1
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Al-Hilaly YK, Hurt C, Rickard JE, Harrington CR, Storey JMD, Wischik CM, Serpell LC, Siemer AB. Solid-state NMR of paired helical filaments formed by the core tau fragment tau(297-391). Front Neurosci 2022; 16:988074. [PMID: 36570831 PMCID: PMC9774000 DOI: 10.3389/fnins.2022.988074] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Aggregation of the tau protein into fibrillar cross-β aggregates is a hallmark of Alzheimer's diseases (AD) and many other neurodegenerative tauopathies. Recently, several core structures of patient-derived tau paired helical filaments (PHFs) have been solved revealing a structural variability that often correlates with a specific tauopathy. To further characterize the dynamics of these fibril cores, to screen for strain-specific small molecules as potential biomarkers and therapeutics, and to develop strain-specific antibodies, recombinant in-vitro models of tau filaments are needed. We recently showed that a 95-residue fragment of tau (from residue 297 to 391), termed dGAE, forms filaments in vitro in the absence of polyanionic co-factors often used for in vitro aggregation of full-length tau. Tau(297-391) was identified as the proteolytic resistant core of tau PHFs and overlaps with the structures characterized by cryo-electron microscopy in ex vivo PHFs, making it a promising model for the study of AD tau filaments in vitro. In the present study, we used solid-state NMR to characterize tau(297-391) filaments and show that such filaments assembled under non-reducing conditions are more dynamic and less ordered than those made in the presence of the reducing agent DTT. We further report the resonance assignment of tau(297-391)+DTT filaments and compare it to existing core structures of tau.
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Affiliation(s)
- Youssra K. Al-Hilaly
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, United Kingdom,Chemistry Department, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Connor Hurt
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Janet E. Rickard
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Charles R. Harrington
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom,TauRx Therapeutics Ltd., Aberdeen, United Kingdom
| | - John M. D. Storey
- TauRx Therapeutics Ltd., Aberdeen, United Kingdom,Department of Chemistry, University of Aberdeen, Aberdeen, United Kingdom
| | - Claude M. Wischik
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom,TauRx Therapeutics Ltd., Aberdeen, United Kingdom
| | - Louise C. Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Ansgar B. Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States,*Correspondence: Ansgar B. Siemer,
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2
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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3
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Abstract
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Thanks to recent
improvements in NMR spectrometer hardware and
pulse sequence design, modern 13C NMR has become a useful
tool for biomolecular applications. The complete assignment of a protein
can be accomplished by using 13C detected multinuclear
experiments and it can provide unique information relevant for the
study of a variety of different biomolecules including paramagnetic
proteins and intrinsically disordered proteins. A wide range of NMR
observables can be measured, concurring to the structural and dynamic
characterization of a protein in isolation, as part of a larger complex,
or even inside a living cell. We present the different properties
of 13C with respect to 1H, which provide the
rationale for the experiments developed and their application, the
technical aspects that need to be faced, and the many experimental
variants designed to address different cases. Application areas where
these experiments successfully complement proton NMR are also described.
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Affiliation(s)
- Isabella C Felli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
| | - Roberta Pierattelli
- Department of Chemistry "Ugo Schiff" and Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Florence), Italy
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4
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Sakhaii P, Bohorc B, Schliedermann U, Bermel W. Boosting the resolution of multidimensional NMR spectra by complete removal of proton spin multiplicities. Sci Rep 2021; 11:21566. [PMID: 34732770 PMCID: PMC8566458 DOI: 10.1038/s41598-021-01041-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/19/2021] [Indexed: 11/23/2022] Open
Abstract
Over decades multidimensional NMR spectroscopy has become an indispensable tool for structure elucidation of natural products, peptides and medium sized to large proteins. Heteronuclear single quantum coherence (HSQC) spectroscopy is one of the work horses in that field often used to map structural connectivity between protons and carbons or other hetero nuclei. In overcrowded HSQC spectra, proton multiplet structures of cross peaks set a limit to the power of resolution and make a straightforward assignment difficult. In this work, we provide a solution to improve these penalties by completely removing the proton spin multiplet structure of HSQC cross peaks. Previously reported sideband artefacts are diminished leading to HSQC spectra with singlet responses for all types of proton multiplicities. For sideband suppression, the idea of restricted random delay (RRD) in chunk interrupted data acquisition is introduced and exemplified. The problem of irreducible residual doublet splitting of diastereotopic CH2 groups is simply solved by using a phase sensitive JRES approach in conjunction with echo processing and real time broadband homodecoupling (BBHD) HSQC, applied as a 3D experiment. Advantages and limitations of the method is presented and discussed.
