1
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Koppe J, Pell AJ. Structure Determination and Refinement of Paramagnetic Materials by Solid-State NMR. ACS PHYSICAL CHEMISTRY AU 2023; 3:419-433. [PMID: 37780542 PMCID: PMC10540298 DOI: 10.1021/acsphyschemau.3c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 10/03/2023]
Abstract
Paramagnetism in solid-state materials has long been considered an additional challenge for structural investigations by using solid-state nuclear magnetic resonance spectroscopy (ssNMR). The strong interactions between unpaired electrons and the surrounding atomic nuclei, on the one hand, are complex to describe, and on the other hand can cause fast decaying signals and extremely broad resonances. However, significant progress has been made over the recent years in developing both theoretical models to understand and calculate the frequency shifts due to paramagnetism and also more sophisticated experimental protocols for obtaining high-resolution ssNMR spectra. While the field is continuously moving forward, to date, the combination of state-of-the-art numerical and experimental techniques enables us to obtain high-quality data for a variety of systems. This involves the determination of several ssNMR parameters that represent different contributions to the frequency shift in paramagnetic solids. These contributions encode structural information on the studied material on various length scales, ranging from crystal morphologies, to the mid- and long-range order, down to the local atomic bonding environment. In this perspective, the different ssNMR parameters characteristic for paramagnetic materials are discussed with a focus on their interpretation in terms of structure. This includes a summary of studies that have explored the information content of these ssNMR parameters, mostly to complement experimental data from other methods, e.g., X-ray diffraction. The presented overview aims to demonstrate how far ssNMR has hitherto been able to determine and refine the structures of materials and to discuss where it currently falls short of its full potential. We attempt to highlight how much further ssNMR can be pushed to determine and refine structure to deliver a comprehensive structural characterization of paramagnetic materials comparable to what is to date achieved by the combined effort of electron microscopy, diffraction, and spectroscopy.
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Affiliation(s)
- Jonas Koppe
- Centre
de RMN à Très Hauts Champs de Lyon (UMR 5082 −
CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon (UMR 5082 −
CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 Rue de la Doua, 69100 Villeurbanne, France
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2
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Huang T, Granick S. Comment on “Following Molecular Mobility during Chemical Reactions: No Evidence for Active Propulsion” and “Molecular Diffusivity of Click Reaction Components: The Diffusion Enhancement Question”. J Am Chem Soc 2022; 144:13431-13435. [DOI: 10.1021/jacs.2c02965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tian Huang
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, South Korea
| | - Steve Granick
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, South Korea
- Departments of Chemistry and Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, South Korea
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3
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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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4
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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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5
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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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6
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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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7
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Gauto D, Dakhlaoui O, Marin-Montesinos I, Hediger S, De Paëpe G. Targeted DNP for biomolecular solid-state NMR. Chem Sci 2021; 12:6223-6237. [PMID: 34084422 PMCID: PMC8115112 DOI: 10.1039/d0sc06959k] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/18/2021] [Indexed: 12/23/2022] Open
Abstract
High-field dynamic nuclear polarization is revolutionizing the scope of solid-state NMR with new applications in surface chemistry, materials science and structural biology. In this perspective article, we focus on a specific DNP approach, called targeted DNP, in which the paramagnets introduced to polarize are not uniformly distributed in the sample but site-specifically located on the biomolecular system. After reviewing the various targeting strategies reported to date, including a bio-orthogonal chemistry-based approach, we discuss the potential of targeted DNP to improve the overall NMR sensitivity while avoiding the use of glass-forming DNP matrix. This is especially relevant to the study of diluted biomolecular systems such as, for instance, membrane proteins within their lipidic environment. We also discuss routes towards extracting structural information from paramagnetic relaxation enhancement (PRE) induced by targeted DNP at cryogenic temperature, and the possibility to recover site-specific information in the vicinity of the paramagnetic moieties using high-resolution selective DNP spectra. Finally, we review the potential of targeted DNP for in-cell NMR studies and how it can be used to extract a given protein NMR signal from a complex cellular background.
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Affiliation(s)
- Diego Gauto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Ons Dakhlaoui
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- Univ. Grenoble Alpes, CNRS, CERMAV Grenoble France
| | - Ildefonso Marin-Montesinos
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- University of Aveiro, CICECO Chem. Dept. Aveiro Portugal
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
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8
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Bari KJ, Sharma S. A Perspective on Biophysical Studies of Crystallin Aggregation and Implications for Cataract Formation. J Phys Chem B 2020; 124:11041-11054. [PMID: 33297682 DOI: 10.1021/acs.jpcb.0c07449] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lens crystallins are subject to various types of damage during their lifetime which triggers protein misfolding and aggregation, ultimately causing cataracts. There are several models for crystallin aggregation, but a comprehensive picture of the mechanism of cataract is still underway. The complex biomolecular interactions underlying crystallin aggregation have motivated major efforts to resolve the structural details and mechanism of aggregation using multiple biophysical techniques at different resolutions. Together, experimental and computational approaches identify and characterize both amyloidogenic and amorphous aggregates leading to an improved understanding of crystallin aggregation. A rigorous characterization of the aggregation-prone intermediates is crucial in cataract-mediated drug discovery. This Perspective summarizes recent biophysical studies on lens crystallin aggregation. We evaluate the outstanding challenges, future outlook, and rewards in this fertile field of research. With lessons learned from protein folding and multiple pathways of aggregation, we highlight the differences in the overall mechanisms of age-related and congenital cataracts. We expect that a correlation between the existing and developing biophysical techniques would provide a platform to study amyloid architecture in the eye lens and reduce the existing gaps in our understanding of crystallin biophysics.
