1
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Chen B. ASAP: An automatic sequential assignment program for congested multidimensional solid state NMR spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 361:107664. [PMID: 38522163 DOI: 10.1016/j.jmr.2024.107664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024]
Abstract
Accurate signal assignments can be challenging for congested solid-state NMR (ssNMR) spectra. We describe an automatic sequential assignment program (ASAP) to partially overcome this challenge. ASAP takes three input files: the residue type assignments (RTAs) determined from the better-resolved NCACX spectrum, the full peak list of the NCOCX spectrum, and the protein sequence. It integrates our auto-residue type assignment strategy (ARTIST) with the Monte Carlo simulated annealing (MCSA) algorithm to overcome the hurdle for accurate signal assignments caused by incomplete side-chain resonances and spectral congestion. Combined, ASAP demonstrates robust performance and accelerates signal assignments of large proteins (>200 residues) that lack crystalline order.
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Affiliation(s)
- Bo Chen
- Department of Physics, University of Central Florida, Orlando 32816, USA.
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2
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Xue K, Sarkar R, Tošner Z, Reif B. Field and magic angle spinning frequency dependence of proton resonances in rotating solids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:47-61. [PMID: 36113917 DOI: 10.1016/j.pnmrs.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Proton detection in solid state NMR is continuously developing and allows one to gain new insights in structural biology. Overall, this progress is a result of the synergy between hardware development, new NMR methodology and new isotope labeling strategies, to name a few factors. Even though current developments are rapid, it is worthwhile to summarize what can currently be achieved employing proton detection in biological solids. We illustrate this by analysing the signal-to-noise ratio (SNR) for spectra obtained for a microcrystalline α-spectrin SH3 domain protein sample by (i) employing different degrees of chemical dilution to replace protons by incorporating deuterons in different sites, by (ii) variation of the magic angle spinning (MAS) frequencies between 20 and 110 kHz, and by (iii) variation of the static magnetic field B0. The experimental SNR values are validated with numerical simulations employing up to 9 proton spins. Although in reality a protein would contain far more than 9 protons, in a deuterated environment this is a sufficient number to achieve satisfactory simulations consistent with the experimental data. The key results of this analysis are (i) with current hardware, deuteration is still necessary to record spectra of optimum quality; (ii) 13CH3 isotopomers for methyl groups yield the best SNR when MAS frequencies above 100 kHz are available; and (iii) sensitivity increases with a factor beyond B0 3/2 with the static magnetic field due to a transition of proton-proton dipolar interactions from a strong to a weak coupling limit.
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Affiliation(s)
- Kai Xue
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology, Am Fassberg. 11, Goettingen, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany
| | - Zdeněk Tošner
- Department of Chemistry, Faculty of Science, Charles University, Hlavova 8, 12842 Praha 2, Czech Republic
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.
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3
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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: 49] [Impact Index Per Article: 24.5] [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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4
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Paluch P, Augustyniak R, Org ML, Vanatalu K, Kaldma A, Samoson A, Stanek J. NMR Assignment of Methyl Groups in Immobilized Proteins Using Multiple-Bond 13C Homonuclear Transfers, Proton Detection, and Very Fast MAS. Front Mol Biosci 2022; 9:828785. [PMID: 35425812 PMCID: PMC9002630 DOI: 10.3389/fmolb.2022.828785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
In nuclear magnetic resonance spectroscopy of proteins, methyl protons play a particular role as extremely sensitive reporters on dynamics, allosteric effects, and protein–protein interactions, accessible even in high-molecular-weight systems approaching 1 MDa. The notorious issue of their chemical shift assignment is addressed here by a joint use of solid-state 1H-detected methods at very fast (nearly 100 kHz) magic-angle spinning, partial deuteration, and high-magnetic fields. The suitability of a series of RF schemes is evaluated for the efficient coherence transfer across entire 13C side chains of methyl-containing residues, which is key for establishing connection between methyl and backbone 1H resonances. The performance of ten methods for recoupling of either isotropic 13C–13C scalar or anisotropic dipolar interactions (five variants of TOBSY, FLOPSY, DIPSI, WALTZ, RFDR, and DREAM) is evaluated experimentally at two state-of-the-art magic-angle spinning (55 and 94.5 kHz) and static magnetic field conditions (18.8 and 23.5 T). Model isotopically labeled compounds (alanine and Met-Leu-Phe tripeptide) and ILV-methyl and amide-selectively protonated, and otherwise deuterated chicken α-spectrin SH3 protein are used as convenient reference systems. Spin dynamics simulations in SIMPSON are performed to determine optimal parameters of these RF schemes, up to recently experimentally attained spinning frequencies (200 kHz) and B0 field strengths (28.2 T). The concept of linearization of 13C side chain by appropriate isotope labeling is revisited and showed to significantly increase sensitivity of methyl-to-backbone correlations. A resolution enhancement provided by 4D spectroscopy with non-uniform (sparse) sampling is demonstrated to remove ambiguities in simultaneous resonance assignment of methyl proton and carbon chemical shifts.
