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Taware PP, Jain MG, Raran-Kurussi S, Agarwal V, Madhu PK, Mote KR. Measuring Dipolar Order Parameters in Nondeuterated Proteins Using Solid-State NMR at the Magic-Angle-Spinning Frequency of 100 kHz. J Phys Chem Lett 2023; 14:3627-3635. [PMID: 37026698 DOI: 10.1021/acs.jpclett.3c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Proteins are dynamic molecules, relying on conformational changes to carry out function. Measurement of these conformational changes can provide insight into how function is achieved. For proteins in the solid state, this can be done by measuring the decrease in the strength of anisotropic interactions due to motion-induced fluctuations. The measurement of one-bond heteronuclear dipole-dipole coupling at magic-angle-spinning (MAS) frequencies >60 kHz is ideal for this purpose. However, rotational-echo double resonance (REDOR), an otherwise gold-standard technique for the quantitative measurement of these couplings, is difficult to implement under these conditions, especially in nondeuterated samples. We present here a combination of strategies based on REDOR variants ϵ-REDOR and DEDOR (deferred REDOR) and simultaneously measure residue-specific 15N-1H and 13Cα-1Hα dipole-dipole couplings in nondeuterated systems at the MAS frequency of 100 kHz. These strategies open up avenues to access dipolar order parameters in a variety of systems at the increasingly fast MAS frequencies that are now available.
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Affiliation(s)
- Pravin P Taware
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Mukul G Jain
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Sreejith Raran-Kurussi
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - P K Madhu
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, Telangana, India
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2
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Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.
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Affiliation(s)
- Yusuke Nishiyama
- JEOL Ltd., Akishima, Tokyo196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa230-0045, Japan
| | - Guangjin Hou
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian116023, China
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad500 046, India
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan41809-1055, United States
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3
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Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. J Struct Biol X 2022; 7:100079. [PMID: 36578472 PMCID: PMC9791609 DOI: 10.1016/j.yjsbx.2022.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.
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Affiliation(s)
- Diego F. Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044 Grenoble, France
- ICSN, CNRS UPR2301, Univ. Paris-Saclay, Gif-sur-Yvette, France
| | - Olga O. Lebedenko
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Lea Marie Becker
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria
| | - Isabel Ayala
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044 Grenoble, France
| | - Roman Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
| | - Nikolai R. Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034, Russia
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
| | - Paul Schanda
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria
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4
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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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5
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Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nat Commun 2022; 13:1927. [PMID: 35395851 PMCID: PMC8993905 DOI: 10.1038/s41467-022-29423-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/14/2022] [Indexed: 02/07/2023] Open
Abstract
Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution.
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Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
- ICSN, CNRS UPR2301, Univ. Paris-Saclay, Gif-sur-Yvette, France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
- Celonic AG, Eulerstrasse 55, 4051, Basel, Switzerland
| | - Duccio Malinverni
- Department of Structural Biology and Center for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
- Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- i3S, Instituto de Investigacao e Inovacao em Saude, Universidade do Porto, Porto, Portugal
| | - Matteo Paloni
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Iva Sučec
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France
| | - Juan Pablo Bustamante
- Instituto de Bioingenieria y Bioinformatica, IBB (CONICET-UNER), Oro Verde, Entre Rios, Argentina
| | - Alessandro Barducci
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, F-38044, Grenoble, France.
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.
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6
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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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7
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Malär AA, Callon M, Smith AA, Wang S, Lecoq L, Pérez-Segura C, Hadden-Perilla JA, Böckmann A, Meier BH. Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR. Front Mol Biosci 2022; 8:807577. [PMID: 35047563 PMCID: PMC8762115 DOI: 10.3389/fmolb.2021.807577] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 01/14/2023] Open
Abstract
Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from 240 copies of the Cp149 core protein. We measure both T1 and T1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.
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Affiliation(s)
| | | | - Albert A Smith
- Institute of Medical Physics and Biophysics, Universität Leipzig, Leipzig, Germany
| | - Shishan Wang
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Jodi A Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS-Université de Lyon, Labex Ecofect, Lyon, France
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Zürich, Switzerland
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8
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Xue K, Nimerovsky E, Tekwani Movellan KA, Becker S, Andreas LB. Backbone Torsion Angle Determination Using Proton Detected Magic-Angle Spinning Nuclear Magnetic Resonance. J Phys Chem Lett 2022; 13:18-24. [PMID: 34957837 PMCID: PMC8762656 DOI: 10.1021/acs.jpclett.1c03267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Protein torsion angles define the backbone secondary structure of proteins. Magic-angle spinning (MAS) NMR methods using carbon detection have been developed to measure torsion angles by determining the relative orientation between two anisotropic interactions─dipolar coupling or chemical shift anisotropy. Here we report a new proton-detection based method to determine the backbone torsion angle by recoupling NH and CH dipolar couplings within the HCANH pulse sequence, for protonated or partly deuterated samples. We demonstrate the efficiency and precision of the method with microcrystalline chicken α spectrin SH3 protein and the influenza A matrix 2 (M2) membrane protein, using 55 or 90 kHz MAS. For M2, pseudo-4D data detect a turn between transmembrane and amphipathic helices.
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9
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China
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10
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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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11
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Abstract
Relaxation in nuclear magnetic resonance is a powerful method for obtaining spatially resolved, timescale-specific dynamics information about molecular systems. However, dynamics in biomolecular systems are generally too complex to be fully characterized based on NMR data alone. This is a familiar problem, addressed by the Lipari-Szabo model-free analysis, a method that captures the full information content of NMR relaxation data in case all internal motion of a molecule in solution is sufficiently fast. We investigate model-free analysis, as well as several other approaches, and find that model-free, spectral density mapping, LeMaster's approach, and our detector analysis form a class of analysis methods, for which behavior of the fitted parameters has a well-defined relationship to the distribution of correlation times of motion, independent of the specific form of that distribution. In a sense, they are all "model-free." Of these methods, only detectors are generally applicable to solid-state NMR relaxation data. We further discuss how detectors may be used for comparison of experimental data to data extracted from molecular dynamics simulation, and how simulation may be used to extract details of the dynamics that are not accessible via NMR, where detector analysis can be used to connect those details to experiments. We expect that combined methodology can eventually provide enough insight into complex dynamics to provide highly accurate models of motion, thus lending deeper insight into the nature of biomolecular dynamics.
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Affiliation(s)
- Kai Zumpfe
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Albert A Smith
- Institute for Medical Physics and Biophysics, Medical Faculty, Leipzig University, Leipzig, Germany
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12
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Gelenter MD, Chen KJ, Hong M. Off-resonance 13C- 2H REDOR NMR for site-resolved studies of molecular motion. JOURNAL OF BIOMOLECULAR NMR 2021; 75:335-345. [PMID: 34342847 PMCID: PMC8830769 DOI: 10.1007/s10858-021-00377-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/19/2021] [Indexed: 06/06/2023]
Abstract
We introduce a 13C-2H Rotational Echo DOuble Resonance (REDOR) technique that uses the difference between on-resonance and off-resonance 2H irradiation to detect dynamic segments in deuterated molecules. By selectively inverting specific regions of the 2H magic-angle spinning (MAS) sideband manifold to recouple some of the deuterons to nearby carbons, we distinguish dynamic and rigid residues in 1D and 2D 13C spectra. We demonstrate this approach on deuterated GB1, H/D exchanged GB1, and perdeuterated bacterial cellulose. Numerical simulations reproduce the measured mixing-time and 2H carrier-frequency dependence of the REDOR dephasing of bacterial cellulose. Combining numerical simulations with experiments thus allow the extraction of motionally averaged quadrupolar couplings from REDOR dephasing values.
