1
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Schönzart J, Han R, Gennett T, Rienstra CM, Stringer JA. Magnetic Susceptibility Modeling of Magic-Angle Spinning Modules for Part Per Billion Scale Field Homogeneity. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 364:107704. [PMID: 38879926 DOI: 10.1016/j.jmr.2024.107704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/18/2024]
Abstract
Magic-angle spinning (MAS) solid-state NMR methods are crucial in many areas of biology and materials science. Conventional probe designs have often been specified with 0.1 part per million (ppm) or 100 part per billion (ppb) magnetic field resolution, which is a limitation for many modern scientific applications. Here we describe a novel 5-mm MAS module design that significantly improves the linewidth and line shape for solid samples by an improved understanding of the magnetic susceptibility of probe materials and geometrical symmetry considerations, optimized to minimize the overall perturbation to the applied magnetic field (B0). The improved spinning module requires only first and second order shimming adjustments to achieve a sub-Hz resolution of 13C resonances of adamantane at 150 MHz Larmor frequency (14.1Tesla magnetic field). Minimal use of third and higher order shims improves experimental reproducibility upon sample changes and the exact placement within the magnet. Furthermore, the shimming procedure is faster, and the required gradients smaller, thus minimizing thermal drift of the room temperature (RT) shims. We demonstrate these results with direct polarization (Bloch decay) and cross polarization experiments on adamantane over a range of sample geometries and with multiple superconducting magnet systems. For a direct polarization experiment utilizing the entire active sample volume of a 5-mm rotor (90 µl), we achieved full width at half maximum (FWHM) of 0.76 Hz (5 ppb) and baseline resolved the 13C satellite peaks for adamantane as a consequent of the 7.31 Hz (59 ppb) width at 2% intensity. We expect these approaches to be increasingly pivotal for high-resolution solid-state NMR spectroscopy at and above 1 GHz 1H frequencies.
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Affiliation(s)
- Jasmin Schönzart
- Department of Chemistry, Colorado School of Mines, Golden, CO 80501, USA; PhoenixNMR, LLC, Loveland, CO 80503, USA.
| | - Ruixian Han
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI 53706, USA
| | - Thomas Gennett
- Department of Chemistry, Colorado School of Mines, Golden, CO 80501, USA
| | - Chad M Rienstra
- Department of Chemistry, University of Wisconsin -Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin -Madison, Madison, WI 53706, USA; National Magnetic Resonance Facility at Madison, University of Wisconsin - Madison Madison, WI 53706, USA
| | - John A Stringer
- Department of Chemistry, Colorado School of Mines, Golden, CO 80501, USA; PhoenixNMR, LLC, Loveland, CO 80503, USA.
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2
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Henkel A, Galchenkova M, Maracke J, Yefanov O, Klopprogge B, Hakanpää J, Mesters JR, Chapman HN, Oberthuer D. JINXED: just in time crystallization for easy structure determination of biological macromolecules. IUCRJ 2023; 10:253-260. [PMID: 36892542 PMCID: PMC10161778 DOI: 10.1107/s2052252523001653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/23/2023] [Indexed: 05/06/2023]
Abstract
Macromolecular crystallography is a well established method in the field of structural biology and has led to the majority of known protein structures to date. After focusing on static structures, the method is now under development towards the investigation of protein dynamics through time-resolved methods. These experiments often require multiple handling steps of the sensitive protein crystals, e.g. for ligand-soaking and cryo-protection. These handling steps can cause significant crystal damage, and hence reduce data quality. Furthermore, in time-resolved experiments based on serial crystallography, which use micrometre-sized crystals for short diffusion times of ligands, certain crystal morphologies with small solvent channels can prevent sufficient ligand diffusion. Described here is a method that combines protein crystallization and data collection in a novel one-step process. Corresponding experiments were successfully performed as a proof-of-principle using hen egg-white lysozyme and crystallization times of only a few seconds. This method, called JINXED (Just IN time Crystallization for Easy structure Determination), promises high-quality data due to the avoidance of crystal handling and has the potential to enable time-resolved experiments with crystals containing small solvent channels by adding potential ligands to the crystallization buffer, simulating traditional co-crystallization approaches.