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Affiliation(s)
- Piotr Paluch
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Łódź, Poland
| | | | - Mai-Liis Org
- Tallin University of Technology, Tallinn, Estonia
| | | | - Ats Kaldma
- Tallin University of Technology, Tallinn, Estonia
| | - Ago Samoson
- Tallin University of Technology, Tallinn, Estonia
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
- *Correspondence: Jan Stanek,
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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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6
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Reif B. Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR. Chem Rev 2021; 122:10019-10035. [PMID: 34870415 DOI: 10.1021/acs.chemrev.1c00681] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B0 field in a perdeuterated environment are compiled.
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Affiliation(s)
- Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at the Department of Chemistry, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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7
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Dubey A, Stoyanov N, Viennet T, Chhabra S, Elter S, Borggräfe J, Viegas A, Nowak RP, Burdzhiev N, Petrov O, Fischer ES, Etzkorn M, Gelev V, Arthanari H. Lokale Deuterierung ermöglicht NMR‐Messung von Methylgruppen in Proteinen aus eukaryotischen und Zell‐freien Expressionssystemen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Abhinav Dubey
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Nikolay Stoyanov
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Thibault Viennet
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Sandeep Chhabra
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Shantha Elter
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Jan Borggräfe
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Aldino Viegas
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Radosław P. Nowak
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Nikola Burdzhiev
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Ognyan Petrov
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Eric S. Fischer
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
| | - Manuel Etzkorn
- Institute of Physical Biology Heinrich-Heine-University Universitätsstr. 1 40225 Düsseldorf Deutschland
- Institute of Biological Information Processing (IBI-7) Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
- JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich GmbH 52425 Jülich Deutschland
| | - Vladimir Gelev
- Faculty of Chemistry and Pharmacy Sofia University 1 James Bourchier Blvd. 1164 Sofia Bulgarien
| | - Haribabu Arthanari
- Cancer Biology Dana-Farber Cancer Institute 450 Brookline Avenue LC-3311 Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology Harvard Medical School 240 Longwood Avenue Boston MA 02215 USA
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8
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Dubey A, Stoyanov N, Viennet T, Chhabra S, Elter S, Borggräfe J, Viegas A, Nowak RP, Burdzhiev N, Petrov O, Fischer ES, Etzkorn M, Gelev V, Arthanari H. Local Deuteration Enables NMR Observation of Methyl Groups in Proteins from Eukaryotic and Cell-Free Expression Systems. Angew Chem Int Ed Engl 2021; 60:13783-13787. [PMID: 33768661 PMCID: PMC8251921 DOI: 10.1002/anie.202016070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/22/2021] [Indexed: 01/13/2023]
Abstract
Therapeutically relevant proteins such as GPCRs, antibodies and kinases face clear limitations in NMR studies due to the challenges in site-specific isotope labeling and deuteration in eukaryotic expression systems. Here we describe an efficient and simple method to observe the methyl groups of leucine residues in proteins expressed in bacterial, eukaryotic or cell-free expression systems without modification of the expression protocol. The method relies on simple stereo-selective 13 C-labeling and deuteration of leucine that alleviates the need for additional deuteration of the protein. The spectroscopic benefits of "local" deuteration are examined in detail through Forbidden Coherence Transfer (FCT) experiments and simulations. The utility of this labeling method is demonstrated in the cell-free synthesis of bacteriorhodopsin and in the insect-cell expression of the RRM2 domain of human RBM39.
