proton-Detected Solid-State Nuclear Magnetic Resonance at Natural Abundance. Anal Chem 2024; 96:4756-4763. [PMID: 38326990 DOI: 10.1021/acs.analchem.3c04040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The integrity of a higher order structure (HOS) is an essential requirement to ensure the efficacy, stability, and safety of protein therapeutics. Solution-state nuclear magnetic resonance (NMR) occupies a unique niche as one of the most promising methods to access atomic-level structural information on soluble biopharmaceutical formulations. Another major class of drugs is poorly soluble, such as microcrystalline suspensions, which poses significant challenges for the characterization of the active ingredient in its native state. Here, we have demonstrated a solid-state NMR method for HOS characterization of biopharmaceutical suspensions employing a selective excitation scheme under fast magic angle spinning (MAS). The applicability of the method is shown on commercial insulin suspensions at natural isotopic abundance. Selective excitation aided with proton detection and non-uniform sampling (NUS) provides improved sensitivity and resolution. The enhanced resolution enabled us to demonstrate the first experimental evidence of a phenol-escaping pathway in insulin, leading to conformational transitions to different hexameric states. This approach has the potential to serve as a valuable means for meticulously examining microcrystalline biopharmaceutical suspensions, which was previously not attainable in their native formulation states and can be seamlessly extended to other classes of biopharmaceuticals such as mAbs and other microcrystalline proteins.
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Affiliation(s)
- Soumya Ranjan Pujahari
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai Mumbai 400076, India
| | - Rudra N Purusottam
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai Mumbai 400076, India
| | - Pramod S Mali
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai Mumbai 400076, India
| | - Sambeda Sarkar
- System and Control Engineering, Indian Institute of Technology, Bombay, Powai Mumbai 400076, India
| | - Navin Khaneja
- System and Control Engineering, Indian Institute of Technology, Bombay, Powai Mumbai 400076, India
| | - Navratna Vajpai
- Biocon Biologics Limited, Biocon SEZ, Plot No. 2 & 3, Phase IV-B.I.A, Bommasandra-Jigani Link Road, Bangalore 560099, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai Mumbai 400076, India
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9
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Venkatesh A, Casano G, Wei R, Rao Y, Lingua H, Karoui H, Yulikov M, Ouari O, Emsley L. Rational Design of Dinitroxide Polarizing Agents for Dynamic Nuclear Polarization to Enhance Overall NMR Sensitivity. Angew Chem Int Ed Engl 2024; 63:e202317337. [PMID: 38193258 DOI: 10.1002/anie.202317337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/10/2024]
Abstract
We evaluate the overall sensitivity gains provided by a series of eighteen nitroxide biradicals for dynamic nuclear polarization (DNP) solid-state NMR at 9.4 T and 100 K, including eight new biradicals. We find that in the best performing group the factors contributing to the overall sensitivity gains, namely the DNP enhancement, the build-up time, and the contribution factor, often compete with each other leading to very similar overall sensitivity across a range of biradicals. NaphPol and HydroPol are found to provide the best overall sensitivity factors, in organic and aqueous solvents respectively. One of the new biradicals, AMUPolCbm, provides high sensitivity for all three solvent formulations measured here, and can be considered to be a "universal" polarizing agent.