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Affiliation(s)
- Khandekar Jishan Bari
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Gopanpally, Hyderabad 500107, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research, Berhampur, Odisha 760010, India
| | - Shrikant Sharma
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Gopanpally, Hyderabad 500107, India.,Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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9
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Solid-state NMR spectroscopy for characterization of RNA and RNP complexes. Biochem Soc Trans 2020; 48:1077-1087. [PMID: 32573690 DOI: 10.1042/bst20191080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022]
Abstract
Ribonucleic acids are driving a multitude of biological processes where they act alone or in complex with proteins (ribonucleoproteins, RNP). To understand these processes both structural and mechanistic information about RNA is necessary. Due to their conformational plasticity RNA pose a challenge for mainstream structural biology methods. Solid-state NMR (ssNMR) spectroscopy is an emerging technique that can be applied to biomolecular complexes of any size in close-to-native conditions. This review outlines recent methodological developments in ssNMR for structural characterization of RNA and protein-RNA complexes and provides relevant examples.
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10
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Zhao W, Fernando LD, Kirui A, Deligey F, Wang T. Solid-state NMR of plant and fungal cell walls: A critical review. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 107:101660. [PMID: 32251983 DOI: 10.1016/j.ssnmr.2020.101660] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 03/17/2020] [Indexed: 05/22/2023]
Abstract
The cell walls of plants and microbes are a central source for bio-renewable energy and the major targets of antibiotics and antifungal agents. It is highly challenging to determine the molecular structure of complex carbohydrates, protein and lignin, and their supramolecular assembly in intact cell walls. This article selectively highlights the recent breakthroughs that employ 13C/15N solid-state NMR techniques to elucidate the architecture of fungal cell walls in Aspergillus fumigatus and the primary and secondary cell walls in a large variety of plant species such as Arabidopsis, Brachypodium, maize, and spruce. Built upon these pioneering studies, we further summarize the underexplored aspects of fungal and plant cell walls. The new research opportunities introduced by innovative methods, such as the detection of proton and quadrupolar nuclei on ultrahigh-field magnets and under fast magic-angle spinning, paramagnetic probes, natural-abundance DNP, and software development, are also critically discussed.
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Affiliation(s)
- Wancheng Zhao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Liyanage D Fernando
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Alex Kirui
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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11
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Kang X, Zhao W, Dickwella Widanage MC, Kirui A, Ozdenvar U, Wang T. CCMRD: a solid-state NMR database for complex carbohydrates. JOURNAL OF BIOMOLECULAR NMR 2020; 74:239-245. [PMID: 32125579 DOI: 10.1007/s10858-020-00304-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/27/2020] [Indexed: 05/03/2023]
Abstract
Carbohydrates are essential to various life activities in living organisms and serve as the central component in many biomaterials. As an emerging technique with steadily improving resolution, solid-state Nuclear Magnetic Resonance (NMR) spectroscopy has the unique capability in revealing the polymorphic structure and heterogeneous dynamics of insoluble complex carbohydrates. Here, we report the first solid-state NMR database for complex carbohydrates, Complex Carbohydrates Magnetic Resonance Database (CCMRD). This database currently holds the chemical shift information of more than four hundred solid-state NMR compounds and expects rapid expansion. CCMRD provides open portals for data deposition and supports search options based on NMR chemical shifts, carbohydrate names, and compound classes. With the timely implementation, this platform will facilitate spectral analysis and structure determination of carbohydrates and promote software development to benefit the research community. The database is freely accessible at www.ccmrd.org.
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Affiliation(s)
- Xue Kang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
| | - Wancheng Zhao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | - Alex Kirui
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Uluc Ozdenvar
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, USA.
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12
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein–RNA Complex by Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic ChemistryLeibniz University Hannover Schneiderberg 38 30167 Hannover Germany
- Group of NMR-based Structural ChemistryHelmholtz Centre for Infection Research Inhoffenstrasse 7 38124 Braunschweig Germany
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13
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Ahmed M, Marchanka A, Carlomagno T. Structure of a Protein-RNA Complex by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2020; 59:6866-6873. [PMID: 32023357 PMCID: PMC7187219 DOI: 10.1002/anie.201915465] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Indexed: 12/17/2022]
Abstract
Solid‐state NMR (ssNMR) is applicable to high molecular‐weight (MW) protein assemblies in a non‐amorphous precipitate. The technique yields atomic resolution structural information on both soluble and insoluble particles without limitations of MW or requirement of crystals. Herein, we propose and demonstrate an approach that yields the structure of protein–RNA complexes (RNP) solely from ssNMR data. Instead of using low‐sensitivity magnetization transfer steps between heteronuclei of the protein and the RNA, we measure paramagnetic relaxation enhancement effects elicited on the RNA by a paramagnetic tag coupled to the protein. We demonstrate that this data, together with chemical‐shift‐perturbation data, yields an accurate structure of an RNP complex, starting from the bound structures of its components. The possibility of characterizing protein–RNA interactions by ssNMR may enable applications to large RNP complexes, whose structures are not accessible by other methods.