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Affiliation(s)
- Abhinav Dubey
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Nikolay Stoyanov
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Thibault Viennet
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Sandeep Chhabra
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Shantha Elter
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Jan Borggräfe
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Aldino Viegas
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Radosław P. Nowak
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Nikola Burdzhiev
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Ognyan Petrov
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Eric S. Fischer
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
| | - Manuel Etzkorn
- Institute of Physical BiologyHeinrich-Heine-UniversityUniversitätsstr. 140225DüsseldorfGermany
- Institute of Biological Information Processing (IBI-7)Forschungszentrum Jülich GmbH52425JülichGermany
- JuStruct: Jülich Center for Structural BiologyForschungszentrum Jülich GmbH52425JülichGermany
| | - Vladimir Gelev
- Faculty of Chemistry and PharmacySofia University1 James Bourchier Blvd.1164SofiaBulgaria
| | - Haribabu Arthanari
- Cancer BiologyDana-Farber Cancer Institute450 Brookline Avenue LC-3311BostonMA02215USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood AvenueBostonMA02215USA
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9
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Nimerovsky E, Movellan KT, Zhang XC, Forster MC, Najbauer E, Xue K, Dervişoǧlu R, Giller K, Griesinger C, Becker S, Andreas LB. Proton Detected Solid-State NMR of Membrane Proteins at 28 Tesla (1.2 GHz) and 100 kHz Magic-Angle Spinning. Biomolecules 2021; 11:752. [PMID: 34069858 PMCID: PMC8157399 DOI: 10.3390/biom11050752] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 12/25/2022] Open
Abstract
The available magnetic field strength for high resolution NMR in persistent superconducting magnets has recently improved from 23.5 to 28 Tesla, increasing the proton resonance frequency from 1 to 1.2 GHz. For magic-angle spinning (MAS) NMR, this is expected to improve resolution, provided the sample preparation results in homogeneous broadening. We compare two-dimensional (2D) proton detected MAS NMR spectra of four membrane proteins at 950 and 1200 MHz. We find a consistent improvement in resolution that scales superlinearly with the increase in magnetic field for three of the four examples. In 3D and 4D spectra, which are now routinely acquired, this improvement indicates the ability to resolve at least 2 and 2.5 times as many signals, respectively.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Loren B. Andreas
- Department for NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany; (E.N.); (K.T.M.); (X.C.Z.); (M.C.F.); (E.N.); (K.X.); (R.D.); (K.G.); (C.G.); (S.B.)
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10
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 182] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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11
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Solid-state NMR approaches to investigate large enzymes in complex with substrates and inhibitors. Biochem Soc Trans 2020; 49:131-144. [PMID: 33367567 DOI: 10.1042/bst20200099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022]
Abstract
Enzyme catalysis is omnipresent in the cell. The mechanisms by which highly evolved protein folds enable rapid and specific chemical transformation of substrates belong to the marvels of structural biology. Targeting of enzymes with inhibitors has immediate application in drug discovery, from chemotherapeutics over antibiotics to antivirals. NMR spectroscopy combines multiple assets for the investigation of enzyme function. The non-invasive technique can probe enzyme structure and dynamics and map interactions with substrates, cofactors and inhibitors at the atomic level. With experiments performed at close to native conditions, catalytic transformations can be monitored in real time, giving access to kinetic parameters. The power of NMR in the solid state, in contrast with solution, lies in the absence of fundamental size limitations, which is crucial for enzymes that are either membrane-embedded or assemble into large soluble complexes exceeding hundreds of kilodaltons in molecular weight. Here we review recent progress in solid-state NMR methodology, which has taken big leaps in the past years due to steady improvements in hardware design, notably magic angle spinning, and connect it to parallel biochemical advances that enable isotope labelling of increasingly complex enzymes. We first discuss general concepts and requirements of the method and then highlight the state-of-the-art in sample preparation, structure determination, dynamics and interaction studies. We focus on examples where solid-state NMR has been instrumental in elucidating enzyme mechanism, alone or in integrative studies.