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Affiliation(s)
- Amrit Venkatesh
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
- Current address: National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Gilles Casano
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire UMR 7273, 13013, Marseille, France
| | - Ran Wei
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Yu Rao
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Hugo Lingua
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire UMR 7273, 13013, Marseille, France
| | - Hakim Karoui
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire UMR 7273, 13013, Marseille, France
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, Department of Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Olivier Ouari
- Aix Marseille Univ, CNRS, Institut de Chimie Radicalaire UMR 7273, 13013, Marseille, France
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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10
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Kumar R, Le Marchand T, Adam L, Bobrovs R, Chen G, Fridmanis J, Kronqvist N, Biverstål H, Jaudzems K, Johansson J, Pintacuda G, Abelein A. Identification of potential aggregation hotspots on Aβ42 fibrils blocked by the anti-amyloid chaperone-like BRICHOS domain. Nat Commun 2024; 15:965. [PMID: 38302480 PMCID: PMC10834949 DOI: 10.1038/s41467-024-45192-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024] Open
Abstract
Protein misfolding can generate toxic intermediates, which underlies several devastating diseases, such as Alzheimer's disease (AD). The surface of AD-associated amyloid-β peptide (Aβ) fibrils has been suggested to act as a catalyzer for self-replication and generation of potentially toxic species. Specifically tailored molecular chaperones, such as the BRICHOS protein domain, were shown to bind to amyloid fibrils and break this autocatalytic cycle. Here, we identify a site on the Aβ42 fibril surface, consisting of three C-terminal β-strands and particularly the solvent-exposed β-strand stretching from residues 26-28, which is efficiently sensed by a designed variant of Bri2 BRICHOS. Remarkably, while only a low amount of BRICHOS binds to Aβ42 fibrils, fibril-catalyzed nucleation processes are effectively prevented, suggesting that the identified site acts as a catalytic aggregation hotspot, which can specifically be blocked by BRICHOS. Hence, these findings provide an understanding how toxic nucleation events can be targeted by molecular chaperones.
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Affiliation(s)
- Rakesh Kumar
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Tanguy Le Marchand
- Université de Lyon, Centre de Resonance Magnétique Nucléaire (CRMN) à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1), 69100, Villeurbanne, France
| | - Laurène Adam
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Raitis Bobrovs
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Jēkabs Fridmanis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Nina Kronqvist
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Henrik Biverstål
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Guido Pintacuda
- Université de Lyon, Centre de Resonance Magnétique Nucléaire (CRMN) à Très Hauts Champs de Lyon (UMR 5082 - CNRS, ENS Lyon, UCB Lyon 1), 69100, Villeurbanne, France
| | - Axel Abelein
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83, Huddinge, Sweden.
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11
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Quan Y, Ouyang Y, Mardini M, Palani RS, Banks D, Kempf J, Wenckebach WT, Griffin RG. Resonant Mixing Dynamic Nuclear Polarization. J Phys Chem Lett 2023; 14:7007-7013. [PMID: 37523253 DOI: 10.1021/acs.jpclett.3c01869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
We propose a mechanism for dynamic nuclear polarization that is different from the well-known Overhauser effect, solid effect, cross effect, and thermal mixing processes. We term it Resonant Mixing (RM), and we show that it arises from the evolution of the density matrix for a simple electron-nucleus coupled spin pair subject to weak microwave irradiation, the same interactions as the solid effect. However, the SE is optimal when the microwave field is off-resonance, whereas RM is optimal when the microwave field is on-resonance and involves the mixing of states by the microwave field together with the electron-nuclear coupling. Finally, we argue that this mechanism is responsible for the observed dispersive-shaped DNP field profile for trityl samples near the electron paramagnetic resonance center.
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Affiliation(s)
- Yifan Quan
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yifu Ouyang
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael Mardini
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ravi Shankar Palani
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel Banks
- Bruker Biospin, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - James Kempf
- Bruker Biospin, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - W Tom Wenckebach
- Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- National High Magnetic Field Laboratory, University of Florida, Gainesville, Florida 32310, United States
| | - Robert G Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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12
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Kent JE, Ackermann BE, Debelouchina GT, Marassi FM. Dynamic Nuclear Polarization Illuminates Key Protein-Lipid Interactions in the Native Bacterial Cell Envelope. Biochemistry 2023; 62:2252-2256. [PMID: 37459255 PMCID: PMC11019665 DOI: 10.1021/acs.biochem.3c00262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Elucidating the structure and interactions of proteins in native environments is a fundamental goal of structural biology. Nuclear magnetic resonance (NMR) spectroscopy is well suited for this task but often suffers from low sensitivity, especially in complex biological settings. Here, we use a sensitivity-enhancement technique called dynamic nuclear polarization (DNP) to overcome this challenge. We apply DNP to capture the membrane interactions of the outer membrane protein Ail, a key component of the host invasion pathway of Yersinia pestis. We show that the DNP-enhanced NMR spectra of Ail in native bacterial cell envelopes are well resolved and enriched in correlations that are invisible in conventional solid-state NMR experiments. Furthermore, we demonstrate the ability of DNP to capture elusive interactions between the protein and the surrounding lipopolysaccharide layer. Our results support a model where the extracellular loop arginine residues remodel the membrane environment, a process that is crucial for host invasion and pathogenesis.