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Affiliation(s)
- Mumdooh Ahmed
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Alexander Marchanka
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany.,Group of NMR-based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
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14
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Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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15
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Lu X, Tsutsumi Y, Huang C, Xu W, Byrn SR, Templeton AC, Buevich AV, Amoureux JP, Su Y. Molecular packing of pharmaceuticals analyzed with paramagnetic relaxation enhancement and ultrafast magic angle pinning NMR. Phys Chem Chem Phys 2020; 22:13160-13170. [DOI: 10.1039/d0cp02049d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Probing molecular details of fluorinated pharmaceutical compounds at a faster acquisition utilizing paramagnetic relaxation enhancement and better resolution from ultrafast magic angle spinning (νrot = 110 kHz) and high magnetic field (B0 = 18.8 T).
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Affiliation(s)
| | | | | | - Wei Xu
- MRL, Merck & Co., Inc
- Kenilworth
- USA
| | - Stephen R. Byrn
- Department of Industrial and Physical Pharmacy
- College of Pharmacy
- Purdue University
- Indiana 47907
- USA
| | | | | | | | - Yongchao Su
- MRL, Merck & Co., Inc
- Kenilworth
- USA
- Department of Industrial and Physical Pharmacy
- College of Pharmacy
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16
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Wen C, Zhang J, Duan Y, Zhang H, Ma H. A Mini‐Review on Brewer's Spent Grain Protein: Isolation, Physicochemical Properties, Application of Protein, and Functional Properties of Hydrolysates. J Food Sci 2019; 84:3330-3340. [DOI: 10.1111/1750-3841.14906] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/30/2019] [Accepted: 10/01/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Chaoting Wen
- School of Food and Biological EngineeringJiangsu Univ. Zhenjiang 212013 China
| | - Jixian Zhang
- School of Food and Biological EngineeringJiangsu Univ. Zhenjiang 212013 China
| | - Yuqing Duan
- School of Food and Biological EngineeringJiangsu Univ. Zhenjiang 212013 China
- Inst. of Food Physical ProcessingJiangsu Univ. Zhenjiang 212013 China
| | - Haihui Zhang
- School of Food and Biological EngineeringJiangsu Univ. Zhenjiang 212013 China
| | - Haile Ma
- School of Food and Biological EngineeringJiangsu Univ. Zhenjiang 212013 China
- Inst. of Food Physical ProcessingJiangsu Univ. Zhenjiang 212013 China
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17
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Jaroniec CP. Two decades of progress in structural and dynamic studies of amyloids by solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:42-47. [PMID: 31311708 PMCID: PMC6703944 DOI: 10.1016/j.jmr.2019.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 06/22/2019] [Accepted: 07/08/2019] [Indexed: 05/09/2023]
Abstract
In this perspective article I briefly highlight the rapid progress made over the past two decades in atomic level structural and dynamic studies of amyloids, which are representative of non-crystalline biomacromolecular assemblies, by magic-angle spinning solid-state NMR spectroscopy. Given new and continuing developments in solid-state NMR instrumentation and methodology, ongoing research in this area promises to contribute to an improved understanding of amyloid structure, polymorphism, interactions, assembly mechanisms, and biological function and toxicity.
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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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18
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Levin K, Kroeker S. Probing Jahn-Teller distortions in Mn(acac) 3 through paramagnetic interactions in solid-state MAS NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 101:101-109. [PMID: 31150959 DOI: 10.1016/j.ssnmr.2019.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/03/2019] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
The structural and electronic properties of solid coordination compounds are of great interest in a wide variety of applications. The sensitivity of solid-state NMR to local structural environments in the presence of a transition metal with unpaired spins is demonstrated through 13C and 1H MAS NMR spectra of tris(acetylacetonato)manganese (III), Mn(acac)3. The spectral assignment is established using a combination of density-functional theory and experimental NMR methods. An analysis of the spin-density distribution throughout the ligands as probed by NMR provides an understanding of the molecular electronic structure. The paramagnetic interaction enhances the spectral resolution and offers the possibility of using these spectra as structural fingerprints. The unique character of Mn(acac)3 to manifest various degrees of Jahn-Teller distortions allows for a discussion of the relation between the electron occupancy, crystal structure, and 13C NMR peak shifts.
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Affiliation(s)
- Kirill Levin
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Scott Kroeker
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
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19
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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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20
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Perez A, Gaalswyk K, Jaroniec CP, MacCallum JL. High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid‐State NMR Restraints. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alberto Perez
- Department of Chemistry University of Florida Gainesville FL USA
| | - Kari Gaalswyk
- Department of Chemistry University of Calgary Calgary Alberta Canada
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21
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Brodrecht M, Herr K, Bothe S, de Oliveira M, Gutmann T, Buntkowsky G. Efficient Building Blocks for Solid-Phase Peptide Synthesis of Spin Labeled Peptides for Electron Paramagnetic Resonance and Dynamic Nuclear Polarization Applications. Chemphyschem 2019; 20:1475-1487. [PMID: 30950574 DOI: 10.1002/cphc.201900211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/22/2019] [Indexed: 11/11/2022]
Abstract
Specific spin labeling allows the site-selective investigation of biomolecules by EPR and DNP enhanced NMR spectroscopy. A novel spin labeling strategy for commercially available Fmoc-amino acids is developed. In this approach, the PROXYL spin label is covalently attached to the hydroxyl side chain of three amino acids hydroxyproline (Hyp), serine (Ser) and tyrosine (Tyr) by a simple three-step synthesis route. The obtained PROXYL containing building-blocks are N-terminally protected by the Fmoc-protection group, which makes them applicable for the use in solid-phase peptide synthesis (SPPS). This approach allows the insertion of the spin label at any desired position during SPPS, which makes it more versatile than the widely used post synthetic spin labeling strategies. For the final building-blocks, the radical activity is proven by EPR. DNP enhanced solid-state NMR experiments employing these building-blocks in a TCE solution show enhancement factors of up to 26 for 1 H and 13 C (1 H→13 C cross-polarization). To proof the viability of the presented building-blocks for insertion of the spin label during SPPS the penta-peptide Acetyl-Gly-Ser(PROXYL)-Gly-Gly-Gly was synthesized employing the spin labeled Ser building-block. This peptide could successfully be isolated and the spin label activity proved by EPR and DNP NMR measurements, showing enhancement factors of 12.1±0.1 for 1 H and 13.9±0.5 for 13 C (direct polarization).