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Affiliation(s)
- Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA
| | - Kelly J Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, MA, 02139, Cambridge, USA.
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13
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Adiram-Filiba N, Ohaion E, Verner G, Schremer A, Nadav-Tsubery M, Lublin-Tennenbaum T, Keinan-Adamsky K, Lucci M, Luchinat C, Ravera E, Goobes G. Structure and Dynamics Perturbations in Ubiquitin Adsorbed or Entrapped in Silica Materials Are Related to Disparate Surface Chemistries Resolved by Solid-State NMR Spectroscopy. Biomacromolecules 2021; 22:3718-3730. [PMID: 34333966 DOI: 10.1021/acs.biomac.1c00495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein immobilization on material surfaces is emerging as a powerful tool in the design of devices and active materials for biomedical and pharmaceutical applications as well as for catalysis. Preservation of the protein's biological functionality is crucial to the design process and is dependent on the ability to maintain its structural and dynamical integrity while removed from the natural surroundings. The scientific techniques to validate the structure of immobilized proteins are scarce and usually provide limited information as a result of poor resolution. In this work, we benchmarked the ability of standard solid-state NMR techniques to resolve the effects of binding to dissimilar silica materials on a model protein. In particular, the interactions between ubiquitin and the surfaces of MCM41, SBA15, and silica formed in situ were tested for their influence on the structure and dynamics of the protein. It is shown that the protein's globular fold in the free state is only slightly perturbed in the three silica materials. Local motions on a residue level that are quenched by immobilization or, conversely, that arise from the process are also detailed. NMR measurements show that these perturbations are unique to each silica material and can serve as reporters of the characteristic surface chemistry.
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Affiliation(s)
| | - Eli Ohaion
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Gilit Verner
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Avital Schremer
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | | | | | | | - Massimo Lucci
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Gil Goobes
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
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14
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Aebischer K, Tošner Z, Ernst M. Effects of radial radio-frequency field inhomogeneity on MAS solid-state NMR experiments. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:523-543. [PMID: 37904774 PMCID: PMC10539735 DOI: 10.5194/mr-2-523-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/14/2021] [Indexed: 11/01/2023]
Abstract
Radio-frequency field inhomogeneity is one of the most common imperfections in NMR experiments. They can lead to imperfect flip angles of applied radio-frequency (rf) pulses or to a mismatch of resonance conditions, resulting in artefacts or degraded performance of experiments. In solid-state NMR under magic angle spinning (MAS), the radial component becomes time-dependent because the rf irradiation amplitude and phase is modulated with integer multiples of the spinning frequency. We analyse the influence of such time-dependent MAS-modulated rf fields on the performance of some commonly used building blocks of solid-state NMR experiments. This analysis is based on analytical Floquet calculations and numerical simulations, taking into account the time dependence of the rf field. We find that, compared to the static part of the rf field inhomogeneity, such time-dependent modulations play a very minor role in the performance degradation of the investigated typical solid-state NMR experiments.
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Affiliation(s)
- Kathrin Aebischer
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Zdeněk Tošner
- Department of Chemistry, Faculty of Science, Charles University, Hlavova 8, 12842 Prague 2, Czech Republic
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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15
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Daskalov A, El Mammeri N, Lends A, Shenoy J, Lamon G, Fichou Y, Saad A, Martinez D, Morvan E, Berbon M, Grélard A, Kauffmann B, Ferber M, Bardiaux B, Habenstein B, Saupe SJ, Loquet A. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective. Front Mol Neurosci 2021; 14:670513. [PMID: 34276304 PMCID: PMC8280340 DOI: 10.3389/fnmol.2021.670513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
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Affiliation(s)
- Asen Daskalov
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Nadia El Mammeri
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Alons Lends
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | | | - Gaelle Lamon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Yann Fichou
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Ahmad Saad
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Denis Martinez
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Estelle Morvan
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | - Melanie Berbon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Axelle Grélard
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Brice Kauffmann
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | | | | | | | - Sven J. Saupe
- CNRS, IBGC UMR 5095, University of Bordeaux, Bordeaux, France
| | - Antoine Loquet
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
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16
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Ji Y, Liang L, Bao X, Hou G. Recent progress in dipolar recoupling techniques under fast MAS in solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 112:101711. [PMID: 33508579 DOI: 10.1016/j.ssnmr.2020.101711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
With the recent advances in NMR hardware and probe design technology, magic-angle spinning (MAS) rates over 100 kHz are accessible now, even on commercial solid NMR probes. Under such fast MAS conditions, excellent spectral resolution has been achieved by efficient suppression of anisotropic interactions, which also opens an avenue to the proton-detected NMR experiments in solids. Numerous methods have been developed to take full advantage of fast MAS during the last decades. Among them, dipolar recoupling techniques under fast MAS play vital roles in the determination of the molecular structure and dynamics, and are also key elements in multi-dimensional correlation NMR experiments. Herein, we review the dipolar recoupling techniques, especially those developed in the past two decades for fast-to-ultrafast MAS conditions. A major focus for our discussion is the ratio of RF field strength (in frequency) to MAS frequency, ν1/νr, in different pulse sequences, which determines whether these dipolar recoupling techniques are suitable for NMR experiments under fast MAS conditions. Systematic comparisons are made among both heteronuclear and homonuclear dipolar recoupling schemes. In addition, the schemes developed specially for proton-detection NMR experiments under ultrafast MAS conditions are highlighted as well.
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Affiliation(s)
- Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinhe Bao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, China.
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17
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Zhang X, Forster MC, Nimerovsky E, Movellan KT, Andreas LB. Transferred-Rotational-Echo Double Resonance. J Phys Chem A 2021; 125:754-769. [PMID: 33464081 PMCID: PMC7884007 DOI: 10.1021/acs.jpca.0c09033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/11/2020] [Indexed: 12/21/2022]
Abstract
Internuclear distance determination is the foundation for NMR-based structure calculation. However, high-precision distance measurement is a laborious process requiring lengthy data acquisitions due to the large set of multidimensional spectra needed at different mixing times. This prevents application to large or challenging molecular systems. Here, we present a new approach, transferred-rotational-echo double resonance (TREDOR), a heteronuclear transfer method in which we simultaneously detect both starting and transferred signals in a single spectrum. This co-acquisition is used to compensate for coherence decay, resulting in accurate and precise distance determination by a single parameter fit using a single spectrum recorded at an ideal mixing time. We showcase TREDOR with the microcrystalline SH3 protein using 3D spectra to resolve resonances. By combining the measured N-C and H-C distances, we calculate the structure of SH3, which converges to the correct fold, with a root-mean-square deviation of 2.1 Å compared to a reference X-ray structure. The TREDOR data used in the structure calculation were acquired in only 4 days on a 600 MHz instrument. This is achieved due to the more than 2-fold time saving afforded by co-acquisition of additional information and demonstrates TREDOR as a fast and straightforward method for determining structures via magic-angle spinning NMR.