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Affiliation(s)
- James E Kent
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Bryce E Ackermann
- Department Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Galia T Debelouchina
- Department Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesca M Marassi
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226-3548, United States
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13
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Mardini M, Palani RS, Ahmad IM, Mandal S, Jawla SK, Bryerton E, Temkin RJ, Sigurdsson ST, Griffin RG. Frequency-swept dynamic nuclear polarization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107511. [PMID: 37385067 PMCID: PMC11549732 DOI: 10.1016/j.jmr.2023.107511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
Dynamic nuclear polarization (DNP) improves the sensitivity of NMR spectroscopy by the transfer of electron polarization to nuclei via irradiation of electron-nuclear transitions with microwaves at the appropriate frequency. For fields > 5 T and using g ∼ 2 electrons as polarizing agents, this requires the availability of microwave sources operating at >140 GHz. Therefore, microwave sources for DNP have generally been continuous-wave (CW) gyrotrons, and more recently solid state, oscillators operating at a fixed frequency and power. This constraint has limited the DNP mechanisms which can be exploited, and stymied the development of new time domain mechanisms. We report here the incorporation of a microwave source enabling facile modulation of frequency, amplitude, and phase at 9 T (250 GHz microwave frequency), and we have used the source for magic-angle spinning (MAS) NMR experiments. The experiments include investigations of CW DNP mechanisms, the advantage of frequency-chirped irradiation, and a demonstration of an Overhauser enhancement of ∼25 with a recently reported water-soluble BDPA radical, highlighting the potential for affordable and compact microwave sources to achieve significant enhancement in aqueous samples, including biological macromolecules. With the development of suitable microwave amplifiers, it should permit exploration of multiple new avenues involving time domain experiments.
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Affiliation(s)
- Michael Mardini
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Ravi Shankar Palani
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Iram M Ahmad
- Department of Chemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Sucharita Mandal
- Department of Chemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Sudheer K Jawla
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Eric Bryerton
- Virginia Diodes Corporation, Charlottesville, VA 22902, United States
| | - Richard J Temkin
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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14
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Golota NC, Fredin ZP, Banks DP, Preiss D, Bahri S, Patil P, Langford WK, Blackburn CL, Strand E, Michael B, Dastrup B, Nelson KA, Gershenfeld N, Griffin R. Diamond rotors. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 352:107475. [PMID: 37224586 PMCID: PMC10504678 DOI: 10.1016/j.jmr.2023.107475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/26/2023]
Abstract
The resolution of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra remains bounded by the spinning frequency, which is limited by the material strength of MAS rotors. Since diamond is capable of withstanding 1.5-2.5x greater MAS frequencies, compared to state-of-the art zirconia, we fabricated rotors from single crystal diamond. When combined with bearings optimized for spinning with helium gas, diamond rotors could achieve the highest MAS frequencies to date. Furthermore, the excellent microwave transmission properties and thermal conductivity of diamond could improve sensitivity enhancements in dynamic nuclear polarization (DNP) experiments. The fabrication protocol we report involves novel laser micromachining and produced rotors that presently spin at ωr/2π = 111.000 ± 0.004 kHz, with stable spinning up to 124 kHz, using N2 gas as the driving fluid. We present the first proton-detected 13C/15N MAS spectra recorded using diamond rotors, a critical step towards studying currently inaccessible ex-vivo protein samples with MAS NMR. Previously, the high aspect ratio of MAS rotors (∼10:1) precluded fabrication of MAS rotors from diamond.