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Affiliation(s)
- Martin Brodrecht
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Kevin Herr
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Sarah Bothe
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Marcos de Oliveira
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Torsten Gutmann
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.,University Kassel, Institute for Chemistry, Heinrich-Plett-Straße 40, D-34132, Kassel
| | - Gerd Buntkowsky
- Institut für Physikalische Chemie, Technische Universität Darmstadt, 64287, Darmstadt, Germany
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22
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Makrinich M, Goldbourt A. 1H-Detected quadrupolar spin-lattice relaxation measurements under magic-angle spinning solid-state NMR. Chem Commun (Camb) 2019; 55:5643-5646. [PMID: 31026003 DOI: 10.1039/c9cc01176e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proton detection and phase-modulated pulse saturation enable the measurement of spin-lattice relaxation times of "invisible" quadrupolar nuclei with extensively large quadrupolar couplings. For nitrogen-14, efficient cross-polarization is obtained with a long-duration preparation pulse. The experiment paves the way to the characterization of a large variety of materials containing halogens, metals and more.
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Affiliation(s)
- Maria Makrinich
- School of Chemistry, Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Tel Aviv, Israel.
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23
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Perez A, Gaalswyk K, Jaroniec CP, MacCallum JL. High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid-State NMR Restraints. Angew Chem Int Ed Engl 2019; 58:6564-6568. [PMID: 30913341 DOI: 10.1002/anie.201811895] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/01/2019] [Indexed: 11/08/2022]
Abstract
There is a pressing need for new computational tools to integrate data from diverse experimental approaches in structural biology. We present a strategy that combines sparse paramagnetic solid-state NMR restraints with physics-based atomistic simulations. Our approach explicitly accounts for uncertainty in the interpretation of experimental data through the use of a semi-quantitative mapping between the data and the restraint energy that is calibrated by extensive simulations. We apply our approach to solid-state NMR data for the model protein GB1 labeled with Cu2+ -EDTA at six different sites. We are able to determine the structure to 0.9 Å accuracy within a single day of computation on a GPU cluster. We further show that in some cases, the data from only a single paramagnetic tag are sufficient for accurate folding.
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Affiliation(s)
- Alberto Perez
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Kari Gaalswyk
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | | | - Justin L MacCallum
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
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25
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Mukhopadhyay D, Gupta C, Theint T, Jaroniec CP. Peptide bond conformation in peptides and proteins probed by dipolar coupling-chemical shift tensor correlation solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 297:152-160. [PMID: 30396157 PMCID: PMC6289736 DOI: 10.1016/j.jmr.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 05/30/2023]
Abstract
Multidimensional magic-angle spinning solid-state NMR experiments are described that permit cis and trans peptide bonds in uniformly 13C,15N-labeled peptides and proteins to be unambiguously distinguished in residue-specific manner by determining the relative orientations of the amide 13C' CSA and 1H-15N dipolar coupling tensors. The experiments are demonstrated for model peptides glycylglycine and 2,5-diketopiperazine containing trans and cis peptide bonds, respectively. Subsequently, the measurements are extended to two representative proteins that contain exclusively trans peptide bonds, microcrystalline B3 immunoglobulin domain of protein G and Y145Stop human prion protein amyloid fibrils, to illustrate their applicability to a wide range of protein systems.
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Affiliation(s)
- Dwaipayan Mukhopadhyay
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Chitrak Gupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Theint Theint
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States.
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26
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Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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27
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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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28
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Leavesley A, Jain S, Kamniker I, Zhang H, Rajca S, Rajca A, Han S. Maximizing NMR signal per unit time by facilitating the e-e-n cross effect DNP rate. Phys Chem Chem Phys 2018; 20:27646-27657. [PMID: 30375593 PMCID: PMC6370975 DOI: 10.1039/c8cp04909b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamic nuclear polarization (DNP) efficiency is critically dependent on the properties of the radical, solvent, and solute constituting the sample system. In this study, we focused on the three spin e-e-n cross effect (CE)'s influence on the nuclear longitudinal relaxation time constant T1n, the build-up time constants of nuclear magnetic resonance (NMR) signal, TDNP and DNP-enhancement of NMR signal. The dipolar interaction strength between the electron spins driving the e-e-n process was systematically modulated using mono-, di-, tri-, and dendritic-nitroxide radicals, while maintaining a constant global electron spin concentration of 10 mM. Experimental results showed that an increase in electron spin clustering led to an increased electron spin depolarization, as mapped by electron double resonance (ELDOR), and a dramatically shortened T1n and TDNP time constants under static and magic angle spinning (MAS) conditions. A theoretical analysis reveals that strong e-e interactions, caused by electron spin clustering, increase the CE rate. The three spin e-e-n CE is a hitherto little recognized mechanism for shortening T1n and TDNP in solid-state NMR experiments at cryogenic temperatures, and offers a design principle to enhance the effective CE DNP enhancement per unit time. Fast CE rates will benefit DNP at liquid helium temperatures, or at higher magnetic fields and pulsed DNP, where slow e-e-n polarization transfer rate is a key bottleneck to achieving maximal DNP performance.