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Affiliation(s)
- Peyman Sakhaii
- NMR Laboratory of SANOFI, Global CMC Early Development, Synthetics Platform, Industrial Park Hoechst, Building G849, 65926, Frankfurt, Germany.
| | - Bojan Bohorc
- NMR Laboratory of SANOFI, Global CMC Early Development, Synthetics Platform, Industrial Park Hoechst, Building G849, 65926, Frankfurt, Germany
| | - Uwe Schliedermann
- NMR Laboratory of SANOFI, Global CMC Early Development, Synthetics Platform, Industrial Park Hoechst, Building G849, 65926, Frankfurt, Germany
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287, Rheinstetten, Germany
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5
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Karunanithy G, Mackenzie HW, Hansen DF. Virtual Homonuclear Decoupling in Direct Detection Nuclear Magnetic Resonance Experiments Using Deep Neural Networks. J Am Chem Soc 2021; 143:16935-16942. [PMID: 34633815 DOI: 10.1021/jacs.1c04010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear magnetic resonance (NMR) experiments are frequently complicated by the presence of homonuclear scalar couplings. For the growing body of biomolecular 13C-detected NMR methods, one-bond 13C-13C couplings significantly reduce sensitivity and resolution. The solution to this problem has typically been to perform virtual decoupling by recording multiple spectra and taking linear combinations. Here, we propose an alternative method of virtual decoupling using deep neural networks, which only requires a single spectrum and gives a significant boost in resolution while reducing the minimum effective phase cycles of the experiments by at least a factor of 2. We successfully apply this methodology to virtually decouple in-phase CON (13CO-15N) protein NMR spectra, 13C-13C correlation spectra of protein side chains, and 13Cα-detected protein 13Cα-13CO spectra where two large homonuclear couplings are present. The deep neural network approach effectively decouples spectra with a high degree of flexibility, including in cases where existing methods fail, and facilitates the use of simpler pulse sequences.
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Affiliation(s)
- Gogulan Karunanithy
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom WC1E 6BT
| | - Harold W Mackenzie
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom WC1E 6BT
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom WC1E 6BT
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6
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Anklin C, Byrd RA. Combined multi-band decoupling in biomolecular NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2021; 75:89-95. [PMID: 33751371 PMCID: PMC8317164 DOI: 10.1007/s10858-021-00360-2] [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: 11/20/2020] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Multi-resonance NMR experiments are powerful analytical and structural tools. Their conceptualization assumes that RF fields may be combined independently to manipulate spin interactions. However, practical implementation can compromise performance. One limitation is the generation of combination bands when two or more RF fields are applied simultaneously within the NMR probe. The combination bands can lead to significant interference with the detection circuitry. A facile approach to combined multi-band decoupling can resolve these problems and increase sensitivity two-fold (or more), by time sharing the application of the individual frequencies rather than time sharing decoupling and data acquisition.
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Affiliation(s)
| | - R Andrew Byrd
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.
