1
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Gigli L, Silva JM, Cerofolini L, Macedo AL, Geraldes CFGC, Suturina EA, Calderone V, Fragai M, Parigi G, Ravera E, Luchinat C. Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins. Inorg Chem 2024; 63:10713-10725. [PMID: 38805564 DOI: 10.1021/acs.inorgchem.4c01274] [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: 05/30/2024]
Abstract
Understanding the fine structural details of inhibitor binding at the active site of metalloenzymes can have a profound impact on the rational drug design targeted to this broad class of biomolecules. Structural techniques such as NMR, cryo-EM, and X-ray crystallography can provide bond lengths and angles, but the uncertainties in these measurements can be as large as the range of values that have been observed for these quantities in all the published structures. This uncertainty is far too large to allow for reliable calculations at the quantum chemical (QC) levels for developing precise structure-activity relationships or for improving the energetic considerations in protein-inhibitor studies. Therefore, the need arises to rely upon computational methods to refine the active site structures well beyond the resolution obtained with routine application of structural methods. In a recent paper, we have shown that it is possible to refine the active site of cobalt(II)-substituted MMP12, a metalloprotein that is a relevant drug target, by matching to the experimental pseudocontact shifts (PCS) those calculated using multireference ab initio QC methods. The computational cost of this methodology becomes a significant bottleneck when the starting structure is not sufficiently close to the final one, which is often the case with biomolecular structures. To tackle this problem, we have developed an approach based on a neural network (NN) and a support vector regression (SVR) and applied it to the refinement of the active site structure of oxalate-inhibited human carbonic anhydrase 2 (hCAII), another prototypical metalloprotein target. The refined structure gives a remarkably good agreement between the QC-calculated and the experimental PCS. This study not only contributes to the knowledge of CAII but also demonstrates the utility of combining machine learning (ML) algorithms with QC calculations, offering a promising avenue for investigating other drug targets and complex biological systems in general.
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Affiliation(s)
- Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Anjos L Macedo
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB─Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Carlos F G C Geraldes
- Department of Life Sciences, Faculty of Science and Technology, 3000-393 Coimbra, Portugal
- Coimbra Chemistry Center─Institute of Molecular Sciences (CCC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- Florence Data Science, University of Florence, Florence 50134, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- Giotto Biotech, S.R.L., Sesto Fiorentino 50019, Italy
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2
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Aguion PI, Marchanka A, Carlomagno T. Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy. J Struct Biol X 2022; 6:100072. [PMID: 36090770 PMCID: PMC9449856 DOI: 10.1016/j.yjsbx.2022.100072] [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] [Received: 06/16/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Solid-state NMR (ssNMR) has become a well-established technique to study large and insoluble protein assemblies. However, its application to nucleic acid-protein complexes has remained scarce, mainly due to the challenges presented by overlapping nucleic acid signals. In the past decade, several efforts have led to the first structure determination of an RNA molecule by ssNMR. With the establishment of these tools, it has become possible to address the problem of structure determination of nucleic acid-protein complexes by ssNMR. Here we review first and more recent ssNMR methodologies that study nucleic acid-protein interfaces by means of chemical shift and peak intensity perturbations, direct distance measurements and paramagnetic effects. At the end, we review the first structure of an RNA-protein complex that has been determined from ssNMR-derived intermolecular restraints.
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Affiliation(s)
- Philipp Innig Aguion
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Alexander Marchanka
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Teresa Carlomagno
- School of Biosciences/College of Life and Enviromental Sciences, Institute of Cancer and Genomic Sciences/College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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3
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Ravera E, Gigli L, Fiorucci L, Luchinat C, Parigi G. The evolution of paramagnetic NMR as a tool in structural biology. Phys Chem Chem Phys 2022; 24:17397-17416. [PMID: 35849063 DOI: 10.1039/d2cp01838a] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paramagnetic NMR data contain extremely accurate long-range information on metalloprotein structures and, when used in the frame of integrative structural biology approaches, they allow for the retrieval of structural details to a resolution that is not achievable using other techniques. Paramagnetic data thus represent an extremely powerful tool to refine protein models in solution, especially when coupled to X-ray or cryoelectron microscopy data, to monitor the formation of complexes and determine the relative arrangements of their components, and to highlight the presence of conformational heterogeneity. More recently, theoretical and computational advancements in quantum chemical calculations of paramagnetic NMR observables are progressively opening new routes in structural biology, because they allow for the determination of the structure within the coordination sphere of the metal center, thus acting as a loupe on sites that are difficult to observe but very important for protein function.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Letizia Fiorucci
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
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4
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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5
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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: 33] [Impact Index Per Article: 16.5] [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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6
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A Low-Spin CoII/Nitroxide Complex for Distance Measurements at Q-Band Frequencies. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pulse dipolar electron paramagnetic resonance spectroscopy (PDS) is continuously furthering the understanding of chemical and biological assemblies through distance measurements in the nanometer range. New paramagnets and pulse sequences can provide structural insights not accessible through other techniques. In the pursuit of alternative spin centers for PDS, we synthesized a low-spin CoII complex bearing a nitroxide (NO) moiety, where both the CoII and NO have an electron spin S of 1/2. We measured CoII-NO distances with the well-established double electron–electron resonance (DEER aka PELDOR) experiment, as well as with the five- and six-pulse relaxation-induced dipolar modulation enhancement (RIDME) spectroscopies at Q-band frequencies (34 GHz). We first identified challenges related to the stability of the complex in solution via DEER and X-ray crystallography and showed that even in cases where complex disproportionation is unavoidable, CoII-NO PDS measurements are feasible and give good signal-to-noise (SNR) ratios. Specifically, DEER and five-pulse RIDME exhibited an SNR of ~100, and while the six-pulse RIDME exhibited compromised SNR, it helped us minimize unwanted signals from the RIDME traces. Last, we demonstrated RIDME at a 10 μM sample concentration. Our results demonstrate paramagnetic CoII to be a feasible spin center in medium magnetic fields with opportunities for PDS studies involving CoII ions.