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Affiliation(s)
- Alisa Leavesley
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
| | - Sheetal Jain
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
| | - Ilia Kamniker
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
| | - Hui Zhang
- Department of Chemistry, University of Nebraska, Lincoln, NE
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, NE
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, NE
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA
- Department of Chemical Engineering, University of California, Santa Barbara, CA
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29
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Theint T, Xia Y, Nadaud PS, Mukhopadhyay D, Schwieters CD, Surewicz K, Surewicz WK, Jaroniec CP. Structural Studies of Amyloid Fibrils by Paramagnetic Solid-State Nuclear Magnetic Resonance Spectroscopy. J Am Chem Soc 2018; 140:13161-13166. [PMID: 30295029 DOI: 10.1021/jacs.8b06758] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Application of paramagnetic solid-state NMR to amyloids is demonstrated, using Y145Stop human prion protein modified with nitroxide spin-label or EDTA-Cu2+ tags as a model. By using sample preparation protocols based on seeding with preformed fibrils, we show that paramagnetic protein analogs can be induced into adopting the wild-type amyloid structure. Measurements of residue-specific intramolecular and intermolecular paramagnetic relaxation enhancements enable determination of protein fold within the fibril core and protofilament assembly. These methods are expected to be widely applicable to other amyloids and protein assemblies.
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Affiliation(s)
- Theint Theint
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Yongjie Xia
- 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
| | - Dwaipayan Mukhopadhyay
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - Charles D Schwieters
- Center for Information Technology , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Krystyna Surewicz
- Department of Physiology and Biophysics , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Witold K Surewicz
- Department of Physiology and Biophysics , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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30
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Walder BJ, Patterson AM, Baltisberger JH, Grandinetti PJ. Hydrogen motional disorder in crystalline iron group chloride dihydrates. J Chem Phys 2018; 149:084503. [PMID: 30193484 DOI: 10.1063/1.5037151] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The principal components and the relative orientation of the 2H paramagnetic shift and quadrupolar coupling tensors have been measured for the MCl2·2D2O family of compounds, M = Mn, Fe, Co, Ni, and Cu, using the two-dimensional shifting-d echo nuclear magnetic resonance experiment in order to determine (1) the degree of unpaired electron delocalization and (2) the number and location of crystallographically distinct hydrogen sites around oxygen and their fractional occupancies. Expressions for the molecular susceptibility of 3d ion systems, where the spin-orbit coupling is a weak perturbation onto the crystal field, are derived using the generalized Van Vleck equation and used to predict molecular susceptibilities. These predicted molecular susceptibilities are combined with various point dipole source configurations modeling unpaired electron delocalization to predict 2H paramagnetic shift tensors at potential deuterium sites. The instantaneous deuterium quadrupolar coupling and shift tensors are then combined with parameterized motional models, developed for trigonally (M = Mn, Fe, Co, and Cu) and pyramidally (M = Ni) coordinated D2O ligands, to obtain the best fit of the experimental 2D spectra. Dipole sources placed onto metal nuclei with a small degree of delocalization onto the chlorine ligands yield good agreement with the experiment for M = Mn, Fe, Co, and Ni, while good agreement for CuCl2·2D2O is obtained with additional delocalization onto the oxygen. Our analysis of the salts with trigonally coordinated water ligands (M = Mn, Fe, Co, and Cu) confirms the presence of bisector flipping and the conclusions from neutron scattering measurements that hydrogen bonding to chlorine on two adjacent chains leads to the water molecule in the [M(D2O)2Cl4] cluster being nearly coplanar with O-M-Cl involving the shortest metal-chlorine bonds of the cluster. In the case of NiCl2·2D2O, the experimental parameters were found to be consistent with a motional model where the D2O ligands are pyramidally coordinated to the metal and undergo bisector flipping while the water ligand additionally hops between two orientations related by a 120° rotation about the Ni-O bond axis. The position of the three crystallographically distinct hydrogen sites in the unit cell was determined along with fractional occupancies. This restricted water ligand motion is likely due to van der Waals interactions and is concerted with the motion of neighboring ligands.