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Affiliation(s)
- Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Julia Maracke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Bjarne Klopprogge
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Johanna Hakanpää
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Jeroen R Mesters
- Institut für Biochemie, Universität zu Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
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3
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Shoeman RL, Hartmann E, Schlichting I. Growing and making nano- and microcrystals. Nat Protoc 2023; 18:854-882. [PMID: 36451055 DOI: 10.1038/s41596-022-00777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 08/22/2022] [Indexed: 12/02/2022]
Abstract
Thanks to recent technological advances in X-ray and micro-electron diffraction and solid-state NMR, structural information can be obtained by using much smaller crystals. Thus, microcrystals have become a valuable commodity rather than a mere stepping stone toward obtaining macroscopic crystals. Microcrystals are particularly useful for structure determination using serial data collection approaches at synchrotrons and X-ray free-electron lasers. The latter's enormous peak brilliance and short X-ray pulse duration mean that structural information can be obtained before the effects of radiation damage are seen; these properties also facilitate time-resolved crystallography. To establish defined reaction initiation conditions, microcrystals with a desired and narrow size distribution are critical. Here, we describe milling and seeding techniques as well as filtration approaches for the reproducible and size-adjustable preparation of homogeneous nano- and microcrystals. Nanocrystals and crystal seeds can be obtained by milling using zirconium beads and the BeadBug homogenizer; fragmentation of large crystals yields micro- or nanocrystals by flowing crystals through stainless steel filters by using an HPLC pump. The approaches can be scaled to generate micro- to milliliter quantities of microcrystals, starting from macroscopic crystals. The procedure typically takes 3-5 d, including the time required to grow the microcrystals.
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4
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Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.
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Affiliation(s)
- Yusuke Nishiyama
- JEOL Ltd., Akishima, Tokyo196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa230-0045, Japan
| | - Guangjin Hou
- State Key Laboratory of Catalysis, Dalian National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian116023, China
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad500 046, India
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan41809-1055, United States
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5
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Mehrabi P, Schulz EC. Sample Preparation for Time-Resolved Serial Crystallography: Practical Considerations. Methods Mol Biol 2023; 2652:361-379. [PMID: 37093487 DOI: 10.1007/978-1-0716-3147-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Time-resolved serial crystallography is an emerging method to elucidate the structure-function relationship of biomolecular systems at up to atomic resolution. However, to make this demanding method a success, a number of experimental requirements have to be met. In this chapter, we summarize general guidelines and protocols towards performing time-resolved crystallography experiments, with a particular emphasis on sample requirements and preparation but also a brief excursion into reaction initiation.
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Affiliation(s)
- Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany.
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
| | - Eike C Schulz
- Max Planck Institute for Structure and Dynamics of Matter, Hamburg, Germany.
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
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6
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Cerofolini L, Parigi G, Ravera E, Fragai M, Luchinat C. Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101828. [PMID: 36240720 DOI: 10.1016/j.ssnmr.2022.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR.
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Affiliation(s)
- Linda Cerofolini
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy; Florence Data Science, Università degli Studi di Firenze, Italy.
| | - Marco Fragai
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Magnetic Resonance Center (CERM), Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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7
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Bruno F, Gigli L, Ferraro G, Cavallo A, Michaelis VK, Goobes G, Fratini E, Ravera E. Lysozyme is Sterically Trapped Within the Silica Cage in Bioinspired Silica-Lysozyme Composites: A Multi-Technique Understanding of Elusive Protein-Material Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8030-8037. [PMID: 35738569 PMCID: PMC9261187 DOI: 10.1021/acs.langmuir.2c00836] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Lysozyme is widely known to promote the formation of condensed silica networks from solutions containing silicic acid, in a reproducible and cost-effective way. However, little is known about the fate of the protein after the formation of the silica particles. Also, the relative arrangement of the different components in the resulting material is a matter of debate. In this study, we investigate the nature of the protein-silica interactions by means of solid-state nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and electron microscopy. We find that lysozyme and silica are in intimate contact and strongly interacting, but their interaction is neither covalent nor electrostatic: lysozyme is mostly trapped inside the silica by steric effects.