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7
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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8
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Zehnder J, Cadalbert R, Yulikov M, Künze G, Wiegand T. Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 332:107075. [PMID: 34597956 DOI: 10.1016/j.jmr.2021.107075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Labeling of biomolecules with a paramagnetic probe for nuclear magnetic resonance (NMR) spectroscopy enables determining long-range distance restraints, which are otherwise not accessible by classically used dipolar coupling-based NMR approaches. Distance restraints derived from paramagnetic relaxation enhancements (PREs) can facilitate the structure determination of large proteins and protein complexes. We herein present the site-directed labeling of the large oligomeric bacterial DnaB helicase from Helicobacter pylori with cysteine-reactive maleimide tags carrying either a nitroxide radical or a lanthanide ion. The success of the labeling reaction was followed by quantitative continuous-wave electron paramagnetic resonance (EPR) experiments performed on the nitroxide-labeled protein. PREs were extracted site-specifically from 2D and 3D solid-state NMR spectra. A good agreement with predicted PRE values, derived by computational modeling of nitroxide and Gd3+ tags in the low-resolution DnaB crystal structure, was found. Comparison of experimental PREs and model-predicted spin label-nucleus distances indicated that the size of the "blind sphere" around the paramagnetic center, in which NMR resonances are not detected, is slightly larger for Gd3+ (∼14 Å) than for nitroxide (∼11 Å) in 13C-detected 2D spectra of DnaB. We also present Gd3+-Gd3+ dipolar electron-electron resonance EPR experiments on DnaB supporting the conclusion that DnaB was present as a hexameric assembly.
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Affiliation(s)
| | | | - Maxim Yulikov
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Georg Künze
- Institute for Drug Discovery, Medical School, Leipzig University, 04103 Leipzig, Germany.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland; Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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9
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Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High-Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021; 60:14960-14966. [PMID: 33595173 DOI: 10.1002/anie.202101149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/13/2022]
Abstract
Metalloproteins constitute a significant fraction of the proteome of all organisms and their characterization is critical for both basic sciences and biomedical applications. A large portion of metalloproteins bind paramagnetic metal ions, and paramagnetic NMR spectroscopy has been widely used in their structural characterization. However, the signals of nuclei in the immediate vicinity of the metal center are often broadened beyond detection. In this work, we show that it is possible to determine the coordination environment of the paramagnetic metal in the protein at a resolution inaccessible to other techniques. Taking the structure of a diamagnetic analogue as a starting point, a geometry optimization is carried out by fitting the pseudocontact shifts obtained from first principles quantum chemical calculations to the experimental ones.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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10
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Ravera E, Gigli L, Suturina EA, Calderone V, Fragai M, Parigi G, Luchinat C. A High‐Resolution View of the Coordination Environment in a Paramagnetic Metalloprotein from its Magnetic Properties. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Lucia Gigli
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff” University of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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11
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Zehnder J, Cadalbert R, Terradot L, Ernst M, Böckmann A, Güntert P, Meier BH, Wiegand T. Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase. Chemistry 2021; 27:7745-7755. [PMID: 33822417 PMCID: PMC8252064 DOI: 10.1002/chem.202100462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg2+ cofactor with Mn2+ or Co2+ . Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF4 - and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn2+ and Co2+ in localizing the ATP cofactor in large oligomeric protein assemblies. 31 P PCSs induced in the Co2+ -containing sample are then used to localize the DNA phosphate groups on the Co2+ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.
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Affiliation(s)
- Johannes Zehnder
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Riccardo Cadalbert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Matthias Ernst
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | | | - Peter Güntert
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
- Institute of Biophysical ChemistryCenter for Biomolecular Magnetic ResonanceGoethe University Frankfurt am Main60438Frankfurt am MainGermany
- Department of ChemistryTokyo Metropolitan UniversityHachiojiTokyo1920397Japan
| | - Beat H. Meier
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
| | - Thomas Wiegand
- Laboratorium für Physikalische ChemieETH ZürichVladimir-Prelog-Weg 28093ZürichSwitzerland
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12
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Bellomo G, Ravera E, Calderone V, Botta M, Fragai M, Parigi G, Luchinat C. Revisiting paramagnetic relaxation enhancements in slowly rotating systems: how long is the long range? MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:25-31. [PMID: 37904766 PMCID: PMC10539754 DOI: 10.5194/mr-2-25-2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/11/2021] [Indexed: 11/01/2023]
Abstract
Cross-relaxation terms in paramagnetic systems that reorient rigidly with slow tumbling times can increase the effective longitudinal relaxation rates of protons of more than 1 order of magnitude. This is evaluated by simulating the time evolution of the nuclear magnetization using a complete relaxation rate-matrix approach. The calculations show that the Solomon dependence of the paramagnetic relaxation rates on the metal-proton distance (as r - 6 ) can be incorrect for protons farther than 15 Å from the metal and thus can cause sizable errors in R 1 -derived distance restraints used, for instance, for protein structure determination. Furthermore, the chemical exchange of these protons with bulk water protons can enhance the relaxation rate of the solvent protons by far more than expected from the paramagnetic Solomon equation. Therefore, it may contribute significantly to the water proton relaxation rates measured at magnetic resonance imaging (MRI) magnetic fields in the presence of slow-rotating nanoparticles containing paramagnetic ions and a large number of exchangeable surface protons.
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Affiliation(s)
- Giovanni Bellomo
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
- present address: Laboratory of Clinical Neurochemistry, Neurology
Clinic, University of Perugia, Piazzale Lucio Severi 1/8, 06132 Perugia
(PG), Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
| | - Mauro Botta
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale “Amedeo Avogadro”, Viale T. Michel 11, 15121 Alessandria, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
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13
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Maiti BK, Govil N, Kundu T, Moura JJG. Designed Metal-ATCUN Derivatives: Redox- and Non-redox-Based Applications Relevant for Chemistry, Biology, and Medicine. iScience 2020; 23:101792. [PMID: 33294799 PMCID: PMC7701195 DOI: 10.1016/j.isci.2020.101792] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The designed “ATCUN” motif (amino-terminal copper and nickel binding site) is a replica of naturally occurring ATCUN site found in many proteins/peptides, and an attractive platform for multiple applications, which include nucleases, proteases, spectroscopic probes, imaging, and small molecule activation. ATCUN motifs are engineered at periphery by conjugation to recombinant proteins, peptides, fluorophores, or recognition domains through chemically or genetically, fulfilling the needs of various biological relevance and a wide range of practical usages. This chemistry has witnessed significant growth over the last few decades and several interesting ATCUN derivatives have been described. The redox role of the ATCUN moieties is also an important aspect to be considered. The redox potential of designed M-ATCUN derivatives is modulated by judicious choice of amino acid (including stereochemistry, charge, and position) that ultimately leads to the catalytic efficiency. In this context, a wide range of M-ATCUN derivatives have been designed purposefully for various redox- and non-redox-based applications, including spectroscopic probes, target-based catalytic metallodrugs, inhibition of amyloid-β toxicity, and telomere shortening, enzyme inactivation, biomolecules stitching or modification, next-generation antibiotic, and small molecule activation.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Nidhi Govil
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Taraknath Kundu
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - José J G Moura
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
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14
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Trindade IB, Invernici M, Cantini F, Louro RO, Piccioli M. PRE-driven protein NMR structures: an alternative approach in highly paramagnetic systems. FEBS J 2020; 288:3010-3023. [PMID: 33124176 DOI: 10.1111/febs.15615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/10/2020] [Accepted: 10/28/2020] [Indexed: 01/29/2023]
Abstract
Metalloproteins play key roles across biology, and knowledge of their structure is essential to understand their physiological role. For those metalloproteins containing paramagnetic states, the enhanced relaxation caused by the unpaired electrons often makes signal detection unfeasible near the metal center, precluding adequate structural characterization right where it is more biochemically relevant. Here, we report a protein structure determination by NMR where two different sets of restraints, one containing Nuclear Overhauser Enhancements (NOEs) and another containing Paramagnetic Relaxation Enhancements (PREs), are used separately and eventually together. The protein PioC from Rhodopseudomonas palustris TIE-1 is a High Potential Iron-Sulfur Protein (HiPIP) where the [4Fe-4S] cluster is paramagnetic in both oxidation states at room temperature providing the source of PREs used as alternative distance restraints. Comparison of the family of structures obtained using NOEs only, PREs only, and the combination of both reveals that the pairwise root-mean-square deviation (RMSD) between them is similar and comparable with the precision within each family. This demonstrates that, under favorable conditions in terms of protein size and paramagnetic effects, PREs can efficiently complement and eventually replace NOEs for the structural characterization of small paramagnetic metalloproteins and de novo-designed metalloproteins by NMR. DATABASES: The 20 conformers with the lowest target function constituting the final family obtained using the full set of NMR restraints were deposited to the Protein Data Bank (PDB ID: 6XYV). The 20 conformers with the lowest target function obtained using NOEs only (PDB ID: 7A58) and PREs only (PDB ID: 7A4L) were also deposited to the Protein Data Bank. The chemical shift assignments were deposited to the BMRB (code 34487).