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Affiliation(s)
- Brennan J Walder
- Department of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | - Alex M Patterson
- Department of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | - Jay H Baltisberger
- Division of Natural Science, Mathematics, and Nursing, Berea College, Berea, Kentucky 40403, USA
| | - Philip J Grandinetti
- Department of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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31
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Paluch P, Pawlak T, Ławniczak K, Trébosc J, Lafon O, Amoureux JP, Potrzebowski MJ. Simple and Robust Study of Backbone Dynamics of Crystalline Proteins Employing 1H- 15N Dipolar Coupling Dispersion. J Phys Chem B 2018; 122:8146-8156. [PMID: 30070484 DOI: 10.1021/acs.jpcb.8b04557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new solid-state multidimensional NMR approach based on the cross-polarization with variable-contact pulse sequence [ Paluch , P. ; Pawlak , T. ; Amoureux , J.-P. ; Potrzebowski , M. J. J. Magn. Reson. 233 , 2013 , 56 ], with 1H inverse detection and very fast magic angle spinning (νR = 60 kHz), dedicated to the measurement of local molecular motions of 1H-15N vectors. The introduced three-dimensional experiments, 1H-15N-1H and hCA(N)H, are particularly useful for the study of molecular dynamics of proteins and other complex structures. The applicability and power of this methodology have been revealed by employing as a model sample the GB-1 small protein doped with Na2CuEDTA. The results clearly prove that the dispersion of 1H-15N dipolar coupling constants well correlates with higher order structure of the protein. Our approach complements the conventional studies and offers a fast and reasonably simple method.
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Affiliation(s)
- Piotr Paluch
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland
| | - Karol Ławniczak
- Department of Theoretical Physics, Faculty of Physics and Applied Informatics , University of Łódź , Pomorska 149/153 , PL-90236 Łódź , Poland
| | - Julien Trébosc
- Unit of Catalysis and Chemistry of Solids (UCCS) , Univ. Lille, UMR 8181 , F-59000 Lille , France
| | - Olivier Lafon
- Unit of Catalysis and Chemistry of Solids (UCCS) , Univ. Lille, UMR 8181 , F-59000 Lille , France
| | - Jean-Paul Amoureux
- Unit of Catalysis and Chemistry of Solids (UCCS) , Univ. Lille, UMR 8181 , F-59000 Lille , France.,Bruker France , 34 rue de l'Industrie , F-67166 Wissembourg , France
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland
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32
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Gaalswyk K, Muniyat MI, MacCallum JL. The emerging role of physical modeling in the future of structure determination. Curr Opin Struct Biol 2018; 49:145-153. [DOI: 10.1016/j.sbi.2018.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/04/2018] [Accepted: 03/05/2018] [Indexed: 10/17/2022]
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33
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Mukhopadhyay D, Nadaud PS, Shannon MD, Jaroniec CP. Rapid Quantitative Measurements of Paramagnetic Relaxation Enhancements in Cu(II)-Tagged Proteins by Proton-Detected Solid-State NMR Spectroscopy. J Phys Chem Lett 2017; 8:5871-5877. [PMID: 29148785 PMCID: PMC5720925 DOI: 10.1021/acs.jpclett.7b02709] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We demonstrate rapid quantitative measurements of site-resolved paramagnetic relaxation enhancements (PREs), which are a source of valuable structural restraints corresponding to electron-nucleus distances in the ∼10-20 Å regime, in solid-state nuclear magnetic resonance (NMR) spectra of proteins containing covalent Cu2+-binding tags. Specifically, using protein GB1 K28C-EDTA-Cu2+ mutant as a model, we show the determination of backbone amide 15N longitudinal and 1H transverse PREs within a few hours of experiment time based on proton-detected 2D or 3D correlation spectra recorded with magic-angle spinning frequencies ≥ ∼ 60 kHz for samples containing ∼10-50 nanomoles of 2H,13C,15N-labeled protein back-exchanged in H2O. Additionally, we show that the electron relaxation time for the Cu2+ center, needed to convert PREs into distances, can be estimated directly from the experimental data. Altogether, these results are important for establishing solid-state NMR based on paramagnetic-tagging as a routine tool for structure determination of natively diamagnetic proteins.
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Rogawski R, Sergeyev IV, Zhang Y, Tran TH, Li Y, Tong L, McDermott AE. NMR Signal Quenching from Bound Biradical Affinity Reagents in DNP Samples. J Phys Chem B 2017; 121:10770-10781. [PMID: 29116793 PMCID: PMC5842680 DOI: 10.1021/acs.jpcb.7b08274] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We characterize the effect of specifically bound biradicals on the NMR spectra of dihydrofolate reductase from E. coli. Dynamic nuclear polarization methods enhance the signal-to-noise of solid state NMR experiments by transferring polarization from unpaired electrons of biradicals to nuclei. There has been recent interest in colocalizing the paramagnetic polarizing agents with the analyte of interest through covalent or noncovalent specific interactions. This experimental approach broadens the scope of dynamic nuclear polarization methods by offering the possibility of selective signal enhancements and the potential to work in a broad range of environments. Paramagnetic compounds can have other effects on the NMR spectroscopy of nearby nuclei, including broadening of nuclear resonances due to the proximity of the paramagnetic agent. Understanding the distance dependence of these interactions is important for the success of the technique. Here we explore paramagnetic signal quenching due to a bound biradical, specifically a biradical-derivatized trimethoprim ligand of E. coli dihydrofolate reductase. Biradical-derivatized trimethoprim has nanomolar affinity for its target, and affords strong and selective signal enhancements in dynamic nuclear polarization experiments. In this work, we show that, although the trimethoprim fragment is well ordered, the biradical (TOTAPOL) moiety is disordered when bound to the protein. The distance dependence in bleaching of NMR signal intensity allows us to detect numerous NMR signals in the protein. We present the possibility that static disorder and electron spin diffusion play roles in this observation, among other contributions. The fact that the majority of signals are observed strengthens the case for the use of high affinity or covalent radicals in dynamic nuclear polarization solid state NMR enhancement.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Ivan V Sergeyev
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Yinglu Zhang
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Yongjun Li
- Department of Chemistry, Columbia University , New York, New York 10027, United States
| | - Liang Tong
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University , New York, New York 10027, United States
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35
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Lilly Thankamony AS, Wittmann JJ, Kaushik M, Corzilius B. Dynamic nuclear polarization for sensitivity enhancement in modern solid-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:120-195. [PMID: 29157490 DOI: 10.1016/j.pnmrs.2017.06.002] [Citation(s) in RCA: 273] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/03/2017] [Accepted: 06/08/2017] [Indexed: 05/03/2023]
Abstract
The field of dynamic nuclear polarization has undergone tremendous developments and diversification since its inception more than 6 decades ago. In this review we provide an in-depth overview of the relevant topics involved in DNP-enhanced MAS NMR spectroscopy. This includes the theoretical description of DNP mechanisms as well as of the polarization transfer pathways that can lead to a uniform or selective spreading of polarization between nuclear spins. Furthermore, we cover historical and state-of-the art aspects of dedicated instrumentation, polarizing agents, and optimization techniques for efficient MAS DNP. Finally, we present an extensive overview on applications in the fields of structural biology and materials science, which underlines that MAS DNP has moved far beyond the proof-of-concept stage and has become an important tool for research in these fields.