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Affiliation(s)
| | | | - Evgeny Nimerovsky
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Kumar Tekwani Movellan
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Loren B. Andreas
- NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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18
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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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19
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Vallet A, Favier A, Brutscher B, Schanda P. ssNMRlib: a comprehensive library and tool box for acquisition of solid-state nuclear magnetic resonance experiments on Bruker spectrometers. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:331-345. [PMID: 37904819 PMCID: PMC10500710 DOI: 10.5194/mr-1-331-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/16/2020] [Indexed: 11/01/2023]
Abstract
We introduce ssNMRlib, a comprehensive suite of pulse sequences and jython scripts for user-friendly solid-state nuclear magnetic resonance (NMR) data acquisition, parameter optimization and storage on Bruker spectrometers. ssNMRlib allows the straightforward setup of even highly complex multi-dimensional solid-state NMR experiments with a few clicks from an intuitive graphical interface directly from the Bruker Topspin acquisition software. ssNMRlib allows the setup of experiments in a magnetic-field-independent manner and thus facilitates the workflow in a multi-spectrometer setting with a centralized library. Safety checks furthermore assist the user in experiment setup. Currently hosting more than 140 1D to 4D experiments, primarily for biomolecular solid-state NMR, the library can be easily customized and new experiments are readily added as new templates. ssNMRlib is part of the previously introduced NMRlib library, which comprises many solution-NMR pulse sequences and macros.
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Affiliation(s)
- Alicia Vallet
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Adrien Favier
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Bernhard Brutscher
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, Avenue des Martyrs, 38044 Grenoble, France
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20
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Nimerovsky E, Soutar CP. A modification of γ-encoded RN symmetry pulses for increasing the scaling factor and more accurate measurements of the strong heteronuclear dipolar couplings. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 319:106827. [PMID: 32950918 DOI: 10.1016/j.jmr.2020.106827] [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: 05/02/2019] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Symmetry based γ-encoded RNnν elements are broadly used in magic-angle spinning solid-state NMR experiments to achieve selective recoupling of the heteronuclear dipolar interactions. The recoupled dipolar couplings in such experiments are scaled by a factor, Ksc, which theoretically depends on the chosen symmetry numbers N, n, and ν. However, the maximum theoretical value of Ksc for γ-encoded RNnν pulses is limited to ~0.25, resulting in long RNnν experiment times. Also, the dependence of Ksc on the experimental parameters can result in systematic errors in the experimental determination of the dipolar couplings, especially at low and moderate MAS rates. In this manuscript, we investigate the use of MODifiEd RNnν symmetry (MODERNnν(ϕM)) pulses that increase the dipolar scaling factor by at least 1.45 fold compared to γ-encoded RNnν. The second advantage of MODERNnν(ϕM) pulses with respect to traditional RNnν pulses is the reduced influence of experimental parameters on Ksc, which allows for more accurate measurement of short-range distances. The robustness of MODERNnν(ϕM) is compared with γ-encoded R1423 symmetry pulses. The enhanced performance is demonstrated on two uniformly-13C-enriched samples, N-acetyl valine and the microcrystalline protein GB1, at a 31.111 kHz MAS rate.
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Affiliation(s)
- Evgeny Nimerovsky
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Corinne P Soutar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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21
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Sala BM, Le Marchand T, Pintacuda G, Camilloni C, Natalello A, Ricagno S. Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution. Biophys J 2020; 119:978-988. [PMID: 32758421 DOI: 10.1016/j.bpj.2020.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 11/29/2022] Open
Abstract
A growing body of evidences has established that in many cases proteins may preserve most of their function and flexibility in a crystalline environment, and several techniques are today capable to characterize molecular properties of proteins in tightly packed lattices. Intriguingly, in the case of amyloidogenic precursors, the presence of transiently populated states (hidden to conventional crystallographic studies) can be correlated to the pathological fate of the native fold; the low fold stability of the native state is a hallmark of aggregation propensity. It remains unclear, however, to which extent biophysical properties of proteins such as the presence of transient conformations or protein stability characterized in crystallo reflect the protein behavior that is more commonly studied in solution. Here, we address this question by investigating some biophysical properties of a prototypical amyloidogenic system, β2-microglobulin in solution and in microcrystalline state. By combining NMR chemical shifts with molecular dynamics simulations, we confirmed that conformational dynamics of β2-microglobulin native state in the crystal lattice is in keeping with what observed in solution. A comparative study of protein stability in solution and in crystallo is then carried out, monitoring the change in protein secondary structure at increasing temperature by Fourier transform infrared spectroscopy. The increased structural order of the crystalline state contributes to provide better resolved spectral components compared to those collected in solution and crucially, the crystalline samples display thermal stabilities in good agreement with the trend observed in solution. Overall, this work shows that protein stability and occurrence of pathological hidden states in crystals parallel their solution counterpart, confirming the interest of crystals as a platform for the biophysical characterization of processes such as unfolding and aggregation.
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Affiliation(s)
| | - Tanguy Le Marchand
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon), Université de Lyon, Villeurbanne, France
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (FRE 2034 CNRS, UCBL, ENS Lyon), Université de Lyon, Villeurbanne, France
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.
| | - Stefano Ricagno
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
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22
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Grohe K, Patel S, Hebrank C, Medina S, Klein A, Rovó P, Vasa SK, Singh H, Vögeli B, Schäfer LV, Linser R. Protein Motional Details Revealed by Complementary Structural Biology Techniques. Structure 2020; 28:1024-1034.e3. [PMID: 32579946 DOI: 10.1016/j.str.2020.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/05/2020] [Accepted: 06/03/2020] [Indexed: 01/16/2023]
Abstract
Proteins depend on defined molecular plasticity for their functionality. How to comprehensively capture dynamics correctly is of ubiquitous biological importance. Approaches commonly used to probe protein dynamics include model-free elucidation of site-specific motion by NMR relaxation, molecular dynamics (MD)-based approaches, and capturing the substates within a dynamic ensemble by recent eNOE-based multiple-structure approaches. Even though MD is sometimes combined with ensemble-averaged NMR restraints, these approaches have largely been developed and used individually. Owing to the different underlying concepts and practical requirements, it has remained unclear how they compare, and how they cross-validate and complement each other. Here, we extract and compare the differential information contents of MD simulations, NMR relaxation measurements, and eNOE-based multi-state structures for the SH3 domain of chicken α-spectrin. The data show that a validated, consistent, and detailed picture is feasible both for timescales and actual conformational states sampled in the dynamic ensemble. This includes the biologically important side-chain plasticity, for which experimentally cross-validated assessment is a significant challenge.