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12
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Zhang R, Nishiyama Y, Ramamoorthy A. Exploiting heterogeneous time scale of dynamics to enhance 2D HETCOR solid-state NMR sensitivity. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 309:106615. [PMID: 31669793 DOI: 10.1016/j.jmr.2019.106615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/11/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
Multidimensional solid-state NMR spectroscopy plays a significant role in offering atomic-level insights into molecular systems. In particular, heteronuclear chemical shift correlation (HETCOR) experiments could provide local chemical and structural information in terms of spatial heteronuclear proximity and through-bond connectivity. In solid state, the transfer of magnetization between heteronuclei, a key step in HETCOR experiments, is usually achieved using cross-polarization (CP) or insensitive nuclei enhanced by polarization transfer (INEPT) depending on the sample characteristics and magic-angle-spinning (MAS) frequency. But, for a multiphase system constituting molecular components that differ in their time scales of mobilities, CP efficiency is pretty low for mobile components because of the averaging of heteronuclear dipolar couplings whereas INEPT is inefficient for immobile components due to the short T2 and can yield through-space connectivity due to strong proton spin diffusion for immobile components especially under moderate spinning speeds. Herein, in this study we present two 2D pulse sequences that enable the sequential acquisition of 13C/1H HETCOR NMR spectra for the rigid and mobile components by taking full advantage of the abundant proton magnetization in a single experiment with barely increasing the overall experimental time. In particular, the 13C-detected HETCOR experiment could be applied under slow MAS conditions, where a multiple-pulse sequence is typically employed to enhance 1H spectral resolution in the indirect dimension. In contrast, the 1H-detected HETCOR experiment should be applied under ultrafast MAS, where CP and heteronuclear nuclear Overhauser effect (NOE) polarization transfer are combined to enhance 13C signal intensities for mobile components. These pulse sequences are experimentally demonstrated on two model systems to obtain 2D 13C/1H chemical shift correlation spectra of rigid and mobile components independently and separately. These pulse sequences can be used for dynamics based spectral editing and resonance assignments. Therefore, we believe the proposed 2D HETCOR NMR pulse sequences will be beneficial for the structural studies of heterogeneous systems containing molecular components that differ in their time scale of motions for understanding the interplay of structures and properties.
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Affiliation(s)
- Rongchun Zhang
- Biophysics and Department of Chemistry, Biomedical Engineering, Maromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Yusuke Nishiyama
- NMR Science and Development Division, RIKEN SPring-8 Center, Nanocrystallography Unit, RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Maromolecular Science and Engineering, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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13
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Zhao S, Yang Y, Zhao Y, Li X, Xue Y, Wang S. High-resolution solid-state NMR spectroscopy of hydrated non-crystallized RNA. Chem Commun (Camb) 2019; 55:13991-13994. [PMID: 31687672 DOI: 10.1039/c9cc06552k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We highlight that sufficient hydration of non-crystallized RNA could provide high-resolution solid-state NMR (SSNMR) spectra, with similar spectral quality to the crystallized RNA. This leads to a greatly simplified RNA preparation approach by ethanol precipitation for high-resolution SSNMR studies. It will greatly broaden the scope of SSNMR applications to the characterization of RNAs.