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Affiliation(s)
- Francesco Bruno
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Lucia Gigli
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Giovanni Ferraro
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia, 3, Sesto Fiorentino 50019, Italy
| | - Andrea Cavallo
- CERTEMA
S.c.a.r.l., S.P. Del
Cipressino Km 10, Cinigiano 58044, Italy
| | | | - Gil Goobes
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Emiliano Fratini
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), via della Lastruccia, 3, Sesto Fiorentino 50019, Italy
| | - Enrico Ravera
- Magnetic
Resonance Center (CERM), University of Florence, via L. Sacconi 6, Sesto Fiorentino 50019, Italy
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via L. Sacconi 6, Sesto Fiorentino 50019, Italy
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8
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Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G. 1H-Detected Biomolecular NMR under Fast Magic-Angle Spinning. Chem Rev 2022; 122:9943-10018. [PMID: 35536915 PMCID: PMC9136936 DOI: 10.1021/acs.chemrev.1c00918] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 02/08/2023]
Abstract
Since the first pioneering studies on small deuterated peptides dating more than 20 years ago, 1H detection has evolved into the most efficient approach for investigation of biomolecular structure, dynamics, and interactions by solid-state NMR. The development of faster and faster magic-angle spinning (MAS) rates (up to 150 kHz today) at ultrahigh magnetic fields has triggered a real revolution in the field. This new spinning regime reduces the 1H-1H dipolar couplings, so that a direct detection of 1H signals, for long impossible without proton dilution, has become possible at high resolution. The switch from the traditional MAS NMR approaches with 13C and 15N detection to 1H boosts the signal by more than an order of magnitude, accelerating the site-specific analysis and opening the way to more complex immobilized biological systems of higher molecular weight and available in limited amounts. This paper reviews the concepts underlying this recent leap forward in sensitivity and resolution, presents a detailed description of the experimental aspects of acquisition of multidimensional correlation spectra with fast MAS, and summarizes the most successful strategies for the assignment of the resonances and for the elucidation of protein structure and conformational dynamics. It finally outlines the many examples where 1H-detected MAS NMR has contributed to the detailed characterization of a variety of crystalline and noncrystalline biomolecular targets involved in biological processes ranging from catalysis through drug binding, viral infectivity, amyloid fibril formation, to transport across lipid membranes.
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Affiliation(s)
- Tanguy Le Marchand
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tobias Schubeis
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Marta Bonaccorsi
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Biochemistry and Biophysics, Stockholm
University, Svante Arrhenius
väg 16C SE-106 91, Stockholm, Sweden
| | - Piotr Paluch
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Daniela Lalli
- Dipartimento
di Scienze e Innovazione Tecnologica, Università
del Piemonte Orientale “A. Avogadro”, Viale Teresa Michel 11, 15121 Alessandria, Italy
| | - Andrew J. Pell
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
- Department
of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Svante Arrhenius väg 16 C, SE-106
91 Stockholm, Sweden
| | - Loren B. Andreas
- Department
for NMR-Based Structural Biology, Max-Planck-Institute
for Multidisciplinary Sciences, Am Fassberg 11, Göttingen 37077, Germany
| | - Kristaps Jaudzems
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006 Latvia
- Faculty
of Chemistry, University of Latvia, Jelgavas 1, Riga LV-1004, Latvia
| | - Jan Stanek
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland
| | - Guido Pintacuda
- Centre
de RMN à Très Hauts Champs de Lyon, UMR 5082 CNRS/ENS
Lyon/Université Claude Bernard Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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9
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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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10