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7
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Djajamuliadi J, Ohgo K, Kumashiro KK. A Two-State Model Describes the Temperature-Dependent Conformational Equilibrium in the Alanine-Rich Domains in Elastin. J Phys Chem B 2020; 124:9017-9028. [PMID: 32936634 DOI: 10.1021/acs.jpcb.0c06811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Elastin is the insoluble elastomeric protein that provides extensibility and resilience to vertebrate tissues. Limited high-resolution structural data for elastin are notably complex. To access this information, this protein is considered in the simplified context of its two general domain types, that is, hydrophobic (HP) and crosslinking (CL). The question of elastin's structure-function has directed the focus of nearly all previous studies in the literature to the unique repeating sequences characteristic of this protein, found primarily in the HP domains. The CL domains were assumed to play a very limited role in biological elasticity due in part to the significant α-helical character that was (incorrectly) predicted for these regions. In this study, the conformational heterogeneity of alanines in native elastin's CL domains is examined in the context of helix-coil transition theory (HCTT) using solid-state nuclear magnetic resonance (SSNMR) spectroscopy in tandem with strategic isotopic labeling. Helix and coil populations are observed at all temperatures, but the former increases significantly at lower temperatures. Below the glass transition temperature (Tg), two major populations of alanines in the CL regions are resolved by two-dimensional SSNMR; one-dimensional methods are used for characterization in nativelike conditions. The spectra of 13CO-Ala in the CL regions are simulated using an HCTT-based statistical mechanical representation. Below Tg, longer segments with significant helical probabilities are consistent with the experimental data. At higher temperatures, the SSNMR lineshapes are best fit with a distribution of shorter (Ala)n segments, most in random coil. These results are used to refine a structure-function model for elastin in the context of HCTT, redirecting attention to the CL domains and their role in elasticity.
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Affiliation(s)
- Jhonsen Djajamuliadi
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kosuke Ohgo
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kristin K Kumashiro
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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8
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Gopinath T, Weber DK, Veglia G. Multi-receiver solid-state NMR using polarization optimized experiments (POE) at ultrafast magic angle spinning. JOURNAL OF BIOMOLECULAR NMR 2020; 74:267-285. [PMID: 32333193 PMCID: PMC7236978 DOI: 10.1007/s10858-020-00316-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/11/2020] [Indexed: 05/04/2023]
Abstract
Ultrafast magic angle spinning (MAS) technology and 1H detection have dramatically enhanced the sensitivity of solid-state NMR (ssNMR) spectroscopy of biopolymers. We previously showed that, when combined with polarization optimized experiments (POE), these advancements enable the simultaneous acquisition of multi-dimensional 1H- or 13C-detected experiments using a single receiver. Here, we propose a new sub-class within the POE family, namely HC-DUMAS, HC-MEIOSIS, and HC-MAeSTOSO, that utilize dual receiver technology for the simultaneous detection of 1H and 13C nuclei. We also expand this approach to record 1H-, 13C-, and 15N-detected homonuclear 2D spectra simultaneously using three independent receivers. The combination of POE and multi-receiver technology will further shorten the total experimental time of ssNMR experiments for biological solids.
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Affiliation(s)
- T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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9
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Dabalos CL, Ohgo K, Kumashiro KK. Detection of Labile Conformations of Elastin’s Prolines by Solid-State Nuclear Magnetic Resonance and Fourier Transform Infrared Techniques. Biochemistry 2019; 58:3848-3860. [DOI: 10.1021/acs.biochem.9b00414] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Chester L. Dabalos
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kosuke Ohgo
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kristin K. Kumashiro
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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10
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Ohgo K, Kumashiro KK. Efficient and accurate determination of 13C T 1 and T 1ρ relaxation time constants of high-mobility polymers from limited-resolution spectra with optimized pulse sequences and data fitting. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 297:161-171. [PMID: 30439590 DOI: 10.1016/j.jmr.2018.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/29/2018] [Accepted: 10/31/2018] [Indexed: 06/09/2023]
Abstract
The pulse sequences for the measurement of 13C T1 and T1ρ relaxation time constants in soft organic solids were modified to include steady-state nuclear Overhauser enhancement with direct polarization (ssNOE/DP). The increased signal intensities with ssNOE are particularly well-suited for highly mobile and structurally heterogeneous polymers and proteins like elastin. The phase cycling of these experiments was modified to yield datasets that require less time, with more accurate results. The "3D-fitting process" was developed and then optimized for natural-abundance 13C spectra of elastin, with its characteristic and significant overlap. A comparison of 3D-fitting with the similarly purposed SPORT (Geppi and Forte, 1999) illustrates that the former is more robust, with smaller uncertainty values and higher precision.