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Affiliation(s)
- Natalie C Golota
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zachary P Fredin
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel P Banks
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David Preiss
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Salima Bahri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Prashant Patil
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William K Langford
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Camron L Blackburn
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Erik Strand
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian Michael
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Blake Dastrup
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Keith A Nelson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil Gershenfeld
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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15
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Kent JE, Ackermann BE, Debelouchina GT, Marassi FM. Dynamic nuclear polarization illuminates key protein-lipid interactions in the native bacterial cell envelope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541325. [PMID: 37292594 PMCID: PMC10245764 DOI: 10.1101/2023.05.18.541325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Elucidating the structure and interactions of proteins in native environments has become a fundamental goal of structural biology. Nuclear magnetic resonance (NMR) spectroscopy is well suited for this task but often suffers from low sensitivity, especially in complex biological settings. Here, we use a sensitivity-enhancement technique called dynamic nuclear polarization (DNP) to overcome this challenge. We apply DNP to capture the membrane interactions of the outer membrane protein Ail, a key component of the host invasion pathway of Yersinia pestis . We show that the DNP-enhanced NMR spectra of Ail in native bacterial cell envelopes are well resolved and enriched in correlations that are invisible in conventional solid-state NMR experiments. Furthermore, we demonstrate the ability of DNP to capture elusive interactions between the protein and the surrounding lipopolysaccharide layer. Our results support a model where the extracellular loop arginine residues remodel the membrane environment, a process that is crucial for host invasion and pathogenesis.
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16
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Kragelj J, Dumarieh R, Xiao Y, Frederick KK. Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins. Protein Sci 2023; 32:e4628. [PMID: 36930141 PMCID: PMC10108432 DOI: 10.1002/pro.4628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023]
Abstract
Protein regions which are intrinsically disordered, exist as an ensemble of rapidly interconverting structures. Cooling proteins to cryogenic temperatures for dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR studies suspends most of the motions, resulting in peaks that are broad but not featureless. To demonstrate that detailed conformational restraints can be retrieved from the peak shapes of frozen proteins alone, we developed and used a simulation framework to assign peak features to conformers in the ensemble. We validated our simulations by comparing them to spectra of α-synuclein acquired under different experimental conditions. Our assignments of peaks to discrete dihedral angle populations suggest that structural constraints are attainable under cryogenic conditions. The ability to infer ensemble populations from peak shapes has important implications for DNP MAS NMR studies of proteins with regions of disorder in living cells because chemical shifts are the most accessible measured parameter.
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Affiliation(s)
- Jaka Kragelj
- Department of BiophysicsUT Southwestern Medical CenterDallasTexas75390‐8816USA
- Present address:
National Institute of ChemistryHajdrihova 191001LjubljanaSlovenia
| | - Rania Dumarieh
- Department of BiophysicsUT Southwestern Medical CenterDallasTexas75390‐8816USA
| | - Yiling Xiao
- Department of BiophysicsUT Southwestern Medical CenterDallasTexas75390‐8816USA
| | - Kendra K. Frederick
- Department of BiophysicsUT Southwestern Medical CenterDallasTexas75390‐8816USA
- Center for Alzheimer's and Neurodegenerative DiseaseUT Southwestern Medical CenterDallasTexas75390USA
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17
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Halbritter T, Harrabi R, Paul S, van Tol J, Lee D, Hediger S, Sigurdsson ST, Mentink-Vigier F, De Paëpe G. PyrroTriPol: a semi-rigid trityl-nitroxide for high field dynamic nuclear polarization. Chem Sci 2023; 14:3852-3864. [PMID: 37035686 PMCID: PMC10074417 DOI: 10.1039/d2sc05880d] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
Magic angle spinning (MAS) dynamic nuclear polarization (DNP) has significantly broadened the scope of solid-state NMR to study biomolecular systems and materials. In recent years, the advent of very high field DNP combined with fast MAS has brought new challenges in the design of polarizing agents (PA) used to enhance nuclear spin polarization. Here, we present a trityl-nitroxide PA family based on a piperazine linker, named PyrroTriPol, for both aqueous and organic solutions. These new radicals have similar properties to that of TEMTriPol-I and can be readily synthesized, and purified in large quantities thereby ensuring widespread application. The family relies on a rigid bridge connecting the trityl and the nitroxide offering a better control of the electron spin-spin interactions thus providing improved performance across a broad range of magnetic fields and MAS frequencies while requiring reduced microwave power compared to bis-nitroxides. We demonstrate the efficiency of the PyrroTriPol family under a magnetic field of 9.4, 14.1 and 18.8 T with respect to TEMTriPol-I. In particular, the superiority of PyrroTriPol was demonstrated on γ-Al2O3 nanoparticles which enabled the acquisition of a high signal-to-noise surface-selective 27Al multiple-quantum MAS experiment at 18.8 T and 40 kHz MAS frequency.