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Li M, Reichert P, Narasimhan C, Sorman B, Xu W, Cote A, Su Y. Investigating Crystalline Protein Suspension Formulations of Pembrolizumab from MAS NMR Spectroscopy. Mol Pharm 2022; 19:936-952. [PMID: 35107019 DOI: 10.1021/acs.molpharmaceut.1c00915] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Developing biological formulations to maintain the chemical and structural integrity of therapeutic antibodies remains a significant challenge. Monoclonal antibody (mAb) crystalline suspension formulation is a promising alternative for high concentration subcutaneous drug delivery. It demonstrates many merits compared to the solution formulation to reach a high concentration at the reduced viscosity and enhanced stability. One main challenge in drug development is the lack of high-resolution characterization of the crystallinity and stability of mAb microcrystals in the native formulations. Conventional analytical techniques often cannot evaluate structural details of mAb microcrystals in the native suspension due to the presence of visible particles, relatively small crystal size, high protein concentration, and multicomponent nature of a liquid formulation. This study demonstrates the first high-resolution characterization of mAb microcrystalline suspension using magic angle spinning (MAS) NMR spectroscopy. Crystalline suspension formulation of pembrolizumab (Keytruda, Merck & Co., Inc., Kenilworth, NJ 07033, U.S.) is utilized as a model system. Remarkably narrow 13C spectral linewidth of approximately 29 Hz suggests a high order of crystallinity and conformational homogeneity of pembrolizumab crystals. The impact of thermal stress and dehydration on the structure, dynamics, and stability of these mAb crystals in the formulation environment is evaluated. Moreover, isotopic labeling and heteronuclear 13C and 15N spectroscopies have been utilized to identify the binding of caffeine in the pembrolizumab crystal lattice, providing molecular insights into the cocrystallization of the protein and ligand. Our study provides valuable structural details for facilitating the design of crystalline suspension formulation of Keytruda and demonstrates the high potential of MAS NMR as an advanced tool for biophysical characterization of biological therapeutics.
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Affiliation(s)
- Mingyue Li
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Paul Reichert
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Bradley Sorman
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Aaron Cote
- Biologics Process Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
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11
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Schulz EC, Yorke BA, Pearson AR, Mehrabi P. Best practices for time-resolved serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2022; 78:14-29. [PMID: 34981758 PMCID: PMC8725164 DOI: 10.1107/s2059798321011621] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments.
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Affiliation(s)
- Eike C. Schulz
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Briony A. Yorke
- School of Chemistry and Bioscience, University of Bradford, Bradford BD7 1DP, United Kingdom
| | - Arwen R. Pearson
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Pedram Mehrabi
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
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12
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Schubeis T, Stanek J, Pintacuda G. Backbone assignment of crystalline E. coli maltose binding protein. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:317-322. [PMID: 33864192 DOI: 10.1007/s12104-021-10023-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
The E.coli maltose binding protein (MBP) is a 42.5 kDa molecule widely employed in many biotechnology applications. Because of its molecular size, it has become the main model system for the development of solution NMR methods adapted to large biomolecular targets. Here, we report virtually complete (~ 90%) backbone resonance assignments obtained on a microcrystalline sample of MBP with 1H-detected solid-state NMR at fast (> 100 kHz) magic-angle spinning. We additionally present the detailed description of the methodology employed for the preparation of the sample and the acquisition and analysis of the NMR spectra. The chemical shifts, obtained with a single uniformly 15N, 13C-labelled and fully-protonated sample and about 2 weeks on a 800 MHz NMR spectrometer, have been deposited to the BMRB under the accession number 50089.
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Affiliation(s)
- Tobias Schubeis
- Centre de Résonance Magnétique Nucléaire à Très Hauts champs (UMR 5082, CNRS/Ecole Normale Supérieure de Lyon/Université Claude Bernard Lyon 1), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Żwirki i Wigury 101, 02089, Warsaw, Poland
| | - Guido Pintacuda
- Centre de Résonance Magnétique Nucléaire à Très Hauts champs (UMR 5082, CNRS/Ecole Normale Supérieure de Lyon/Université Claude Bernard Lyon 1), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.