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Affiliation(s)
- Sha Zhao
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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14
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Xue K, Sarkar R, Tosner Z, Lalli D, Motz C, Koch B, Pintacuda G, Reif B. MAS dependent sensitivity of different isotopomers in selectively methyl protonated protein samples in solid state NMR. JOURNAL OF BIOMOLECULAR NMR 2019; 73:625-631. [PMID: 31515660 DOI: 10.1007/s10858-019-00274-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Sensitivity and resolution together determine the quality of NMR spectra in biological solids. For high-resolution structure determination with solid-state NMR, proton-detection emerged as an attractive strategy in the last few years. Recent progress in probe technology has extended the range of available MAS frequencies up to above 100 kHz, enabling the detection of resolved resonances from sidechain protons, which are important reporters of structure. Here we characterise the interplay between MAS frequency in the newly available range of 70-110 kHz and proton content on the spectral quality obtainable on a 1 GHz spectrometer for methyl resonances. Variable degrees of proton densities are tested on microcrystalline samples of the α-spectrin SH3 domain with selectively protonated methyl isotopomers (CH3, CH2D, CHD2) in a perdeuterated matrix. The experimental results are supported by simulations that allow the prediction of the sensitivity outside this experimental frequency window. Our results facilitate the selection of the appropriate labelling scheme at a given MAS rotation frequency.
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Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
| | - Zdenek Tosner
- Department of Chemistry, Faculty of Science, Charles University, Hlavova 8, 12842, Prague 2, Czech Republic
| | - Daniela Lalli
- Centre de Résonance Magnétique Nucléaire a Très hauts Champs (FRE 2034, CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100, Villeurbanne, France
| | - Carina Motz
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Benita Koch
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire a Très hauts Champs (FRE 2034, CNRS, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100, Villeurbanne, France
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale Amedeo Avogadro, Viale Teresa Michel, 15121, Alessandria, Italy
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
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15
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Prabhakar A, Puglisi EV, Puglisi JD. Single-Molecule Fluorescence Applied to Translation. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032714. [PMID: 29891562 DOI: 10.1101/cshperspect.a032714] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Single-molecule fluorescence methods have illuminated the dynamics of the translational machinery. Structural and bulk biochemical experiments have provided detailed atomic and global mechanistic views of translation, respectively. Single-molecule studies of translation have bridged these views by temporally connecting the conformational and compositional states defined from structural data within the mechanistic framework of translation produced from biochemical studies. Here, we discuss the context for applying different single-molecule fluorescence experiments, and present recent applications to studying prokaryotic and eukaryotic translation. We underscore the power of observing single translating ribosomes to delineate and sort complex mechanistic pathways during initiation and elongation, and discuss future applications of current and improved technologies.
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Affiliation(s)
- Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Program in Biophysics, Stanford University, Stanford, California 94305
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
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16
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Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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17
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Zinke M, Fricke P, Lange S, Zinn‐Justin S, Lange A. Protein-Protein Interfaces Probed by Methyl Labeling and Proton-Detected Solid-State NMR Spectroscopy. Chemphyschem 2018; 19:2457-2460. [PMID: 29917302 PMCID: PMC6220863 DOI: 10.1002/cphc.201800542] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 12/18/2022]
Abstract
Proton detection and fast magic-angle spinning have advanced biological solid-state NMR, allowing for the backbone assignment of complex protein assemblies with high sensitivity and resolution. However, so far no method has been proposed to detect intermolecular interfaces in these assemblies by proton detection. Herein, we introduce a concept based on methyl labeling that allows for the assignment of these moieties and for the study of protein-protein interfaces at atomic resolution.