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Affiliation(s)
- Aany Sofia Lilly Thankamony
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Johannes J Wittmann
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Monu Kaushik
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany.
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36
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van der Wel PCA. Insights into protein misfolding and aggregation enabled by solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 88:1-14. [PMID: 29035839 PMCID: PMC5705391 DOI: 10.1016/j.ssnmr.2017.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 05/17/2023]
Abstract
The aggregation of proteins and peptides into a variety of insoluble, and often non-native, aggregated states plays a central role in many devastating diseases. Analogous processes undermine the efficacy of polypeptide-based biological pharmaceuticals, but are also being leveraged in the design of biologically inspired self-assembling materials. This Trends article surveys the essential contributions made by recent solid-state NMR (ssNMR) studies to our understanding of the structural features of polypeptide aggregates, and how such findings are informing our thinking about the molecular mechanisms of misfolding and aggregation. A central focus is on disease-related amyloid fibrils and oligomers involved in neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntington's disease. SSNMR-enabled structural and dynamics-based findings are surveyed, along with a number of resulting emerging themes that appear common to different amyloidogenic proteins, such as their compact alternating short-β-strand/β-arc amyloid core architecture. Concepts, methods, future prospects and challenges are discussed.
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Affiliation(s)
- Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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37
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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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38
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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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39
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Pilla KB, Gaalswyk K, MacCallum JL. Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28648524 DOI: 10.1016/j.bbapap.2017.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The 3D atomic structures of biomolecules and their complexes are key to our understanding of biomolecular function, recognition, and mechanism. However, it is often difficult to obtain structures, particularly for systems that are complex, dynamic, disordered, or exist in environments like cell membranes. In such cases sparse data from a variety of paramagnetic NMR experiments offers one possible source of structural information. These restraints can be incorporated in computer modeling algorithms that can accurately translate the sparse experimental data into full 3D atomic structures. In this review, we discuss various types of paramagnetic NMR/computational hybrid modeling techniques that can be applied to successful modeling of not only the atomic structure of proteins but also their interacting partners. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
| | - Kari Gaalswyk
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
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40
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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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41
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Pilla KB, Otting G, Huber T. Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts. Structure 2017; 25:559-568. [DOI: 10.1016/j.str.2017.01.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 01/17/2017] [Accepted: 01/29/2017] [Indexed: 11/26/2022]
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42
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Wiegand T, Lacabanne D, Keller K, Cadalbert R, Lecoq L, Yulikov M, Terradot L, Jeschke G, Meier BH, Böckmann A. Solid-state NMR and EPR Spectroscopy of Mn 2+ -Substituted ATP-Fueled Protein Engines. Angew Chem Int Ed Engl 2017; 56:3369-3373. [PMID: 28191714 DOI: 10.1002/anie.201610551] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Indexed: 12/16/2022]
Abstract
Paramagnetic metal ions deliver structural information both in EPR and solid-state NMR experiments, offering a profitable synergetic approach to study bio-macromolecules. We demonstrate the spectral consequences of Mg2+ / Mn2+ substitution and the resulting information contents for two different ATP:Mg2+ -fueled protein engines, a DnaB helicase from Helicobacter pylori active in the bacterial replisome, and the ABC transporter BmrA, a bacterial efflux pump. We show that, while EPR spectra report on metal binding and provide information on the geometry of the metal centers in the proteins, paramagnetic relaxation enhancements identified in the NMR spectra can be used to localize residues at the binding site. Protein engines are ubiquitous and the methods described herein should be applicable in a broad context.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | | | | | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Maxim Yulikov
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
| | - Gunnar Jeschke
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367, Lyon, France
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43
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Wiegand T, Lacabanne D, Keller K, Cadalbert R, Lecoq L, Yulikov M, Terradot L, Jeschke G, Meier BH, Böckmann A. Festkörper-NMR- und EPR-Spektroskopie an Mn2+-substituierten ATP-angetriebenen Proteinmaschinen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry; Labex Ecofect; UMR 5086 CNRS/Université de Lyon; 69367 Lyon Frankreich
| | | | | | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry; Labex Ecofect; UMR 5086 CNRS/Université de Lyon; 69367 Lyon Frankreich
| | - Maxim Yulikov
- Physikalische Chemie; ETH Zürich; 8093 Zürich Schweiz
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry; Labex Ecofect; UMR 5086 CNRS/Université de Lyon; 69367 Lyon Frankreich