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Affiliation(s)
- Inês B Trindade
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Michele Invernici
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
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15
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Tang M, Lam D. Paramagnetic solid-state NMR of proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 103:9-16. [PMID: 31585788 DOI: 10.1016/j.ssnmr.2019.101621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
The paramagnetic properties of metal ions and stable radicals can affect NMR spectra, which can lead to changes in peak intensities, relaxation times and chemical shifts. The changes from paramagnetic effects provide intriguing opportunities for solid-state NMR studies of proteins. In this review, we summarized the trends and progress of paramagnetic solid-state NMR of proteins in the past decade, and showed that paramagnetic effects have great potential applications for sensitivity enhancement, structure determination and topological analysis for microcrystalline proteins, protein complexes, protein aggregates and membrane proteins.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Dennis Lam
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
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16
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Miao Q, Liu WM, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double-Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019; 58:13093-13100. [PMID: 31314159 PMCID: PMC6771572 DOI: 10.1002/anie.201906049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/15/2019] [Indexed: 01/20/2023]
Abstract
Synthetic metal complexes can be used as paramagnetic probes for the study of proteins and protein complexes. Herein, two transition metal NMR probes (TraNPs) are reported. TraNPs are attached through two arms to a protein to generate a pseudocontact shift (PCS) using cobalt(II), or paramagnetic relaxation enhancement (PRE) with manganese(II). The PCS analysis of TraNPs attached to three different proteins shows that the size of the anisotropic component of the magnetic susceptibility depends on the probe surroundings at the surface of the protein, contrary to what is observed for lanthanoid‐based probes. The observed PCS are relatively small, making cobalt‐based probes suitable for localized studies, such as of an active site. The obtained PREs are stronger than those obtained with nitroxide spin labels and the possibility to generate both PCS and PRE offers advantages. The properties of TraNPs in comparison with other cobalt‐based probes are discussed.
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Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wei-Min Liu
- Department of Chemistry, Fu Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New, Taipei City, 24205, Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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17
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Miao Q, Liu W, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double‐Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Wei‐Min Liu
- Department of Chemistry Fu Jen Catholic University No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205 Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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18
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Öster C, Kosol S, Lewandowski JR. Quantifying Microsecond Exchange in Large Protein Complexes with Accelerated Relaxation Dispersion Experiments in the Solid State. Sci Rep 2019; 9:11082. [PMID: 31366983 PMCID: PMC6668460 DOI: 10.1038/s41598-019-47507-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/16/2019] [Indexed: 01/20/2023] Open
Abstract
Solid state NMR is a powerful method to obtain information on the structure and dynamics of protein complexes that, due to solubility and size limitations, cannot be achieved by other methods. Here, we present an approach that allows the quantification of microsecond conformational exchange in large protein complexes by using a paramagnetic agent to accelerate 15N R1ρ relaxation dispersion measurements and overcome sensitivity limitations. The method is validated on crystalline GB1 and then applied to a >300 kDa precipitated complex of GB1 with full length human immunoglobulin G (IgG). The addition of a paramagnetic agent increased the signal to noise ratio per time unit by a factor of 5, which allowed full relaxation dispersion curves to be recorded on a sample containing less than 50 μg of labelled material in 5 and 10 days on 850 and 700 MHz spectrometers, respectively. We discover a similar exchange process across the β-sheet in GB1 in crystals and in complex with IgG. However, the slow motion observed for a number of residues in the α-helix of crystalline GB1 is not detected in the complex.
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Affiliation(s)
- Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Simone Kosol
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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19
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Pell AJ, Pintacuda G, Grey CP. Paramagnetic NMR in solution and the solid state. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 111:1-271. [PMID: 31146806 DOI: 10.1016/j.pnmrs.2018.05.001] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 05/22/2023]
Abstract
The field of paramagnetic NMR has expanded considerably in recent years. This review addresses both the theoretical description of paramagnetic NMR, and the way in which it is currently practised. We provide a review of the theory of the NMR parameters of systems in both solution and the solid state. Here we unify the different languages used by the NMR, EPR, quantum chemistry/DFT, and magnetism communities to provide a comprehensive and coherent theoretical description. We cover the theory of the paramagnetic shift and shift anisotropy in solution both in the traditional formalism in terms of the magnetic susceptibility tensor, and using a more modern formalism employing the relevant EPR parameters, such as are used in first-principles calculations. In addition we examine the theory first in the simple non-relativistic picture, and then in the presence of spin-orbit coupling. These ideas are then extended to a description of the paramagnetic shift in periodic solids, where it is necessary to include the bulk magnetic properties, such as magnetic ordering at low temperatures. The description of the paramagnetic shift is completed by describing the current understanding of such shifts due to lanthanide and actinide ions. We then examine the paramagnetic relaxation enhancement, using a simple model employing a phenomenological picture of the electronic relaxation, and again using a more complex state-of-the-art theory which incorporates electronic relaxation explicitly. An additional important consideration in the solid state is the impact of bulk magnetic susceptibility effects on the form of the spectrum, where we include some ideas from the field of classical electrodynamics. We then continue by describing in detail the solution and solid-state NMR methods that have been deployed in the study of paramagnetic systems in chemistry, biology, and the materials sciences. Finally we describe a number of case studies in paramagnetic NMR that have been specifically chosen to highlight how the theory in part one, and the methods in part two, can be used in practice. The systems chosen include small organometallic complexes in solution, solid battery electrode materials, metalloproteins in both solution and the solid state, systems containing lanthanide ions, and multi-component materials used in pharmaceutical controlled-release formulations that have been doped with paramagnetic species to measure the component domain sizes.