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Affiliation(s)
- Maximilian Zinke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Pascal Fricke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sascha Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sophie Zinn‐Justin
- Institute for Integrative Biology of the Cell (I2BC) CEA, CNRSUniversité Paris-Sud Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Adam Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- Institut für BiologieHumboldt-Universität zu BerlinBerlinGermany
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18
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Choi J, Grosely R, Prabhakar A, Lapointe CP, Wang J, Puglisi JD. How Messenger RNA and Nascent Chain Sequences Regulate Translation Elongation. Annu Rev Biochem 2018; 87:421-449. [PMID: 29925264 PMCID: PMC6594189 DOI: 10.1146/annurev-biochem-060815-014818] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Translation elongation is a highly coordinated, multistep, multifactor process that ensures accurate and efficient addition of amino acids to a growing nascent-peptide chain encoded in the sequence of translated messenger RNA (mRNA). Although translation elongation is heavily regulated by external factors, there is clear evidence that mRNA and nascent-peptide sequences control elongation dynamics, determining both the sequence and structure of synthesized proteins. Advances in methods have driven experiments that revealed the basic mechanisms of elongation as well as the mechanisms of regulation by mRNA and nascent-peptide sequences. In this review, we highlight how mRNA and nascent-peptide elements manipulate the translation machinery to alter the dynamics and pathway of elongation.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
- Department of Applied Physics, Stanford University, Stanford, California 94305-4090, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
| | - Arjun Prabhakar
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
- Program in Biophysics, Stanford University, Stanford, California 94305, USA
| | - Christopher P Lapointe
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA; , , , , ,
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19
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Atomic structural details of a protein grafted onto gold nanoparticles. Sci Rep 2017; 7:17934. [PMID: 29263419 PMCID: PMC5738368 DOI: 10.1038/s41598-017-18109-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
The development of a methodology for the structural characterization at atomic detail of proteins conjugated to nanoparticles would be a breakthrough in nanotechnology. Solution and solid-state NMR spectroscopies are currently used to investigate molecules and peptides grafted onto nanoparticles, but the strategies used so far fall short in the application to proteins, which represent a thrilling development in theranostics. We here demonstrate the feasibility of highly-resolved multidimensional heteronuclear spectra of a large protein assembly conjugated to PEGylated gold nanoparticles. The spectra have been obtained by direct proton detection under fast MAS and allow for both a fast fingerprinting for the assessment of the preservation of the native fold and for resonance assignment. We thus demonstrate that the structural characterization and the application of the structure-based methodologies to proteins bound to gold nanoparticles is feasible and potentially extensible to other hybrid protein-nanomaterials.
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20
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Cala-De Paepe D, Stanek J, Jaudzems K, Tars K, Andreas LB, Pintacuda G. Is protein deuteration beneficial for proton detected solid-state NMR at and above 100 kHz magic-angle spinning? SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:126-136. [PMID: 28802890 DOI: 10.1016/j.ssnmr.2017.07.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/14/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
1H-detection in solid-state NMR of proteins has been traditionally combined with deuteration for both resolution and sensitivity reasons, with the optimal level of proton dilution being dependent on MAS rate. Here we present 1H-detected 15N and 13C CP-HSQC spectra on two microcrystalline samples acquired at 60 and 111 kHz MAS and at ultra-high field. We critically compare the benefits of three labeling schemes yielding different levels of proton content in terms of resolution, coherence lifetimes and feasibility of scalar-based 2D correlations under these experimental conditions. We observe unexpectedly high resolution and sensitivity of aromatic resonances in 2D 13C-1H correlation spectra of protonated samples. Ultrafast MAS reduces or even removes the necessity of 1H dilution for high-resolution 1H-detection in biomolecular solid-state NMR. It yields 15N,1H and 13C,1H fingerprint spectra of exceptional resolution for fully protonated samples, with notably superior 1H and 13C lineshapes for side-chain resonances.
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Affiliation(s)
- Diane Cala-De Paepe
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Jan Stanek
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Kristaps Jaudzems
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Kaspars Tars
- Biomedical Research and Study Centre, Rātsupītes 1, LV1067, Riga, Latvia
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France; Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077, Göttingen, Germany
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.