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Affiliation(s)
- Thomas Halbritter
- Department of Chemistry, University of Iceland, Science Institute Dunhaga 3 107 Reykjavik Iceland
| | - Rania Harrabi
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Subhradip Paul
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Johan van Tol
- National High Magnetic Field Laboratory, Florida State University Tallahassee FL 32310 USA
| | - Daniel Lee
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
- Department of Chemical Engineering, University of Manchester Manchester M13 9PL UK
| | - Sabine Hediger
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Snorri Th Sigurdsson
- Department of Chemistry, University of Iceland, Science Institute Dunhaga 3 107 Reykjavik Iceland
| | | | - Gaël De Paëpe
- IRIG, MEM, Univ. Grenoble Alpes, CEA, CNRS 38000 Grenoble France
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18
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Sun X, Dyson HJ, Wright PE. Role of conformational dynamics in pathogenic protein aggregation. Curr Opin Chem Biol 2023; 73:102280. [PMID: 36878172 PMCID: PMC10033434 DOI: 10.1016/j.cbpa.2023.102280] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/13/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
The accumulation of pathogenic protein oligomers and aggregates is associated with several devastating amyloid diseases. As protein aggregation is a multi-step nucleation-dependent process beginning with unfolding or misfolding of the native state, it is important to understand how innate protein dynamics influence aggregation propensity. Kinetic intermediates composed of heterogeneous ensembles of oligomers are frequently formed on the aggregation pathway. Characterization of the structure and dynamics of these intermediates is critical to the understanding of amyloid diseases since oligomers appear to be the main cytotoxic agents. In this review, we highlight recent biophysical studies of the roles of protein dynamics in driving pathogenic protein aggregation, yielding new mechanistic insights that can be leveraged for design of aggregation inhibitors.
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Affiliation(s)
- Xun Sun
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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19
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Liu J, Wu XL, Zeng YT, Hu ZH, Lu JX. Solid-state NMR studies of amyloids. Structure 2023; 31:230-243. [PMID: 36750098 DOI: 10.1016/j.str.2023.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/10/2022] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Amyloids have special structural properties and are involved in many aspects of biological function. In particular, amyloids are the cause or hallmarks of a group of notorious and incurable neurodegenerative diseases. The extraordinary high molecular weight and aggregation states of amyloids have posed a challenge for researchers studying them. Solid-state NMR (SSNMR) has been extensively applied to study the structures and dynamics of amyloids for the past 20 or more years and brought us tremendous progress in understanding their structure and related diseases. These studies, at the same time, helped to push SSNMR technical developments in sensitivity and resolution. In this review, some interesting research studies and important technical developments are highlighted to give the reader an overview of the current state of this field.
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Affiliation(s)
- Jing Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xia-Lian Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu-Teng Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhi-Heng Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jun-Xia Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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20
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Palani RS, Mardini M, Delage-Laurin L, Banks D, Ouyang Y, Bryerton E, Kempf JG, Swager TM, Griffin RG. Amplified Overhauser DNP with Selective Deuteration: Attenuation of Double-Quantum Cross-Relaxation. J Phys Chem Lett 2023; 14:95-100. [PMID: 36573841 PMCID: PMC9903202 DOI: 10.1021/acs.jpclett.2c03087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
We recently used selective 2H labeling of BDPA to investigate the Overhauser Effect (OE) dynamic nuclear polarization (DNP) mechanism in insulating solids doped with 1,3-bis(diphenylene)-2-phenylallyl (BDPA), and established that the α and γ 1H spins on the fluorene rings are responsible for generating a zero quantum (ZQ) mediated positive bulk polarization. Here, we establish that the phenyl 1H spins relax via double-quantum (DQ) processes and therefore contribute negative enhancements which attenuate the OE-DNP. With measurements at different magnetic field strengths, we show that phenyl-d5-BDPA offers >50% improvement in OE-DNP enhancement compared to h21-BDPA attaining a maximum of ∼90 at 14.1 T and 5 kHz MAS, the highest observed OE-DNP enhancement to date under these conditions. The approach may be utilized to optimize other polarizing agents exhibiting an OE, an important DNP mechanism with a favorable field and spinning frequency dependence.