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Affiliation(s)
- Kristof Grohe
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Snehal Patel
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Cornelia Hebrank
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Sara Medina
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Alexander Klein
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Petra Rovó
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Suresh K Vasa
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Himanshu Singh
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Lars V Schäfer
- Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Rasmus Linser
- Faculty for Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227 Dortmund, Germany.
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23
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Siemer AB. Advances in studying protein disorder with solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 106:101643. [PMID: 31972419 PMCID: PMC7202078 DOI: 10.1016/j.ssnmr.2020.101643] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 05/26/2023]
Abstract
Solution NMR is a key tool to study intrinsically disordered proteins (IDPs), whose importance for biological function is widely accepted. However, disordered proteins are not limited to solution and are also found in non-soluble systems such as fibrils and membrane proteins. In this Trends article, I will discuss how solid-state NMR can be used to study disorder in non-soluble proteins. Techniques based on dipolar couplings can study static protein disorder which either occurs naturally as e.g. in spider silk or can be induced by freeze trapping IDPs or unfolded proteins. In this case, structural ensembles are directly reflected by a static distribution of dihedral angels that can be determined by the distribution of chemical shifts or other methods. Techniques based on J-couplings can detect dynamic protein disorder under MAS. In this case, only average chemical shifts are measured but disorder can be characterized with a variety of data including secondary chemical shifts, relaxation rates, paramagnetic relaxation enhancements, or residual dipolar couplings. I describe both technical aspects and examples of solid-state NMR on protein disorder and end the article with a discussion of challenges and opportunities of this emerging field.
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Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Univeristy of Southern California, 1501 San Pablo Street, Los Angeles, CA, 90033, USA.
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24
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Jain MG, Rajalakshmi G, Madhu PK, Agarwal V, Mote KR. Overcoming Prohibitively Large Radiofrequency Demands for the Measurement of Internuclear Distances with Solid-State NMR under Fast Magic-Angle Spinning. J Phys Chem B 2020; 124:1444-1451. [DOI: 10.1021/acs.jpcb.9b11849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Mukul G. Jain
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
| | - G. Rajalakshmi
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
| | - P. K. Madhu
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
| | - Kaustubh R. Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad, Telangana 500107, India
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25
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Mance D, Comas-Vives A, Copéret C. Proton-Detected Multidimensional Solid-State NMR Enables Precise Characterization of Vanadium Surface Species at Natural Abundance. J Phys Chem Lett 2019; 10:7898-7904. [PMID: 31770488 DOI: 10.1021/acs.jpclett.9b02872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Heterogeneous catalysts fulfill vital roles in industrial processes; however, the nature of the catalytic surfaces, typically either containing a low abundance of active sites or being amorphous in nature, leads to difficulties when attempting to study the structure of the active sites. In this work, we show how making use of fast MAS ssNMR allows one to efficiently detect well-resolved 1H-detected spectra of heterogeneous catalysts. This approach was applied to study the structure of surface species resulting from the grafting of VO(OiPr)3 onto a partially dehydroxylated silica using the surface organometallic chemistry approach. The use of 1H sensitivity enabled detection of various hetero- and homonuclear correlation spectra in order to study the structure of this system and to resolve the structure of the grafted vanadium complex. More specifically, VO(OiPr)3 grafts through both protonolysis and opening of siloxane bridges to generate a bis-grafted species.
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Affiliation(s)
- Deni Mance
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog Weg 1-5 , CH-8093 Zürich , Switzerland
| | - Aleix Comas-Vives
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog Weg 1-5 , CH-8093 Zürich , Switzerland
| | - Christophe Copéret
- Department of Chemistry and Applied Biosciences , ETH Zürich , Vladimir-Prelog Weg 1-5 , CH-8093 Zürich , Switzerland
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26
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Jain MG, Rajalakshmi G, Agarwal V, Madhu PK, Mote KR. On the direct relation between REDOR and DIPSHIFT experiments in solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106563. [PMID: 31353014 DOI: 10.1016/j.jmr.2019.07.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
Rotational-echo double resonance (REDOR) and Dipolar-coupling chemical-shift correlation (DIPSHIFT) are commonly used experiments to probe heteronuclear dipole-dipole couplings between isolated pairs of spin-12 nuclei in magic-angle-spinning (MAS) solid-state NMR. Their widespread use is due to their robustness to experimental imperfections and a straightforward interpretation of data. Both of these experiments use rotor-synchronised π pulses to recouple the heteronuclear dipole-dipole couplings, and the observed intensity of resonances is modulated by a recoupled phase factor depending on the position or duration of the recoupling pulses. Several modifications to both of these experiments have been proposed, for example, the development of DIPSHIFT which employs strategies that mimic the multi-rotor-period nature of REDOR. We show here that REDOR and DIPSHIFT are in fact alternate implementations of the same experiment. The overt similarity in the design of REDOR and DIPSHIFT is also reflected in their theoretical description. Dipolar dephasing curves in REDOR are obtained by increasing the recoupling duration whilst keeping the position of the pulses constant, which results in a dephasing factor that is a function of only the dephasing time. DIPSHIFT, on the other hand, is a constant-time version of REDOR; the dipolar dephasing is a function of the position of the pulses with respect to the rotor period. We discuss the advantages and disadvantages of each implementation and suggest domains of applicability for these sequences.
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Affiliation(s)
- Mukul G Jain
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India
| | - G Rajalakshmi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India.
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Serilingampally, Hyderabad 500107, Telangana, India.
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27
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Xue K, Mamone S, Koch B, Sarkar R, Reif B. Determination of methyl order parameters using solid state NMR under off magic angle spinning. JOURNAL OF BIOMOLECULAR NMR 2019; 73:471-475. [PMID: 31407204 DOI: 10.1007/s10858-019-00253-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/07/2019] [Indexed: 06/10/2023]
Abstract
Quantification of dipolar couplings in biological solids is important for the understanding of dynamic processes. Under Magic Angle Spinning (MAS), order parameters are normally obtained by recoupling of anisotropic interactions involving the application of radio frequency pulses. We have recently shown that amide backbone order parameters can be estimated accurately in a spin-echo experiment in case the rotor spinning angle is slightly mis-calibrated. In this work, we apply this method to determine methyl order parameters in a deuterated sample of the SH3 domain of chicken α-spectrin in which the methyl containing side chains valine and leucine are selectively protonated.
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Affiliation(s)
- Kai Xue
- 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
| | - Salvatore Mamone
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Benita Koch
- 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
| | - 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.
| | - 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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28
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Barnes CA, Robertson AJ, Louis JM, Anfinrud P, Bax A. Observation of β-Amyloid Peptide Oligomerization by Pressure-Jump NMR Spectroscopy. J Am Chem Soc 2019; 141:13762-13766. [DOI: 10.1021/jacs.9b06970] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- C. Ashley Barnes
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J. Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Philip Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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29
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Smith AA, Ernst M, Riniker S, Meier BH. Localized and Collective Motions in HET-s(218-289) Fibrils from Combined NMR Relaxation and MD Simulation. Angew Chem Int Ed Engl 2019; 58:9383-9388. [PMID: 31070275 PMCID: PMC6618077 DOI: 10.1002/anie.201901929] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/17/2019] [Indexed: 12/20/2022]
Abstract
Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET-s(218-289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale-specific information. An analogous analysis is performed on MD trajectories. Because specific MD predictions can be verified as agreeing with the NMR data, MD was used for further interpretation of NMR results: for the different timescales, cross-correlation coefficients were derived to quantify the correlation of the motion between different residues. Short timescales are the result of very local motions, while longer timescales are found for longer-range correlated motion. Similar trends on ns- and μs-timescales suggest that μs motion in fibrils is the result of motion correlated over many fibril layers.