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21
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Xue K, Sarkar R, Motz C, Asami S, Camargo DCR, Decker V, Wegner S, Tosner Z, Reif B. Limits of Resolution and Sensitivity of Proton Detected MAS Solid-State NMR Experiments at 111 kHz in Deuterated and Protonated Proteins. Sci Rep 2017; 7:7444. [PMID: 28785098 PMCID: PMC5547042 DOI: 10.1038/s41598-017-07253-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/21/2017] [Indexed: 01/23/2023] Open
Abstract
MAS solid-state NMR is capable of determining structures of protonated solid proteins using proton-detected experiments. These experiments are performed at MAS rotation frequency of around 110 kHz, employing 0.5 mg of material. Here, we compare 1H, 13C correlation spectra obtained from protonated and deuterated microcrystalline proteins at MAS rotation frequency of 111 kHz, and show that the spectral quality obtained from deuterated samples is superior to those acquired using protonated samples in terms of resolution and sensitivity. In comparison to protonated samples, spectra obtained from deuterated samples yield a gain in resolution on the order of 3 and 2 in the proton and carbon dimensions, respectively. Additionally, the spectrum from the deuterated sample yields approximately 2–3 times more sensitivity compared to the spectrum of a protonated sample. This gain could be further increased by a factor of 2 by making use of stereospecific precursors for biosynthesis. Although the overall resolution and sensitivity of 1H, 13C correlation spectra obtained using protonated solid samples with rotation frequencies on the order of 110 kHz is high, the spectral quality is still poor when compared to the deuterated samples. We believe that experiments involving large protein complexes in which sensitivity is limiting will benefit from the application of deuteration schemes.
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Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
| | - Carina Motz
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Sam Asami
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Diana C Rodriguez Camargo
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Venita Decker
- Bruker BioSpin, Silberstreifen 4, 76287, Rheinstetten, Germany
| | | | - Zdenek Tosner
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.,Deptartment of chemistry, Faculty of Science, Charles University, Hlavova 8, 12842, Praha 2, Czech Republic
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
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22
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Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Protonendetektierte Festkörper-NMR-Spektroskopie an einem Zinktransporter-Membranprotein in nativen Nanoscheiben. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Beate Bersch
- CEA, CNRS; Université Grenoble Alpes; Institut de Biologie Structurale; 71, avenue des martyrs 38044 Grenoble Frankreich
| | - Jonas M. Dörr
- Membrane Biochemistry and Biophysics; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht Niederlande
| | - Audrey Hessel
- CEA, CNRS; Université Grenoble Alpes; Institut de Biologie Structurale; 71, avenue des martyrs 38044 Grenoble Frankreich
| | - J. Antoinette Killian
- Membrane Biochemistry and Biophysics; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht Niederlande
| | - Paul Schanda
- CEA, CNRS; Université Grenoble Alpes; Institut de Biologie Structurale; 71, avenue des martyrs 38044 Grenoble Frankreich
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23
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Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs. Angew Chem Int Ed Engl 2017; 56:2508-2512. [PMID: 28128538 DOI: 10.1002/anie.201610441] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/13/2016] [Indexed: 12/30/2022]
Abstract
The structure, dynamics, and function of membrane proteins are intimately linked to the properties of the membrane environment in which the proteins are embedded. For structural and biophysical characterization, membrane proteins generally need to be extracted from the membrane and reconstituted in a suitable membrane-mimicking environment. Ensuring functional and structural integrity in these environments is often a major concern. The styrene/maleic acid co-polymer has recently been shown to be able to extract lipid/membrane protein patches directly from native membranes to form nanosize discoidal proteolipid particles, also referred to as native nanodiscs. In this work, we show that high-resolution solid-state NMR spectra can be obtained from an integral membrane protein in native nanodiscs, as exemplified by the 2×34 kDa bacterial cation diffusion facilitator CzcD.
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Affiliation(s)
- Beate Bersch
- CEA, CNRS, Univ. Grenoble Alpes, Institut de Biologie Structurale, 71, avenue des martyrs, 38044, Grenoble, France
| | - Jonas M Dörr
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Audrey Hessel
- CEA, CNRS, Univ. Grenoble Alpes, Institut de Biologie Structurale, 71, avenue des martyrs, 38044, Grenoble, France
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Paul Schanda
- CEA, CNRS, Univ. Grenoble Alpes, Institut de Biologie Structurale, 71, avenue des martyrs, 38044, Grenoble, France
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