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Affiliation(s)
- Andrew J Pell
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106 91 Stockholm, Sweden.
| | - Guido Pintacuda
- Institut des Sciences Analytiques (CNRS UMR 5280, ENS de Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Clare P Grey
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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20
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Metal centers in biomolecular solid-state NMR. J Struct Biol 2018; 206:99-109. [PMID: 30502494 DOI: 10.1016/j.jsb.2018.11.013] [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] [Received: 07/16/2018] [Revised: 09/25/2018] [Accepted: 11/27/2018] [Indexed: 01/03/2023]
Abstract
Solid state NMR (SSNMR) has earned a substantial success in the characterization of paramagnetic systems over the last decades. Nowadays, the resolution and sensitivity of solid state NMR in biological molecules has improved significantly and these advancements can be translated into the study of paramagnetic biomolecules. However, the electronic properties of different metal centers affect the quality of their SSNMR spectra differently, and not all systems turn out to be equally easy to approach by this technique. In this review we will try to give an overview of the properties of different paramagnetic centers and how they can be used to increase the chances of experimental success.
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21
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Paramagnetic NMR as a new tool in structural biology. Emerg Top Life Sci 2018; 2:19-28. [DOI: 10.1042/etls20170084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/25/2022]
Abstract
NMR (nuclear magnetic resonance) investigation through the exploitation of paramagnetic effects is passing from an approach limited to few specialists in the field to a generally applicable method that must be considered, especially for the characterization of systems hardly affordable with other techniques. This is mostly due to the fact that paramagnetic data are long range in nature, thus providing information for the structural and dynamic characterization of complex biomolecular architectures in their native environment. On the other hand, this information usually needs to be complemented by data from other sources. Integration of paramagnetic NMR with other techniques, and the development of protocols for a joint analysis of all available data, is fundamental for achieving a comprehensive characterization of complex biological systems. We describe here a few examples of the new possibilities offered by paramagnetic data used in integrated structural approaches.
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22
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Ravera E, Parigi G, Luchinat C. Perspectives on paramagnetic NMR from a life sciences infrastructure. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 282:154-169. [PMID: 28844254 DOI: 10.1016/j.jmr.2017.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 05/17/2023]
Abstract
The effects arising in NMR spectroscopy because of the presence of unpaired electrons, collectively referred to as "paramagnetic NMR" have attracted increasing attention over the last decades. From the standpoint of the structural and mechanistic biology, paramagnetic NMR provides long range restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements through NMR and X-ray data. These restraints also provide information on structure rearrangements and conformational variability in biomolecular systems. Theoretical improvements in quantum chemistry calculations can nowadays allow for accurate calculations of the paramagnetic data from a molecular structural model, thus providing a tool to refine the metal coordination environment by matching the paramagnetic effects observed far away from the metal. Furthermore, the availability of an improved technology (higher fields and faster magic angle spinning) has promoted paramagnetic NMR applications in the fast-growing area of biomolecular solid-state NMR. Major improvements in dynamic nuclear polarization have been recently achieved, especially through the exploitation of the Overhauser effect occurring through the contact-driven relaxation mechanism: the very large enhancement of the 13C signal observed in a variety of liquid organic compounds at high fields is expected to open up new perspectives for applications of solution NMR.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy.
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23
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Öster C, Kosol S, Hartlmüller C, Lamley JM, Iuga D, Oss A, Org ML, Vanatalu K, Samoson A, Madl T, Lewandowski JR. Characterization of Protein-Protein Interfaces in Large Complexes by Solid-State NMR Solvent Paramagnetic Relaxation Enhancements. J Am Chem Soc 2017; 139:12165-12174. [PMID: 28780861 PMCID: PMC5590091 DOI: 10.1021/jacs.7b03875] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Solid-state NMR is becoming a viable
alternative for obtaining
information about structures and dynamics of large biomolecular complexes,
including ones that are not accessible to other high-resolution biophysical
techniques. In this context, methods for probing protein–protein
interfaces at atomic resolution are highly desirable. Solvent paramagnetic
relaxation enhancements (sPREs) proved to be a powerful method for
probing protein–protein interfaces in large complexes in solution
but have not been employed toward this goal in the solid state. We
demonstrate that 1H and 15N relaxation-based
sPREs provide a powerful tool for characterizing intermolecular interactions
in large assemblies in the solid state. We present approaches for
measuring sPREs in practically the entire range of magic angle spinning
frequencies used for biomolecular studies and discuss their benefits
and limitations. We validate the approach on crystalline GB1, with
our experimental results in good agreement with theoretical predictions.
Finally, we use sPREs to characterize protein–protein interfaces
in the GB1 complex with immunoglobulin G (IgG). Our results suggest
the potential existence of an additional binding site and provide
new insights into GB1:IgG complex structure that amend and revise
the current model available from studies with IgG fragments. We demonstrate
sPREs as a practical, widely applicable, robust, and very sensitive
technique for determining intermolecular interaction interfaces in
large biomolecular complexes in the solid state.
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Affiliation(s)
- Carl Öster
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Simone Kosol
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Christoph Hartlmüller
- Center for Integrated Protein Science, Department of Chemistry, Munich Technische Universität München , Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Jonathan M Lamley
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Dinu Iuga
- Department of Physics, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Andres Oss
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Mai-Liis Org
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Kalju Vanatalu
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Ago Samoson
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Tobias Madl
- Center for Integrated Protein Science, Department of Chemistry, Munich Technische Universität München , Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz , Harrachgasse 21, 8010 Graz, Austria
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
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24
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Rogawski R, McDermott AE. New NMR tools for protein structure and function: Spin tags for dynamic nuclear polarization solid state NMR. Arch Biochem Biophys 2017; 628:102-113. [PMID: 28623034 PMCID: PMC5815514 DOI: 10.1016/j.abb.2017.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/05/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022]
Abstract
Magic angle spinning solid state NMR studies of biological macromolecules [1-3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University, NY, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, NY, NY 10027, United States.