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Affiliation(s)
| | | | | | - Daniel Banks
- Bruker Biospin Corporation, Billerica, Massachusetts 01821, United States
| | | | - Eric Bryerton
- Virginia Diodes Corporation, Charlottesville, Virginia 22902, United States
| | - James G Kempf
- Bruker Biospin Corporation, Billerica, Massachusetts 01821, United States
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21
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Yan Z, Zhang R. Multiple acquisitions in a single scan: exhausting abundant 1H polarization at fast MAS. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 346:107338. [PMID: 36463686 DOI: 10.1016/j.jmr.2022.107338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Proton-detected solid-state NMR spectroscopy is emerging as a unique tool for atomic characterization of organic solids due to the boost of resolution and sensitivity afforded by the combined use of high magnetic field and ultrafast magic angle spinning (MAS). Here, we proposed a new set of proton-detected solid-state NMR sequences that hybrid multi-dimensional 1H-1H homonuclear chemical shift correlation (HOMCOR) and two-dimensional 1H-13C heteronuclear chemical shift correlation (HETCOR) sequences into a single experiment, enabling the simultaneous acquisition of multidimensional HOMCOR and HETCOR spectra and thus significant time savings. Based on the core idea of exhausting 1H polarization in each transient scan, we firstly demonstrated that 3D 1H multiple-quantum (MQ) HOMCOR sequence can be combined with 2D HETCOR sequence into a single experiment, leading to the simultaneous acquisition of a 3D 1H MQ HOMCOR and a 2D 1H-13C HETCOR spectrum. Besides, we also showed that 2D 1H/1H double-quantum/single-quantum (DQ/SQ) and single-quantum/single-quantum (SQ/SQ) HOMCOR sequence can be simultaneously combined with HETCOR sequence either, and thus three spectra can be simultaneously obtained from one experiment, including 2D 1H DQ/SQ, 2D 1H SQ/SQ and 2D 1H-13C HETCOR spectra. Since there is only one recycle delay in each experiment, experimental time is substantially reduced compared to separate acquisition of each multi-dimensional solid-state NMR spectrum. Furthermore, those new sequences can be implemented on any standard solid-state spectrometer with only one receiver. Thus, we foresee that these approaches can be valuable for the study of a broad range of molecular systems, including polymers, pharmaceuticals, covalent-organic frameworks (COF) and so on.
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Affiliation(s)
- Zhiwei Yan
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter (SESM), South China University of Technology, Guangzhou 510640, PR China
| | - Rongchun Zhang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter (SESM), South China University of Technology, Guangzhou 510640, PR China; Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, PR China.
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22
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Michaelis VK, Keeler EG, Bahri S, Ong TC, Daviso E, Colvin MT, Griffin RG. Biradical Polarizing Agents at High Fields. J Phys Chem B 2022; 126:7847-7856. [PMID: 36194539 PMCID: PMC9886493 DOI: 10.1021/acs.jpcb.2c03985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The sensitivity enhancements available from dynamic nuclear polarization (DNP) are rapidly reshaping the research landscape and expanding the field of nuclear magnetic resonance (NMR) spectroscopy as a tool for solving complex chemical and structural problems. The past decade has seen considerable advances in this burgeoning method, while efforts to further improve its capabilities continue along many avenues. In this report, we examine the influence of static magnetic field strength and temperature on the reported 1H DNP enhancements from three conventional organic biradicals: TOTAPOL, AMUPol, and SPIROPOL. In contrast to the conventional wisdom, our findings show that at liquid nitrogen temperatures and 700 MHz/460.5 GHz, these three bisnitroxides all provide similar 1H DNP enhancements, ε ≈ 60. Furthermore, we investigate the influence of temperature, microwave power, magnetic field strength, and protein sample deuteration on the NMR experimental results.