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Affiliation(s)
- Albert A. Smith
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 28093ZurichSwitzerland
- Present address: Institut für Medizinische Physik und BiophysikUniversität LeipzigHärtelstraße 16–1804107LeipzigGermany
| | - Matthias Ernst
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 28093ZurichSwitzerland
| | - Sereina Riniker
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 28093ZurichSwitzerland
| | - Beat H. Meier
- Physical ChemistryETH ZurichVladimir-Prelog-Weg 28093ZurichSwitzerland
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30
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Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific 1H- 13C Labeling and Fast Magic-Angle Spinning NMR. J Am Chem Soc 2019; 141:11183-11195. [PMID: 31199882 DOI: 10.1021/jacs.9b04219] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize the dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artifact-free dynamics measurements, and allows probing motions effectively without molecular weight limitations. The application to the TET2 enzyme assembly of ∼0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (picoseconds to milliseconds). We quantitatively probe ring-flip motions and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as the exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.
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Affiliation(s)
- Diego F Gauto
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Pavel Macek
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Alessandro Barducci
- Centre de Biochimie Structurale (CBS) , INSERM, CNRS, Université de Montpellier , Montpellier , France
| | - Hugo Fraga
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France.,Departamento de Biomedicina , Faculdade de Medicina da Universidade do Porto , Porto , Portugal.,i3S, Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal
| | - Audrey Hessel
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Tsutomu Terauchi
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,SI Innovation Center , Taiyo Nippon Sanso Corp. , 2008-2 Wada , Tama-city , Tokyo 206-0001 , Japan
| | - David Gajan
- Université de Lyon , Centre de RMN à Hauts Champs de Lyon CRMN, FRE 2034, Université de Lyon, CNRS, ENS Lyon, UCB Lyon 1 , 69100 Villeurbanne , France
| | - Yohei Miyanoiri
- Institute of Protein Research , Osaka University , 3-2 Yamadaoka , Suita , Osaka 565-0871 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Jerome Boisbouvier
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
| | - Roman Lichtenecker
- Institute of Organic Chemistry , University of Vienna , Währinger Str. 38 , 1090 Vienna , Austria
| | - Masatsune Kainosho
- Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-ohsawa , Hachioji , Tokyo 192-0397 , Japan.,Structural Biology Research Center, Graduate School of Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - Paul Schanda
- Univ. Grenoble Alpes, CEA, CNRS , Institut de Biologie Structurale (IBS) , 71, avenue des martyrs , F-38044 Grenoble , France
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31
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Smith AA, Ernst M, Riniker S, Meier BH. Localized and Collective Motions in HET‐s(218‐289) Fibrils from Combined NMR Relaxation and MD Simulation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Albert A. Smith
- Physical ChemistryETH Zurich Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
- Present address: Institut für Medizinische Physik und BiophysikUniversität Leipzig Härtelstraße 16–18 04107 Leipzig Germany
| | - Matthias Ernst
- Physical ChemistryETH Zurich Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Sereina Riniker
- Physical ChemistryETH Zurich Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Beat H. Meier
- Physical ChemistryETH Zurich Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
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32
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Xue K, Mühlbauer M, Mamone S, Sarkar R, Reif B. Accurate Determination of
1
H‐
15
N Dipolar Couplings Using Inaccurate Settings of the Magic Angle in Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und Umwelt Ingolstädter Landstr. 1 85764 Neuherberg Germany
| | - Max Mühlbauer
- Helmholtz-Zentrum München (HMGU)Deutsches Forschungszentrum für Gesundheit und Umwelt Ingolstädter Landstr. 1 85764 Neuherberg Germany
| | - Salvatore Mamone
- Max Planck Institute for Biophysical Chemistry Göttingen 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), Department ChemieTechnische Universität München (TUM) Lichtenbergstr. 4 85747 Garching Germany
| | - 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), Department ChemieTechnische Universität München (TUM) Lichtenbergstr. 4 85747 Garching Germany
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33
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Xue K, Mühlbauer M, Mamone S, Sarkar R, Reif B. Accurate Determination of 1 H- 15 N Dipolar Couplings Using Inaccurate Settings of the Magic Angle in Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2019; 58:4286-4290. [PMID: 30694593 DOI: 10.1002/anie.201814314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Indexed: 11/10/2022]
Abstract
Magic-angle spinning (MAS) is an essential ingredient in a wide variety of solid-state NMR experiments. The standard procedures to adjust the rotor angle are not highly accurate, resulting in a slight misadjustment of the rotor from the magic angle ( θ R L = tan - 1 2 ) on the order of a few millidegrees. This small missetting has no significant impact on the overall spectral resolution, but is sufficient to reintroduce anisotropic interactions. Shown here is that site-specific 1 H-15 N dipolar couplings can be accurately measured in a heavily deuterated protein. This method can be applied at arbitrarily high MAS frequencies, since neither rotor synchronization nor particularly high radiofrequency field strengths are required. The off-MAS method allows the quantification of order parameters for very dynamic residues, which often escape an analysis using existing methods.
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Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Max Mühlbauer
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Salvatore Mamone
- Max Planck Institute for Biophysical Chemistry, Göttingen, 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), Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - 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), Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
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34
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Penzel S, Oss A, Org ML, Samoson A, Böckmann A, Ernst M, Meier BH. Spinning faster: protein NMR at MAS frequencies up to 126 kHz. JOURNAL OF BIOMOLECULAR NMR 2019; 73:19-29. [PMID: 30680507 PMCID: PMC6441448 DOI: 10.1007/s10858-018-0219-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 12/05/2018] [Indexed: 05/05/2023]
Abstract
We report linewidth and proton T1, T1ρ and T2' relaxation data of the model protein ubiquitin acquired at MAS frequencies up to 126 kHz. We find a predominantly linear improvement in linewidths and coherence decay times of protons with increasing spinning frequency in the range from 93 to 126 kHz. We further attempt to gain insight into the different contributions to the linewidth at fast MAS using site-specific analysis of proton relaxation parameters and present bulk relaxation times as a function of the MAS frequency. For microcrystalline fully-protonated ubiquitin, inhomogeneous contributions are only a minor part of the proton linewidth, and at 126 kHz MAS coherent effects are still dominating. We furthermore present site-specific proton relaxation rate constants during a spinlock at 126 kHz MAS, as well as MAS-dependent bulk T1ρ (1HN).