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Affiliation(s)
- Kosuke Ohgo
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, HI 96822, USA.
| | - Kristin K Kumashiro
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, HI 96822, USA
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11
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Djajamuliadi J, Ohgo K, Kumashiro KK. Targeting Alanines in the Hydrophobic and Cross-Linking Domains of Native Elastin with Isotopic Enrichment and Solid-State NMR Spectroscopy. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jhonsen Djajamuliadi
- Department of Chemistry, University of Hawaii,
2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kosuke Ohgo
- Department of Chemistry, University of Hawaii,
2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kristin K. Kumashiro
- Department of Chemistry, University of Hawaii,
2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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12
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Chinthalapalli S, Bornet A, Carnevale D, Jannin S, Bodenhausen G. Homonuclear decoupling for spectral simplification of carbon-13 enriched molecules in solution-state NMR enhanced by dissolution DNP. Phys Chem Chem Phys 2016; 18:11480-7. [PMID: 27058951 DOI: 10.1039/c5cp07884a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Complex overlapping multiplets due to scalar couplings (n)J((13)C, (13)C) in fully (13)C-enriched molecules can be simplified by polychromatic irradiation of selected spins. The signal intensities of the remaining non-irradiated signals are proportional to the concentrations, as shown in this work for the anomeric (13)C signals of the α- and β-conformers of glucose. Homonuclear decoupling can therefore be useful for quantitative NMR studies. The resulting decoupled lineshapes show residual fine structures that have been investigated by means of numerical simulations. Simulations also show that homonuclear decoupling schemes remain effective despite inhomogeneous static fields that tend to hamper in cellulo and in vivo studies. Homonuclear decoupling schemes can be combined with dissolution DNP to obtain signal enhancements of more than four orders of magnitude. Polychromatic irradiation of selected spins does not cause significant losses of hyperpolarization of the remaining non-irradiated spins.
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Affiliation(s)
- Srinivas Chinthalapalli
- Institut des sciences et ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland and Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Gulbarga, 585311 Karnataka, India
| | - Aurélien Bornet
- Institut des sciences et ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Diego Carnevale
- Institut des sciences et ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland and Neuchâtel Platform of Analytical Chemistry (NPAC), Institut de Chimie, Université de Neuchâtel, Avenue de Bellevaux 51, 2000 Neuchâtel, Switzerland.
| | - Sami Jannin
- Institut des sciences et ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Geoffrey Bodenhausen
- Institut des sciences et ingénierie chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland and École Normale Supérieure-PSL Research University, Département de Chimie, 24 rue Lhomond, F-75005 Paris, France and Sorbonne Universités, UPMC Univ Paris 06, LBM, 4 place Jussieu, F-75005, Paris, France and CNRS, UMR 7203 LBM, F-75005, Paris, France
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13
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Kiraly P, Adams RW, Paudel L, Foroozandeh M, Aguilar JA, Timári I, Cliff MJ, Nilsson M, Sándor P, Batta G, Waltho JP, Kövér KE, Morris GA. Real-time pure shift ¹⁵N HSQC of proteins: a real improvement in resolution and sensitivity. JOURNAL OF BIOMOLECULAR NMR 2015; 62:43-52. [PMID: 25737243 PMCID: PMC4432093 DOI: 10.1007/s10858-015-9913-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/20/2015] [Indexed: 06/01/2023]
Abstract
Spectral resolution in proton NMR spectroscopy is reduced by the splitting of resonances into multiplets due to the effect of homonuclear scalar couplings. Although these effects are often hidden in protein NMR spectroscopy by low digital resolution and routine apodization, behind the scenes homonuclear scalar couplings increase spectral overcrowding. The possibilities for biomolecular NMR offered by new pure shift NMR methods are illustrated here. Both resolution and sensitivity are improved, without any increase in experiment time. In these experiments, free induction decays are collected in short bursts of data acquisition, with durations short on the timescale of J-evolution, interspersed with suitable refocusing elements. The net effect is real-time (t 2) broadband homodecoupling, suppressing the multiplet structure caused by proton-proton interactions. The key feature of the refocusing elements is that they discriminate between the resonances of active (observed) and passive (coupling partner) spins. This can be achieved either by using band-selective refocusing or by the BIRD element, in both cases accompanied by a nonselective 180° proton pulse. The latter method selects the active spins based on their one-bond heteronuclear J-coupling to (15)N, while the former selects a region of the (1)H spectrum. Several novel pure shift experiments are presented, and the improvements in resolution and sensitivity they provide are evaluated for representative samples: the N-terminal domain of PGK; ubiquitin; and two mutants of the small antifungal protein PAF. These new experiments, delivering improved sensitivity and resolution, have the potential to replace the current standard HSQC experiments.