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25
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Soss SE, Flynn PF, Iuliucci RJ, Young RP, Mueller LJ, Hartman J, Beran GJO, Harper JK. Measuring and Modeling Highly Accurate
15
N Chemical Shift Tensors in a Peptide. Chemphyschem 2017; 18:2225-2232. [DOI: 10.1002/cphc.201700357] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/08/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Sarah E. Soss
- Department of Chemistry University of Utah Salt Lake City UT 84112 USA
| | - Peter F. Flynn
- Department of Chemistry University of Utah Salt Lake City UT 84112 USA
| | - Robbie J. Iuliucci
- Department of Chemistry Washington and Jefferson College 60 Lincoln Street Washington PA 15301 USA
| | - Robert P. Young
- Department of Chemistry University of California Riverside CA 92521 USA
| | | | - Joshua Hartman
- Department of Chemistry University of California Riverside CA 92521 USA
| | | | - James K. Harper
- Department of Chemistry University of Central Florida 4111 Libra Drive Orlando FL 32816 USA
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26
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Oligomeric Structure of Anabaena Sensory Rhodopsin in a Lipid Bilayer Environment by Combining Solid-State NMR and Long-range DEER Constraints. J Mol Biol 2017; 429:1903-1920. [DOI: 10.1016/j.jmb.2017.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/27/2017] [Accepted: 05/06/2017] [Indexed: 11/22/2022]
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27
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Nitsche C, Otting G. Pseudocontact shifts in biomolecular NMR using paramagnetic metal tags. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 98-99:20-49. [PMID: 28283085 DOI: 10.1016/j.pnmrs.2016.11.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 05/14/2023]
Affiliation(s)
- Christoph Nitsche
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia. http://www.rsc.anu.edu.au/~go/index.html
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28
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Sala D, Giachetti A, Luchinat C, Rosato A. A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions. JOURNAL OF BIOMOLECULAR NMR 2016; 66:175-185. [PMID: 27771862 DOI: 10.1007/s10858-016-0065-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.
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Affiliation(s)
- Davide Sala
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Andrea Giachetti
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Antonio Rosato
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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29
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Benda L, Mareš J, Ravera E, Parigi G, Luchinat C, Kaupp M, Vaara J. Pseudo-Contact NMR Shifts over the Paramagnetic Metalloprotein CoMMP-12 from First Principles. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608829] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ladislav Benda
- Institut für Chemie, Theoretische Chemie; Technische Universität Berlin; Sekr. C7, Straße des 17. Juni 135 10623 Berlin Germany
- Institut des Sciences Analytiques; UMR 5280 CNRS/ ENS Lyon/ UCB Lyon 1; 5 rue de la Doua 69100 Villeurbanne France
| | - Jiří Mareš
- NMR Research Unit; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Enrico Ravera
- Magnetic Resonance Center; University of Florence and; Interuniversity Consortium for Magnetic Resonance of Metalloproteins; Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center; University of Florence and; Interuniversity Consortium for Magnetic Resonance of Metalloproteins; Sesto Fiorentino Italy
- Department of Chemistry; University of Florence; Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center; University of Florence and; Interuniversity Consortium for Magnetic Resonance of Metalloproteins; Sesto Fiorentino Italy
- Department of Chemistry; University of Florence; Sesto Fiorentino Italy
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie; Technische Universität Berlin; Sekr. C7, Straße des 17. Juni 135 10623 Berlin Germany
| | - Juha Vaara
- NMR Research Unit; University of Oulu; P.O. Box 3000 90014 Oulu Finland
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30
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Benda L, Mareš J, Ravera E, Parigi G, Luchinat C, Kaupp M, Vaara J. Pseudo-Contact NMR Shifts over the Paramagnetic Metalloprotein CoMMP-12 from First Principles. Angew Chem Int Ed Engl 2016; 55:14713-14717. [PMID: 27781358 DOI: 10.1002/anie.201608829] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 11/08/2022]
Abstract
Long-range pseudo-contact NMR shifts (PCSs) provide important restraints for the structure refinement of proteins when a paramagnetic metal center is present, either naturally or introduced artificially. Here we show that ab initio quantum-chemical methods and a modern version of the Kurland-McGarvey approach for paramagnetic NMR (pNMR) shifts in the presence of zero-field splitting (ZFS) together provide accurate predictions of all PCSs in a metalloprotein (high-spin cobalt-substituted MMP-12 as a test case). Computations of 314 13 C PCSs using g- and ZFS tensors based on multi-reference methods provide a reliable bridge between EPR-parameter- and susceptibility-based pNMR formalisms. Due to the high sensitivity of PCSs to even small structural differences, local structures based either on X-ray diffraction or on various DFT optimizations could be evaluated critically by comparing computed and experimental PCSs. Many DFT functionals provide insufficiently accurate structures. We also found the available 1RMZ PDB X-ray structure to exhibit deficiencies related to binding of a hydroxamate inhibitor. This has led to a newly refined PDB structure for MMP-12 (5LAB) that provides a more accurate coordination arrangement and PCSs.
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Affiliation(s)
- Ladislav Benda
- Institut für Chemie, Theoretische Chemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623, Berlin, Germany.,Institut des Sciences Analytiques, UMR 5280 CNRS/ ENS Lyon/ UCB Lyon 1, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Jiří Mareš
- NMR Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Enrico Ravera
- Magnetic Resonance Center, University of Florence and, Interuniversity Consortium for Magnetic Resonance of Metalloproteins, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center, University of Florence and, Interuniversity Consortium for Magnetic Resonance of Metalloproteins, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center, University of Florence and, Interuniversity Consortium for Magnetic Resonance of Metalloproteins, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Juha Vaara
- NMR Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
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31
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Tang M, Mao K, Li S, Zhuang J, Diallo K. Paramagnetic effects on the NMR spectra of isotropic bicelles with headgroup modified chelator lipids and metal ions. Phys Chem Chem Phys 2016; 18:15524-7. [PMID: 27240538 DOI: 10.1039/c6cp01443g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We characterized the paramagnetic effects of nine metal ions on NMR signals of isotropic bicelles with headgroup-modified lipids. We found that Mn(2+), Gd(3+) and Dy(3+) show evidence for influencing NMR signals on the surface more than inside and on the disc edge, providing distance information in the bilayers.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, College of Staten Island - PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA.
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32
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Liu J, Liu C, Fan Y, Munro RA, Ladizhansky V, Brown LS, Wang S. Sparse (13)C labelling for solid-state NMR studies of P. pastoris expressed eukaryotic seven-transmembrane proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 65:7-13. [PMID: 27121590 DOI: 10.1007/s10858-016-0033-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
We demonstrate a novel sparse (13)C labelling approach for methylotrophic yeast P. pastoris expression system, towards solid-state NMR studies of eukaryotic membrane proteins. The labelling scheme was achieved by co-utilizing natural abundance methanol and specifically (13)C labelled glycerol as carbon sources in the expression medium. This strategy improves the spectral resolution by 1.5 fold, displays site-specific labelling patterns, and has advantages for collecting long-range distance restraints for structure determination of large eukaryotic membrane proteins by solid-state NMR.