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Affiliation(s)
- Susanne Penzel
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Andres Oss
- NMR Instituut, Tartu Teaduspark, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia
| | - Mai-Liis Org
- NMR Instituut, Tartu Teaduspark, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia
| | - Ago Samoson
- NMR Instituut, Tartu Teaduspark, Tehnomeedikum, Tallinn University of Technology, Akadeemia tee 15a, 19086, Tallinn, Estonia.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/Université de Lyon 1, Labex ECOFECT, 7, Passage du Vercors, 69367, Lyon, France.
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
| | - Beat H Meier
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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35
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Caulkins BG, Cervantes SA, Isas JM, Siemer AB. Dynamics of the Proline-Rich C-Terminus of Huntingtin Exon-1 Fibrils. J Phys Chem B 2018; 122:9507-9515. [PMID: 30252478 DOI: 10.1021/acs.jpcb.8b09213] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Intrinsically disordered protein domains not only are found in soluble proteins but also can be part of large protein complexes or protein aggregates. For example, several amyloid fibrils have intrinsically disordered domains framing a rigid β-sheet-rich core. These disordered domains can often be observed using solution NMR methods in combination with modest magic angle spinning and without perdeuteration. But how can these regions be detected using solution NMR methods when they are part of a fibril that is not tumbling isotropically in solution? Here we addressed this question by investigating the dynamic C-terminus of huntingtin exon-1 (HTTex1) fibrils that are important in Huntington's disease. We assigned the most dynamic regions of the C-terminus of three HTTex1 variants. On the basis of this assignment, we measured site-specific secondary chemical shifts, peak intensities, and R1, R'2, and R1ρ 15N relaxation rates. In addition, we determined the residual 1H-15N dipolar couplings of this region. Our results show that the dipolar couplings are averaged to a very high degree, resulting in an order parameter that is essentially zero. Together, our data show that the C-terminus of HTTex1 is intrinsically disordered and undergoes motions in the high picosecond to low nanosecond range.
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Affiliation(s)
- Bethany G Caulkins
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute , Keck School of Medicine of USC , 1501 San Pablo St. , Los Angeles , California 90033 , United States
| | - Silvia A Cervantes
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute , Keck School of Medicine of USC , 1501 San Pablo St. , Los Angeles , California 90033 , United States
| | - J Mario Isas
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute , Keck School of Medicine of USC , 1501 San Pablo St. , Los Angeles , California 90033 , United States
| | - Ansgar B Siemer
- Department of Physiology & Neuroscience, Zilkha Neurogenetic Institute , Keck School of Medicine of USC , 1501 San Pablo St. , Los Angeles , California 90033 , United States
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36
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Paluch P, Pawlak T, Ławniczak K, Trébosc J, Lafon O, Amoureux JP, Potrzebowski MJ. Simple and Robust Study of Backbone Dynamics of Crystalline Proteins Employing 1H- 15N Dipolar Coupling Dispersion. J Phys Chem B 2018; 122:8146-8156. [PMID: 30070484 DOI: 10.1021/acs.jpcb.8b04557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new solid-state multidimensional NMR approach based on the cross-polarization with variable-contact pulse sequence [ Paluch , P. ; Pawlak , T. ; Amoureux , J.-P. ; Potrzebowski , M. J. J. Magn. Reson. 233 , 2013 , 56 ], with 1H inverse detection and very fast magic angle spinning (νR = 60 kHz), dedicated to the measurement of local molecular motions of 1H-15N vectors. The introduced three-dimensional experiments, 1H-15N-1H and hCA(N)H, are particularly useful for the study of molecular dynamics of proteins and other complex structures. The applicability and power of this methodology have been revealed by employing as a model sample the GB-1 small protein doped with Na2CuEDTA. The results clearly prove that the dispersion of 1H-15N dipolar coupling constants well correlates with higher order structure of the protein. Our approach complements the conventional studies and offers a fast and reasonably simple method.
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Affiliation(s)
- Piotr Paluch
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland
| | - Karol Ławniczak
- Department of Theoretical Physics, Faculty of Physics and Applied Informatics , University of Łódź , Pomorska 149/153 , PL-90236 Łódź , Poland
| | - Julien Trébosc
- Unit of Catalysis and Chemistry of Solids (UCCS) , Univ. Lille, UMR 8181 , F-59000 Lille , France
| | - Olivier Lafon
- Unit of Catalysis and Chemistry of Solids (UCCS) , Univ. Lille, UMR 8181 , F-59000 Lille , France
| | - Jean-Paul Amoureux
- Unit of Catalysis and Chemistry of Solids (UCCS) , Univ. Lille, UMR 8181 , F-59000 Lille , France.,Bruker France , 34 rue de l'Industrie , F-67166 Wissembourg , France
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland
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37
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Smith AA, Ernst M, Meier BH. Optimized "detectors" for dynamics analysis in solid-state NMR. J Chem Phys 2018; 148:045104. [PMID: 29390848 DOI: 10.1063/1.5013316] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Relaxation in nuclear magnetic resonance (NMR) results from stochastic motions that modulate anisotropic NMR interactions. Therefore, measurement of relaxation-rate constants can be used to characterize molecular-dynamic processes. The motion is often characterized by Markov processes using an auto-correlation function, which is assumed to be a sum of multiple decaying exponentials. We have recently shown that such a model can lead to severe misrepresentation of the real motion, when the real correlation function is more complex than the model. Furthermore, multiple distributions of motion may yield the same set of dynamics data. Therefore, we introduce optimized dynamics "detectors" to characterize motions which are linear combinations of relaxation-rate constants. A detector estimates the average or total amplitude of motion for a range of motional correlation times. The information obtained through the detectors is less specific than information obtained using an explicit model, but this is necessary because the information contained in the relaxation data is ambiguous, if one does not know the correct motional model. On the other hand, if one has a molecular dynamics trajectory, one may calculate the corresponding detector responses, allowing direct comparison to experimental NMR dynamics analysis. We describe how to construct a set of optimized detectors for a given set of relaxation measurements. We then investigate the properties of detectors for a number of different data sets, thus gaining an insight into the actual information content of the NMR data. Finally, we show an example analysis of ubiquitin dynamics data using detectors, using the DIFRATE software.
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Affiliation(s)
- Albert A Smith
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Matthias Ernst
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Beat H Meier
- ETH Zurich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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38
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Schubeis T, Le Marchand T, Andreas LB, Pintacuda G. 1H magic-angle spinning NMR evolves as a powerful new tool for membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 287:140-152. [PMID: 29413327 DOI: 10.1016/j.jmr.2017.11.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 06/08/2023]
Abstract
Building on a decade of continuous advances of the community, the recent development of very fast (60 kHz and above) magic-angle spinning (MAS) probes has revolutionised the field of solid-state NMR. This new spinning regime reduces the 1H-1H dipolar couplings, so that direct detection of the larger magnetic moment available from 1H is now possible at high resolution, not only in deuterated molecules but also in fully-protonated substrates. Such capabilities allow rapid "fingerprinting" of samples with a ten-fold reduction of the required sample amounts with respect to conventional approaches, and permit extensive, robust and expeditious assignment of small-to-medium sized proteins (up to ca. 300 residues), and the determination of inter-nuclear proximities, relative orientations of secondary structural elements, protein-cofactor interactions, local and global dynamics. Fast MAS and 1H detection techniques have nowadays been shown to be applicable to membrane-bound systems. This paper reviews the strategies underlying this recent leap forward in sensitivity and resolution, describing its potential for the detailed characterization of membrane proteins.