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Affiliation(s)
- Vladimir K. Michaelis
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Department of Chemistry, University of Alberta, Edmonton T6G 2G2 Alberta, Canada
| | - Eric G. Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; New York Structural Biology Center, New York 10027, New York, United States
| | - Salima Bahri
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584CH, The Netherlands
| | - Ta-Chung Ong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles 90095 California, United States
| | - Eugenio Daviso
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Department of Scientific Support and Applications Development, Covaris LLC, Woburn 01801 Massachusetts, United States
| | - Michael T. Colvin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States; Ortho Clinical Diagnostics, Rochester 14626 New York, United States
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139 Massachusetts, United States
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23
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Tognetti J, Franks WT, Lewandowski JR, Brown SP. Optimisation of 1H PMLG homonuclear decoupling at 60 kHz MAS to enable 15N- 1H through-bond heteronuclear correlation solid-state NMR spectroscopy. Phys Chem Chem Phys 2022; 24:20258-20273. [PMID: 35975627 PMCID: PMC9429863 DOI: 10.1039/d2cp01041k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022]
Abstract
The Lee-Goldburg condition for homonuclear decoupling in 1H magic-angle spinning (MAS) solid-state NMR sets the angle θ, corresponding to arctan of the ratio of the rf nutation frequency, ν1, to the rf offset, to be the magic angle, θm, equal to tan-1(√2) = 54.7°. At 60 kHz MAS, we report enhanced decoupling compared to MAS alone in a 1H spectrum of 15N-glycine with at θ = 30° for a ν1 of ∼100 kHz at a 1H Larmor frequency, ν0, of 500 MHz and 1 GHz, corresponding to a high chemical shift scaling factor (λCS) of 0.82. At 1 GHz, we also demonstrate enhanced decoupling compared to 60 kHz MAS alone for a lower ν1 of 51 kHz, i.e., a case where the nutation frequency is less than the MAS frequency, with θ = 18°, λCS = 0.92. The ratio of the rotor period to the decoupling cycle time, Ψ = τr/τc, is in the range 0.53 to 0.61. Windowed decoupling using the optimised parameters for a ν1 of ∼100 kHz also gives good performance in a 1H spin-echo experiment, enabling implementation in a 1H-detected 15N-1H cross polarisation (CP)-refocused INEPT heteronuclear correlation NMR experiment. Specifically, initial 15N transverse magnetisation as generated by 1H-15N CP is transferred back to 1H using a refocused INEPT pulse sequence employing windowed 1H decoupling. Such an approach ensures the observation of through-bond N-H connectivities. For 15N-glycine, while the CP-refocused INEPT experiment has a lower sensitivity (∼50%) as compared to a double CP experiment (with a 200 μs 15N to 1H CP contact time), there is selectivity for the directly bonded NH3+ moiety, while intensity is observed for the CH21H resonances in the double CP experiment. Two-dimensional 15N-1H correlation MAS NMR spectra are presented for the dipeptide β-AspAla and the pharmaceutical cimetidine at 60 kHz MAS, both at natural isotopic abundance. For the dipeptide β-AspAla, different build-up dependence on the first spin-echo duration is observed for the NH and NH3+ moieties demonstrating that the experiment could be used to distinguish resonances for different NHx groups.
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Affiliation(s)
- Jacqueline Tognetti
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
| | - W Trent Franks
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
| | | | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK.
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24
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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25
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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26
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Tan KO, Griffin RG. Observation of a Four-Spin Solid Effect. J Chem Phys 2022; 156:174201. [PMID: 35525661 PMCID: PMC9068241 DOI: 10.1063/5.0091663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The two-spin solid effect (2SSE) is one of the established continuous wave dynamic nuclear polarization mechanisms that enables enhancement of nuclear magnetic resonance signals. It functions via a state-mixing mechanism that mediates the excitation of forbidden transitions in an electron–nuclear spin system. Specifically, microwave irradiation at frequencies ωμw ∼ ω0S ± ω0I, where ω0S and ω0I are electron and nuclear Larmor frequencies, respectively, yields enhanced nuclear spin polarization. Following the recent rediscovery of the three-spin solid effect (3SSE) [Tan et al., Sci. Adv. 5, eaax2743 (2019)], where the matching condition is given by ωμw = ω0S ± 2ω0I, we report here the first direct observation of the four-spin solid effect (4SSE) at ωμw = ω0S ± 3ω0I. The forbidden double- and quadruple-quantum transitions were observed in samples containing trityl radicals dispersed in a glycerol–water mixture at 0.35 T/15 MHz/9.8 GHz and 80 K. We present a derivation of the 4SSE effective Hamiltonian, matching conditions, and transition probabilities. Finally, we show that the experimental observations agree with the results from numerical simulations and analytical theory.
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Affiliation(s)
| | - Robert G. Griffin
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, United States of America
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