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Affiliation(s)
- Jing Liu
- Beijing NMR Centre, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Beijing, China
| | - Chang Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ying Fan
- The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Physics, University of Guelph, Guelph, ON, Canada
| | - Rachel A Munro
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Shenlin Wang
- Beijing NMR Centre, Peking University, Beijing, China.
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Beijing National Laboratory for Molecular Sciences, Beijing, China.
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33
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Carlon A, Ravera E, Andrałojć W, Parigi G, Murshudov GN, Luchinat C. How to tackle protein structural data from solution and solid state: An integrated approach. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:54-70. [PMID: 26952192 DOI: 10.1016/j.pnmrs.2016.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 05/17/2023]
Abstract
Long-range NMR restraints, such as diamagnetic residual dipolar couplings and paramagnetic data, can be used to determine 3D structures of macromolecules. They are also used to monitor, and potentially to improve, the accuracy of a macromolecular structure in solution by validating or "correcting" a crystal model. Since crystal structures suffer from crystal packing forces they may not be accurate models for the macromolecular structures in solution. However, the presence of real differences should be tested for by simultaneous refinement of the structure using both crystal and solution NMR data. To achieve this, the program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic and paramagnetic NMR data and/or diamagnetic residual dipolar couplings. Inconsistencies between crystal structures and solution NMR data, if any, may be due either to structural rearrangements occurring on passing from the solution to solid state, or to a greater degree of conformational heterogeneity in solution with respect to the crystal. In the case of multidomain proteins, paramagnetic restraints can provide the correct mutual orientations and positions of domains in solution, as well as information on the conformational variability experienced by the macromolecule.
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Affiliation(s)
- Azzurra Carlon
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Witold Andrałojć
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Garib N Murshudov
- MRC Laboratory for Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
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34
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van der Cruijsen EAW, Koers EJ, Sauvée C, Hulse RE, Weingarth M, Ouari O, Perozo E, Tordo P, Baldus M. Biomolecular DNP-Supported NMR Spectroscopy using Site-Directed Spin Labeling. Chemistry 2015; 21:12971-7. [DOI: 10.1002/chem.201501376] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 12/24/2022]
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35
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Andrałojć W, Berlin K, Fushman D, Luchinat C, Parigi G, Ravera E, Sgheri L. Information content of long-range NMR data for the characterization of conformational heterogeneity. JOURNAL OF BIOMOLECULAR NMR 2015; 62:353-71. [PMID: 26044033 PMCID: PMC4782772 DOI: 10.1007/s10858-015-9951-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/25/2015] [Indexed: 05/16/2023]
Abstract
Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by steric alignment and of both RDCs and pseudocontact shifts caused by paramagnetic alignment, and found that, despite the substantial differences, they contain a similar amount of information. Furthermore, using several synthetic tests we find that both sets of data are equally good towards recovering the major state(s) in conformational distributions.
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Affiliation(s)
- Witold Andrałojć
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Konstantin Berlin
- Department of Chemistry and Biochemistry, Center for Biomolecular
Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular
Structure and Organization, University of Maryland, College Park, MD 20742, USA
- Corresponding authors: David Fushman, ,
Claudio Luchinat,
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Corresponding authors: David Fushman, ,
Claudio Luchinat,
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Luca Sgheri
- Istituto per le Applicazioni del Calcolo, Sezione di Firenze,
CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
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36
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Opella SJ. Solid-state NMR and membrane proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:129-37. [PMID: 25681966 PMCID: PMC4372479 DOI: 10.1016/j.jmr.2014.11.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/17/2014] [Accepted: 11/30/2014] [Indexed: 05/15/2023]
Abstract
The native environment for a membrane protein is a phospholipid bilayer. Because the protein is immobilized on NMR timescales by the interactions within a bilayer membrane, solid-state NMR methods are essential to obtain high-resolution spectra. Approaches have been developed for both unoriented and oriented samples, however, they all rest on the foundation of the most fundamental aspects of solid-state NMR, and the chemical shift and homo- and hetero-nuclear dipole-dipole interactions. Solid-state NMR has advanced sufficiently to enable the structures of membrane proteins to be determined under near-native conditions in phospholipid bilayers.
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Affiliation(s)
- Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
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37
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Jaroniec CP. Structural studies of proteins by paramagnetic solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:50-9. [PMID: 25797004 PMCID: PMC4371136 DOI: 10.1016/j.jmr.2014.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/17/2014] [Indexed: 05/03/2023]
Abstract
Paramagnetism-based nuclear pseudocontact shifts and spin relaxation enhancements contain a wealth of information in solid-state NMR spectra about electron-nucleus distances on the ∼20 Å length scale, far beyond that normally probed through measurements of nuclear dipolar couplings. Such data are especially vital in the context of structural studies of proteins and other biological molecules that suffer from a sparse number of experimentally-accessible atomic distances constraining their three-dimensional fold or intermolecular interactions. This perspective provides a brief overview of the recent developments and applications of paramagnetic magic-angle spinning NMR to biological systems, with primary focus on the investigations of metalloproteins and natively diamagnetic proteins modified with covalent paramagnetic tags.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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38
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Ravera E, Schubeis T, Martelli T, Fragai M, Parigi G, Luchinat C. NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:60-70. [PMID: 25797005 DOI: 10.1016/j.jmr.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/06/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tobias Schubeis
- Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tommaso Martelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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Wang S, Ladizhansky V. Recent advances in magic angle spinning solid state NMR of membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 82:1-26. [PMID: 25444696 DOI: 10.1016/j.pnmrs.2014.07.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 07/16/2014] [Accepted: 07/20/2014] [Indexed: 05/14/2023]
Abstract
Membrane proteins mediate many critical functions in cells. Determining their three-dimensional structures in the native lipid environment has been one of the main objectives in structural biology. There are two major NMR methodologies that allow this objective to be accomplished. Oriented sample NMR, which can be applied to membrane proteins that are uniformly aligned in the magnetic field, has been successful in determining the backbone structures of a handful of membrane proteins. Owing to methodological and technological developments, Magic Angle Spinning (MAS) solid-state NMR (ssNMR) spectroscopy has emerged as another major technique for the complete characterization of the structure and dynamics of membrane proteins. First developed on peptides and small microcrystalline proteins, MAS ssNMR has recently been successfully applied to large membrane proteins. In this review we describe recent progress in MAS ssNMR methodologies, which are now available for studies of membrane protein structure determination, and outline a few examples, which highlight the broad capability of ssNMR spectroscopy.