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Affiliation(s)
- Tobias Schubeis
- 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
| | - Tanguy Le Marchand
- 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
| | - Loren B Andreas
- 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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39
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Hellwagner J, Wili N, Ibáñez LF, Wittmann JJ, Meier BH, Ernst M. Transient effects in π-pulse sequences in MAS solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 287:65-73. [PMID: 29289819 DOI: 10.1016/j.jmr.2017.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
Dipolar recoupling techniques that use isolated rotor-synchronized π pulses are commonly used in solid-state NMR spectroscopy to gain insight into the structure of biological molecules. These sequences excel through their simplicity, stability towards radio-frequency (rf) inhomogeneity, and low rf requirements. For a theoretical understanding of such sequences, we present a Floquet treatment based on an interaction-frame transformation including the chemical-shift offset dependence. This approach is applied to the homonuclear dipolar-recoupling sequence Radio-Frequency Driven Recoupling (RFDR) and the heteronuclear recoupling sequence Rotational Echo Double Resonance (REDOR). Based on the Floquet approach, we show the influence of effective fields caused by pulse transients and discuss the advantages of pulse-transient compensation. We demonstrate experimentally that the transfer efficiency for homonuclear recoupling can be doubled in some cases in model compounds as well as in simple peptides if pulse-transient compensation is applied to the π pulses. Additionally, we discuss the influence of various phase cycles on the recoupling efficiency in order to reduce the magnitude of effective fields. Based on the findings from RFDR, we are able to explain why the REDOR sequence does not suffer in the recoupling efficiency despite the presence of effective fields.
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Affiliation(s)
- Johannes Hellwagner
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Nino Wili
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | | | - Johannes J Wittmann
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland.
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40
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Wittmann T, Mondal A, Tschense CBL, Wittmann JJ, Klimm O, Siegel R, Corzilius B, Weber B, Kaupp M, Senker J. Probing Interactions of N-Donor Molecules with Open Metal Sites within Paramagnetic Cr-MIL-101: A Solid-State NMR Spectroscopic and Density Functional Theory Study. J Am Chem Soc 2018; 140:2135-2144. [DOI: 10.1021/jacs.7b10148] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Thomas Wittmann
- Inorganic
Chemistry III, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Arobendo Mondal
- Institute
of Chemistry, Theoretical Chemistry/Quantum Chemistry, Technical University of Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Carsten B. L. Tschense
- Inorganic
Chemistry III, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Johannes J. Wittmann
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7-9, 60438 Frankfurt am Main, Germany
| | - Ottokar Klimm
- Inorganic
Chemistry II, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Renée Siegel
- Inorganic
Chemistry III, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Björn Corzilius
- Institute
of Physical and Theoretical Chemistry and Institute of Biophysical
Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7-9, 60438 Frankfurt am Main, Germany
| | - Birgit Weber
- Inorganic
Chemistry II, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - Martin Kaupp
- Institute
of Chemistry, Theoretical Chemistry/Quantum Chemistry, Technical University of Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Juergen Senker
- Inorganic
Chemistry III, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
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41
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Quinn CM, Wang M, Polenova T. NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology. Methods Mol Biol 2018; 1688:1-35. [PMID: 29151202 PMCID: PMC6217836 DOI: 10.1007/978-1-4939-7386-6_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
As a result of profound gains in sensitivity and resolution afforded by ultrahigh magnetic fields, transformative applications in the fields of structural biology and materials science are being realized. The development of dual low temperature superconducting (LTS)/high-temperature superconducting (HTS) magnets has enabled the achievement of magnetic fields above 1 GHz (23.5 T), which will open doors to an unprecedented new range of applications. In this contribution, we discuss the promise of ultrahigh field magnetic resonance. We highlight several methodological developments pertinent at high-magnetic fields including measurement of 1H-1H distances and 1H chemical shift anisotropy in the solid state as well as studies of quadrupolar nuclei such as 17O. Higher magnetic fields have advanced heteronuclear detection in solution NMR, valuable for applications including metabolomics and disordered proteins, as well as expanded use of proton detection in the solid state in conjunction with ultrafast magic angle spinning. We also present several recent applications to structural studies of the AP205 bacteriophage, the M2 channel from Influenza A, and biomaterials such as human bone. Gains in sensitivity and resolution from increased field strengths will enable advanced applications of NMR spectroscopy including in vivo studies of whole cells and intact virions.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, 036 Brown Laboratories, Newark, DE, 19716, USA.
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave, Pittsburgh, PA, 15261, USA.
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42
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Barbet-Massin E, van der Sluis E, Musial J, Beckmann R, Reif B. Reconstitution of Isotopically Labeled Ribosomal Protein L29 in the 50S Large Ribosomal Subunit for Solution-State and Solid-State NMR. Methods Mol Biol 2018; 1764:87-100. [PMID: 29605910 DOI: 10.1007/978-1-4939-7759-8_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Solid-state nuclear magnetic resonance (NMR) has recently emerged as a method of choice to study structural and dynamic properties of large biomolecular complexes at atomic resolution. Indeed, recent technological and methodological developments have enabled the study of ever more complex systems in the solid-state. However, to explore multicomponent protein complexes by NMR, specific labeling schemes need to be developed that are dependent on the biological question to be answered. We show here how to reconstitute an isotopically labeled protein within the unlabeled 50S or 70S ribosomal subunit. In particular, we focus on the 63-residue ribosomal protein L29 (~7 kDa), which is located at the exit of the tunnel of the large 50S ribosomal subunit (~1.5 MDa). The aim of this work is the preparation of a suitable sample to investigate allosteric conformational changes in a ribosomal protein that are induced by the nascent polypeptide chain and that trigger the interaction with different chaperones (e.g., trigger factor or SRP).
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Affiliation(s)
- Emeline Barbet-Massin
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Garching, Germany.,Dynamic Biosensors, Planegg, Germany
| | - Eli van der Sluis
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Bionanoscience, Faculty of Applied Sciences, TU Delft, Delft, The Netherlands
| | - Joanna Musial
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bernd Reif
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Garching, Germany. .,Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz-Zentrum München (HMGU), Neuherberg, Germany.
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43
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Gauto DF, Hessel A, Rovó P, Kurauskas V, Linser R, Schanda P. Protein conformational dynamics studied by 15N and 1H R 1ρ relaxation dispersion: Application to wild-type and G53A ubiquitin crystals. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:86-95. [PMID: 28438365 PMCID: PMC5531261 DOI: 10.1016/j.ssnmr.2017.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/01/2017] [Accepted: 04/12/2017] [Indexed: 05/12/2023]
Abstract
Solid-state NMR spectroscopy can provide site-resolved information about protein dynamics over many time scales. Here we combine protein deuteration, fast magic-angle spinning (~45-60kHz) and proton detection to study dynamics of ubiquitin in microcrystals, and in particular a mutant in a region that undergoes microsecond motions in a β-turn region in the wild-type protein. We use 15N R1ρ relaxation measurements as a function of the radio-frequency (RF) field strength, i.e. relaxation dispersion, to probe how the G53A mutation alters these dynamics. We report a population-inversion of conformational states: the conformation that in the wild-type protein is populated only sparsely becomes the predominant state. We furthermore explore the potential to use amide-1H R1ρ relaxation to obtain insight into dynamics. We show that while quantitative interpretation of 1H relaxation remains beyond reach under the experimental conditions, due to coherent contributions to decay, one may extract qualitative information about flexibility.