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Affiliation(s)
- Peter Kiraly
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Ralph W. Adams
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Liladhar Paudel
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington, 850 Republican St, Seattle, WA 98109 USA
| | | | - Juan A. Aguilar
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE UK
| | - István Timári
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Mathias Nilsson
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Péter Sándor
- Agilent Technologies R&D and Marketing GmbH & Co. KG, Hewlett-Packard Strasse 8, 76337 Waldbronn, Germany
| | - Gyula Batta
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary
| | - Jonathan P. Waltho
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Katalin E. Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary
| | - Gareth A. Morris
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
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14
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Felli IC, Pierattelli R. Spin-state-selective methods in solution- and solid-state biomolecular 13C NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 84-85:1-13. [PMID: 25669738 DOI: 10.1016/j.pnmrs.2014.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 10/26/2014] [Indexed: 06/04/2023]
Abstract
Spin-state-selective methods to achieve homonuclear decoupling in the direct acquisition dimension of (13)C detected NMR experiments have been one of the key contributors to converting (13)C detected NMR experiments into really useful tools for studying biomolecules. We discuss here in detail the various methods that have been proposed, summarize the large array of new experiments that have been developed and present applications to different kinds of proteins in different aggregation states.
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Affiliation(s)
- Isabella C Felli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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15
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Ying J, Li F, Lee JH, Bax A. ¹³Cα decoupling during direct observation of carbonyl resonances in solution NMR of isotopically enriched proteins. JOURNAL OF BIOMOLECULAR NMR 2014; 60:15-21. [PMID: 25129622 PMCID: PMC4156133 DOI: 10.1007/s10858-014-9853-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/04/2014] [Indexed: 05/23/2023]
Abstract
Direct detection of (13)C can be advantageous when studying uniformly enriched proteins, in particular for paramagnetic proteins or when hydrogen exchange with solvent is fast. A scheme recently introduced for long-observation-window band-selective homonuclear decoupling in solid state NMR, LOW-BASHD (Struppe et al. in J Magn Reson 236:89-94, 2013) is shown to be effective for (13)C(α) decoupling during direct (13)C' observation in solution NMR experiments too. For this purpose, adjustment of the decoupling pulse parameters and delays is demonstrated to be important for increasing spectral resolution, to reduce three-spin effects, and to decrease the intensity of decoupling side-bands. LOW-BASHD then yields (13)C' line widths comparable to those obtained with the popular IPAP method, while enhancing sensitivity by ca 35 %. As a practical application of LOW-BASHD decoupling, requiring quantitative intensity measurement over a wide dynamic range, the impact of lipid binding on the (13)C'-detected NCO spectrum of the intrinsically disordered protein α-synuclein is compared with that on the (1)H-detected (1)H-(15)N HSQC spectrum. Results confirm that synuclein's "dark state" behavior is not caused by paramagnetic relaxation or rapid hydrogen exchange.
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Affiliation(s)
- Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
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