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Affiliation(s)
- Shenlin Wang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada; Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
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40
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Ivanir H, Goldbourt A. Solid state NMR chemical shift assignment and conformational analysis of a cellulose binding protein facilitated by optimized glycerol enrichment. JOURNAL OF BIOMOLECULAR NMR 2014; 59:185-197. [PMID: 24824437 DOI: 10.1007/s10858-014-9838-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/04/2014] [Indexed: 06/03/2023]
Abstract
Magic-angle spinning solid-state NMR has been applied to study CBM3b-Cbh9A (CBM3b), a cellulose binding module protein belonging to family 3b. It is a 146-residue protein having a unique nine-stranded β-sandwich fold, in which 35% of the structure is in a β-sheet conformation and the remainder of the protein is composed of loops and unstructured regions. Yet, the protein can be crystalized and it forms elongated needles. Close to complete chemical shift assignment of the protein was obtained by combining two- and three-dimensional experiments using a fully labeled sample and a glycerol-labeled sample. The use of an optimized protocol for glycerol-based sparse labeling reduces sample preparation costs and facilitates the assignment of the large number of aromatic signals in this protein. Conformational analysis shows good correlation between the NMR-predicted secondary structure and the reported X-ray crystal structure, in particular in the structured regions. Residues which show high B-factor values are situated mainly in unstructured regions, and are missing in our spectra indicating conformational flexibility rather than heterogeneity. Interestingly, long-range contacts, which could be clearly detected for tyrosine residues, could not be observed for aromatic phenylalanine residues pointing into the hydrophobic core, suggesting possible high ring mobility. These studies will allow us to further investigate the cellulose-bound form of CBM proteins.
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Affiliation(s)
- Hadar Ivanir
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Ramat Aviv, 69978, Tel Aviv, Israel
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41
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Rinaldelli M, Ravera E, Calderone V, Parigi G, Murshudov GN, Luchinat C. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:958-67. [PMID: 24699641 PMCID: PMC4306559 DOI: 10.1107/s1399004713034160] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 12/18/2013] [Indexed: 11/12/2022]
Abstract
The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.
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Affiliation(s)
- Mauro Rinaldelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Vito Calderone
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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42
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43
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Varghese S, Yang F, Pacheco V, Wrede K, Medvedev A, Ogata H, Knipp M, Heise H. Expression, purification, and solid-state NMR characterization of the membrane binding heme protein nitrophorin 7 in two electronic spin states. Biochemistry 2013; 52:7031-40. [PMID: 24033104 DOI: 10.1021/bi401020t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nitrophorins (NPs) comprise a group of NO transporting ferriheme b proteins found in the saliva of the blood sucking insect Rhodnius prolixus . In contrast to other nitrophorins (NP1-4), the recently identified membrane binding isoform NP7 tends to form oligomers and precipitates at higher concentrations in solution. Hence, solid-state NMR (ssNMR) was employed as an alternative method to gain structural insights on the precipitated protein. We report the expression and purification of (13)C,(15)N isotopically labeled protein together with the first ssNMR characterization of NP7. Because the size of NP7 (21 kDa) still provides a challenge for ssNMR, the samples were reverse labeled with Lys and Val to reduce the number of crosspeaks in two-dimensional spectra. The two electronic spin states with S = 1/2 and S = 0 at the ferriheme iron were generated by the complexation with imidazole and NO, respectively. ssNMR spectra of both forms are well resolved, which allows for sequential resonance assignments of 22 residues. Importantly, the ssNMR spectra demonstrate that aggregation does not affect the protein fold. Comparison of the spectra of the two electronic spin states allows the determination of paramagnetically shifted cross peaks due to pseudocontact shifts, which assists the assignment of residues close to the heme center.
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Affiliation(s)
- Sabu Varghese
- ICS-6 Institute of Complex Systems-Structural Biochemistry, Forschungszentrum Jülich , D-2425 Jülich, Germany
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Sengupta I, Nadaud PS, Jaroniec CP. Protein structure determination with paramagnetic solid-state NMR spectroscopy. Acc Chem Res 2013; 46:2117-26. [PMID: 23464364 DOI: 10.1021/ar300360q] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2+)-tagged GB1 mutants to rapidly determine the global protein fold in a de novo fashion. Remarkably, these studies required quantitative measurements of only approximately four or five backbone amide (15)N longitudinal paramagnetic relaxation enhancements per residue, in the complete absence of the usual internuclear distance restraints. Importantly, this paramagnetic solid-state NMR methodology is general and can be directly applied to larger proteins and protein complexes for which a significant fraction of the signals can be assigned in standard 2D and 3D MAS NMR chemical shift correlation spectra.
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Affiliation(s)
- Ishita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Philippe S. Nadaud
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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45
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Weingarth M, Baldus M. Solid-state NMR-based approaches for supramolecular structure elucidation. Acc Chem Res 2013; 46:2037-46. [PMID: 23586937 DOI: 10.1021/ar300316e] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Supramolecular chemistry provides structural and conformational information about complexes formed from multiple molecules. While the molecule is held together by strong intramolecular contacts like covalent bonds, supramolecular structures can be further stabilized by weaker or transient intermolecular interactions. These interactions can confer a great diversity and sensitivity to exogenous factors like temperature, pressure, or ionic strength to multimolecular arrangements. Solid-state nuclear magnetic resonance (ssNMR) can provide atomic-scale structural and dynamical information in highly disordered or heterogeneous biological systems, even in complex environments such as cellular membranes or whole cells. In these systems, the molecule of interest no longer exists as a separate unit, but it entangles with its surroundings in a dynamic interplay. Researchers have long accounted for the complexity of these intermolecular arrangements through a rather phenomenological description. But now the focus is shifting toward a detailed understanding of supramolecular structure at atomic resolution, constantly expanding our understanding of the stunning influence of the environment. In this Account, we discuss how ssNMR can help to dissect the remarkable interplay between intra- and intermolecular interactions. We describe biochemical and spectroscopic strategies that tailor ssNMR spectroscopic methods to the challenge of supramolecular structure investigation. In particular, we consider protein-protein interactions or the protein-membrane topology, and we review recent applications of these techniques. Furthermore, we summarize methods for integrating ssNMR information with other experimental techniques or computational methods, and we offer perspectives on how this overall information allows us to target increasingly large and intricate supramolecular structures of biomolecules. Advancements in ssNMR methodology and instrumentation, including the incorporation of signal enhancement methods such as dynamic nuclear polarization will further increase the potential of ssNMR spectroscopy, and together with additional developments in the field of NMR-hybrid strategies, ssNMR may become an ideal tool to study the heterogeneous, dynamic, and often transient nature of molecular interactions in complex biological systems.