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Affiliation(s)
- Diego F Gauto
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Audrey Hessel
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Petra Rovó
- Ludwig-Maximilians-Universität, Department Chemie, D-81377 München, Germany
| | - Vilius Kurauskas
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Rasmus Linser
- Ludwig-Maximilians-Universität, Department Chemie, D-81377 München, Germany
| | - Paul Schanda
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France; CEA, Institut de Biologie Structurale, F-38044 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
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44
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Chevelkov V, Giller K, Becker S, Lange A. Measurement of backbone hydrogen-deuterium exchange in the type III secretion system needle protein PrgI by solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 283:110-116. [PMID: 28985499 DOI: 10.1016/j.jmr.2017.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/15/2017] [Accepted: 08/27/2017] [Indexed: 06/07/2023]
Abstract
In this report we present site-specific measurements of amide hydrogen-deuterium exchange rates in a protein in the solid state phase by MAS NMR. Employing perdeuteration, proton detection and a high external magnetic field we could adopt the highly efficient Relax-EXSY protocol previously developed for liquid state NMR. According to this method, we measured the contribution of hydrogen exchange on apparent 15N longitudinal relaxation rates in samples with differing D2O buffer content. Differences in the apparent T1 times allowed us to derive exchange rates for multiple residues in the type III secretion system needle protein.
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Affiliation(s)
- Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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45
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Smith AA, Ernst M, Meier BH. Because the Light is Better Here: Correlation-Time Analysis by NMR Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707316] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Albert A. Smith
- Physical Chemistry; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Matthias Ernst
- Physical Chemistry; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Beat H. Meier
- Physical Chemistry; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
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46
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Smith AA, Ernst M, Meier BH. Because the Light is Better Here: Correlation-Time Analysis by NMR Spectroscopy. Angew Chem Int Ed Engl 2017; 56:13590-13595. [PMID: 28856783 DOI: 10.1002/anie.201707316] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Indexed: 11/05/2022]
Abstract
Relaxation data in NMR spectra are often used for dynamics analysis, by modeling motion in the sample with a correlation function consisting of one or more decaying exponential terms, each described by an order parameter, and a correlation time. This method has its origins in the Lipari-Szabo model-free approach, which originally considered overall tumbling plus one internal motion and was later expanded to several internal motions. Considering several of these cases in the solid state it is found that if the real motion is more complex than the assumed model, model fitting is biased towards correlation times where the relaxation data are most sensitive. This leads to unexpected distortions in the resulting dynamics description. Therefore dynamics detectors should be used, which characterize different ranges of correlation times and can help in the analysis of protein motion without assuming a specific model of the correlation function.
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Affiliation(s)
- Albert A Smith
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
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47
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Asami S, Reif B. Comparative Study of REDOR and CPPI Derived Order Parameters by 1H-Detected MAS NMR and MD Simulations. J Phys Chem B 2017; 121:8719-8730. [DOI: 10.1021/acs.jpcb.7b06812] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sam Asami
- Munich
Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany
| | - Bernd Reif
- Munich
Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter
Landstr. 1, 85764 Neuherberg, Germany
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48
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Jain MG, Rajalakshmi G, Equbal A, Mote KR, Agarwal V, Madhu PK. Sine-squared shifted pulses for recoupling interactions in solid-state NMR. J Chem Phys 2017; 146:244201. [PMID: 28668030 DOI: 10.1063/1.4986791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Rotational-Echo DOuble-Resonance (REDOR) is a versatile experiment for measuring internuclear distance between two heteronuclear spins in solid-state NMR. At slow to intermediate magic-angle spinning (MAS) frequencies, the measurement of distances between strongly coupled spins is challenging due to rapid dephasing of magnetisation. This problem can be remedied by employing the pulse-shifted version of REDOR known as Shifted-REDOR (S-REDOR) that scales down the recoupled dipolar coupling. In this study, we propose a new variant of the REDOR sequence where the positions of the π pulses are determined by a sine-squared function. This new variant has scaling properties similar to S-REDOR. We use theory, numerical simulations, and experiments to compare the dipolar recoupling efficiencies and the experimental robustness of the three REDOR schemes. The proposed variant has advantages in terms of radiofrequency field requirements at fast MAS frequencies.
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Affiliation(s)
- Mukul G Jain
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - G Rajalakshmi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Asif Equbal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
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49
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Lakomek NA, Penzel S, Lends A, Cadalbert R, Ernst M, Meier BH. Microsecond Dynamics in Ubiquitin Probed by Solid-State 15
N NMR Spectroscopy R
1ρ
Relaxation Experiments under Fast MAS (60-110 kHz). Chemistry 2017; 23:9425-9433. [DOI: 10.1002/chem.201701738] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Nils-Alexander Lakomek
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Susanne Penzel
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Alons Lends
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Matthias Ernst
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
| | - Beat H. Meier
- Laboratory of Physical Chemistry; ETH Zurich; Vladimir-Prelog Weg 2 8093 Zurich Switzerland
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50
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Fritz M, Quinn CM, Wang M, Hou G, Lu X, Koharudin LMI, Polenova T, Gronenborn AM. Toward Closing the Gap: Quantum Mechanical Calculations and Experimentally Measured Chemical Shifts of a Microcrystalline Lectin. J Phys Chem B 2017; 121:3574-3585. [PMID: 28001418 PMCID: PMC5465307 DOI: 10.1021/acs.jpcb.6b09479] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NMR chemical shifts are exquisitely sensitive probes for conformation and dynamics in molecules and supramolecular assemblies. Although isotropic chemical shifts are easily measured with high accuracy and precision in conventional NMR experiments, they remain challenging to calculate quantum mechanically, particularly in inherently dynamic biological systems. Using a model benchmark protein, the 133-residue agglutinin from Oscillatoria agardhii (OAA), which has been extensively characterized by us previously, we have explored the integration of X-ray crystallography, solution NMR, MAS NMR, and quantum mechanics/molecular mechanics (QM/MM) calculations for analysis of 13Cα and 15NH isotropic chemical shifts. The influence of local interactions, quaternary contacts, and dynamics on the accuracy of calculated chemical shifts is analyzed. Our approach is broadly applicable and expected to be beneficial in chemical shift analysis and chemical-shift-based structure refinement for proteins and protein assemblies.
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Affiliation(s)
- Matthew Fritz
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Leonardus M. I. Koharudin
- Pittsburgh center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine,3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
- Pittsburgh center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine,3501 Fifth Ave., Pittsburgh, PA 15261, United States
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