| | | | - Beat H. Meier
- Physikalische Chemie; ETH Zürich; 8093 Zürich Schweiz
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry; Labex Ecofect; UMR 5086 CNRS/Université de Lyon; 69367 Lyon Frankreich
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44
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Wang T, Chen Y, Tabuchi A, Cosgrove DJ, Hong M. The Target of β-Expansin EXPB1 in Maize Cell Walls from Binding and Solid-State NMR Studies. PLANT PHYSIOLOGY 2016; 172:2107-2119. [PMID: 27729469 PMCID: PMC5129719 DOI: 10.1104/pp.16.01311] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/07/2016] [Indexed: 05/18/2023]
Abstract
The wall-loosening actions of β-expansins are known primarily from studies of EXPB1 extracted from maize (Zea mays) pollen. EXPB1 selectively loosens cell walls (CWs) of grasses, but its specific binding target is unknown. We characterized EXPB1 binding to sequentially extracted maize CWs, finding that the protein primarily binds glucuronoarabinoxylan (GAX), the major matrix polysaccharide in grass CWs. This binding is strongly reduced by salts, indicating that it is predominantly electrostatic in nature. For direct molecular evidence of EXPB1 binding, we conducted solid-state nuclear magnetic resonance experiments using paramagnetic relaxation enhancement (PRE), which is sensitive to distances between unpaired electrons and nuclei. By mixing 13C-enriched maize CWs with EXPB1 functionalized with a Mn2+ tag, we measured Mn2+-induced PRE Strong 1H and 13C PREs were observed for the carboxyls of GAX, followed by more moderate PREs for carboxyl groups in homogalacturonan and rhamnogalacturonan-I, indicating that EXPB1 preferentially binds GAX In contrast, no PRE was observed for cellulose, indicating very weak interaction of EXPB1 with cellulose. Dynamics experiments show that EXPB1 changes GAX mobility in a complex manner: the rigid fraction of GAX became more rigid upon EXPB1 binding while the dynamic fraction became more mobile. Combining these data with previous results, we propose that EXPB1 loosens grass CWs by disrupting noncovalent junctions between highly substituted GAX and GAX of low substitution, which binds cellulose. This study provides molecular evidence of β-expansin's target in grass CWs and demonstrates a new strategy for investigating ligand binding for proteins that are difficult to express heterologously.
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Affiliation(s)
- Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Yuning Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Akira Tabuchi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Daniel J Cosgrove
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
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45
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Affiliation(s)
- Benjamin J. Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Hoa Q. Do
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Collin G. Borcik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Emily P. Hardy
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
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46
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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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47
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Habenstein B, Loquet A. Solid-state NMR: An emerging technique in structural biology of self-assemblies. Biophys Chem 2016; 210:14-26. [DOI: 10.1016/j.bpc.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022]
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48
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Tamaki H, Egawa A, Kido K, Kameda T, Kamiya M, Kikukawa T, Aizawa T, Fujiwara T, Demura M. Structure determination of uniformly (13)C, (15)N labeled protein using qualitative distance restraints from MAS solid-state (13)C-NMR observed paramagnetic relaxation enhancement. JOURNAL OF BIOMOLECULAR NMR 2016; 64:87-101. [PMID: 26728076 DOI: 10.1007/s10858-015-0010-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/29/2015] [Indexed: 06/05/2023]
Abstract
Magic angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) is a powerful method for structure determination of insoluble biomolecules. However, structure determination by MAS solid-state NMR remains challenging because it is difficult to obtain a sufficient amount of distance restraints owing to spectral complexity. Collection of distance restraints from paramagnetic relaxation enhancement (PRE) is a promising approach to alleviate this barrier. However, the precision of distance restraints provided by PRE is limited in solid-state NMR because of incomplete averaged interactions and intermolecular PREs. In this report, the backbone structure of the B1 domain of streptococcal protein G (GB1) has been successfully determined by combining the CS-Rosetta protocol and qualitative PRE restraints. The derived structure has a Cα RMSD of 1.49 Å relative to the X-ray structure. It is noteworthy that our protocol can determine the correct structure from only three cysteine-EDTA-Mn(2+) mutants because this number of PRE sites is insufficient when using a conventional structure calculation method based on restrained molecular dynamics and simulated annealing. This study shows that qualitative PRE restraints can be employed effectively for protein structure determination from a limited conformational sampling space using a protein fragment library.
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Affiliation(s)
- Hajime Tamaki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Ayako Egawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kouki Kido
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Tomoshi Kameda
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masakatsu Kamiya
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Tomoyasu Aizawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | | | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
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Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins. J Mol Biol 2016; 428:522-32. [DOI: 10.1016/j.jmb.2016.01.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/08/2016] [Accepted: 01/08/2016] [Indexed: 01/23/2023]
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