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Affiliation(s)
- Markus Weingarth
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marc Baldus
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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46
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Parthasarathy S, Nishiyama Y, Ishii Y. Sensitivity and resolution enhanced solid-state NMR for paramagnetic systems and biomolecules under very fast magic angle spinning. Acc Chem Res 2013; 46:2127-35. [PMID: 23889329 DOI: 10.1021/ar4000482] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent research in fast magic angle spinning (MAS) methods has drastically improved the resolution and sensitivity of NMR spectroscopy of biomolecules and materials in solids. In this Account, we summarize recent and ongoing developments in this area by presenting (13)C and (1)H solid-state NMR (SSNMR) studies on paramagnetic systems and biomolecules under fast MAS from our laboratories. First, we describe how very fast MAS (VFMAS) at the spinning speed of at least 20 kHz allows us to overcome major difficulties in (1)H and (13)C high-resolution SSNMR of paramagnetic systems. As a result, we can enhance both sensitivity and resolution by up to a few orders of magnitude. Using fast recycling (∼ms/scan) with short (1)H T1 values, we can perform (1)H SSNMR microanalysis of paramagnetic systems on the microgram scale with greatly improved sensitivity over that observed for diamagnetic systems. Second, we discuss how VFMAS at a spinning speed greater than ∼40 kHz can enhance the sensitivity and resolution of (13)C biomolecular SSNMR measurements. Low-power (1)H decoupling schemes under VFMAS offer excellent spectral resolution for (13)C SSNMR by nominal (1)H RF irradiation at ∼10 kHz. By combining the VFMAS approach with enhanced (1)H T1 relaxation by paramagnetic doping, we can achieve extremely fast recycling in modern biomolecular SSNMR experiments. Experiments with (13)C-labeled ubiquitin doped with 10 mM Cu-EDTA demonstrate how effectively this new approach, called paramagnetic assisted condensed data collection (PACC), enhances the sensitivity. Lastly, we examine (13)C SSNMR measurements for biomolecules under faster MAS at a higher field. Our preliminary (13)C SSNMR data of Aβ amyloid fibrils and GB1 microcrystals acquired at (1)H NMR frequencies of 750-800 MHz suggest that the combined use of the PACC approach and ultrahigh fields could allow for routine multidimensional SSNMR analyses of proteins at the 50-200 nmol level. Also, we briefly discuss the prospects for studying bimolecules using (13)C SSNMR under ultrafast MAS at the spinning speed of ∼100 kHz.
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Affiliation(s)
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishimashi, Tokyo 196-8558, Japan
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47
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Knight MJ, Felli IC, Pierattelli R, Emsley L, Pintacuda G. Magic angle spinning NMR of paramagnetic proteins. Acc Chem Res 2013; 46:2108-16. [PMID: 23506094 DOI: 10.1021/ar300349y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Metal ions are ubiquitous in biochemical and cellular processes. Since many metal ions are paramagnetic due to the presence of unpaired electrons, paramagnetic molecules are an important class of targets for research in structural biology and related fields. Today, NMR spectroscopy plays a central role in the investigation of the structure and chemical properties of paramagnetic metalloproteins, linking the observed paramagnetic phenomena directly to electronic and molecular structure. A major step forward in the study of proteins by solid-state NMR came with the advent of ultrafast magic angle spinning (MAS) and the ability to use (1)H detection. Combined, these techniques have allowed investigators to observe nuclei that previously were invisible in highly paramagnetic metalloproteins. In addition, these techniques have enabled quantitative site-specific measurement of a variety of long-range paramagnetic effects. Instead of limiting solid-state NMR studies of biological systems, paramagnetism provides an information-rich phenomenon that can be exploited in these studies. This Account emphasizes state-of-the-art methods and applications of solid-state NMR in paramagnetic systems in biological chemistry. In particular, we discuss the use of ultrafast MAS and (1)H-detection in perdeuterated paramagnetic metalloproteins. Current methodology allows us to determine the structure and dynamics of metalloenzymes, and, as an example, we describe solid-state NMR studies of microcrystalline superoxide dismutase, a 32 kDa dimer. Data were acquired with remarkably short times, and these experiments required only a few milligrams of sample.
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Affiliation(s)
- Michael J. Knight
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Isabella C. Felli
- Department of Chemistry “Ugo Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6 − 50019 Sesto Fiorentino, FI, Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6 − 50019 Sesto Fiorentino, FI, Italy
| | - Lyndon Emsley
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Guido Pintacuda
- Université de Lyon, Institut de Sciences Analytiques (CNRS / ENS-Lyon / UCB Lyon 1), Centre de RMN à Très Hauts Champs, 5 rue de la Doua, 69100 Villeurbanne, France
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48
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Zhou L, Li S, Su Y, Yi X, Zheng A, Deng F. Interaction between Histidine and Zn(II) Metal Ions over a Wide pH as Revealed by Solid-State NMR Spectroscopy and DFT Calculations. J Phys Chem B 2013; 117:8954-65. [DOI: 10.1021/jp4041937] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lei Zhou
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
- Graduate School, the Chinese Academy of Sciences, Beijing 100029, China
| | - Shenhui Li
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Yongchao Su
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Xianfeng Yi
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
- Graduate School, the Chinese Academy of Sciences, Beijing 100029, China
| | - Anmin Zheng
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
| | - Feng Deng
- State Key
Laboratory of Magnetic
Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic
Resonance, Key Laboratory of Magnetic Resonance in Biological Systems,
Wuhan Institute of Physics and Mathematics, the Chinese Academy of Sciences, Wuhan 430071, China
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49
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Li J, Pilla KB, Li Q, Zhang Z, Su X, Huber T, Yang J. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts. J Am Chem Soc 2013; 135:8294-303. [DOI: 10.1021/ja4021149] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jianping Li
- Key Laboratory of Magnetic Resonance
in Biological Systems, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance,
Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Kala Bharath Pilla
- Research School
of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Qingfeng Li
- State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin300071,
PR China
| | - Zhengfeng Zhang
- Key Laboratory of Magnetic Resonance
in Biological Systems, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance,
Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin300071,
PR China
| | - Thomas Huber
- Research School
of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Jun Yang
- Key Laboratory of Magnetic Resonance
in Biological Systems, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance,
Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China
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50
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Comellas G, Rienstra CM. Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils. Annu Rev Biophys 2013; 42:515-36. [DOI: 10.1146/annurev-biophys-083012-130356] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology,
- Department of Chemistry, and
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; ,
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