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13
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Chen Y, Ling J, Li M, Su Y, Arte KS, Mutukuri TT, Taylor LS, Munson EJ, Topp EM, Zhou QT. Understanding the Impact of Protein-Excipient Interactions on Physical Stability of Spray-Dried Protein Solids. Mol Pharm 2021; 18:2657-2668. [PMID: 34096731 PMCID: PMC10042268 DOI: 10.1021/acs.molpharmaceut.1c00189] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mannitol, leucine, and trehalose have been widely used in spray-dried formulations, especially for inhalation formulations. The individual contribution of these excipients on protein physical stability in spray-dried solids was studied here using bovine serum albumin (BSA) as a model protein. The spray-dried solids were characterized with scanning electron microscopy, powder X-ray diffraction, and solid-state Fourier-transform infrared spectroscopy to analyze particle morphology, crystallinity, and secondary structure change, respectively. Advanced solid-state characterizations were conducted with solid-state hydrogen-deuterium exchange (ssHDX) and solid-state nuclear magnetic resonance (ssNMR) to explore protein conformation and molecular interactions in the context of the system physical stability. Trehalose remained amorphous after spray-drying and was miscible with BSA, forming hydrogen bonds to maintain protein conformation, whereby this system showed the least monomer loss in the stability study. As indicated by ssNMR, both crystalline and amorphous forms of mannitol existed in the spray-dried BSA-mannitol solids, which explained its partial stabilizing effect on BSA. Leucine showed the strongest crystallization tendency after spray-drying and did not provide a stabilizing effect due to substantial immiscibility and phase separation with BSA as a result of crystal formation. This work showed novel applications of ssNMR in examining protein conformation and protein-excipient interaction in dry formulations. Overall, our results demonstrate the pivotal role of advanced solid-state characterization techniques in understanding the physical stability of spray-dried protein solids.
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Affiliation(s)
- Yuan Chen
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Jing Ling
- Discovery Pharmaceutical Sciences, Merck & Comapny, Inc., South San Francisco, California 94080, United States
| | - Mingyue Li
- Pharmaceutical Sciences, Merck & Company, Inc., Rahway, New Jersey 07065, United States
| | - Yongchao Su
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.,Pharmaceutical Sciences, Merck & Company, Inc., Rahway, New Jersey 07065, United States
| | - Kinnari Santosh Arte
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Tarun Tejasvi Mutukuri
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Lynne S Taylor
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Eric J Munson
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.,National Institute for Bioprocessing Research and Training, Belfield, Blackrock, Company, Dublin A94 X099, Ireland
| | - Qi Tony Zhou
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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14
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Norton-Baker B, Mehrabi P, Boger J, Schönherr R, von Stetten D, Schikora H, Kwok AO, Martin RW, Miller RJD, Redecke L, Schulz EC. A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip. Acta Crystallogr D Struct Biol 2021; 77:820-834. [PMID: 34076595 PMCID: PMC8171066 DOI: 10.1107/s2059798321003855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/10/2021] [Indexed: 11/12/2022] Open
Abstract
Fixed-target serial crystallography has become an important method for the study of protein structure and dynamics at synchrotrons and X-ray free-electron lasers. However, sample homogeneity, consumption and the physical stress on samples remain major challenges for these high-throughput experiments, which depend on high-quality protein microcrystals. The batch crystallization procedures that are typically applied require time- and sample-intensive screening and optimization. Here, a simple protein crystallization method inside the features of the HARE serial crystallography chips is reported that circumvents batch crystallization and allows the direct transfer of canonical vapor-diffusion conditions to in-chip crystallization. Based on conventional hanging-drop vapor-diffusion experiments, the crystallization solution is distributed into the wells of the HARE chip and equilibrated against a reservoir with mother liquor. Using this simple method, high-quality microcrystals were generated with sufficient density for the structure determination of four different proteins. A new protein variant was crystallized using the protein concentrations encountered during canonical crystallization experiments, enabling structure determination from ∼55 µg of protein. Additionally, structure determination from intracellular crystals grown in insect cells cultured directly in the features of the HARE chips is demonstrated. In cellulo crystallization represents a comparatively unexplored space in crystallization, especially for proteins that are resistant to crystallization using conventional techniques, and eliminates any need for laborious protein purification. This in-chip technique avoids harvesting the sensitive crystals or any further physical handling of the crystal-containing cells. These proof-of-principle experiments indicate the potential of this method to become a simple alternative to batch crystallization approaches and also as a convenient extension to canonical crystallization screens.
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Affiliation(s)
- Brenna Norton-Baker
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Pedram Mehrabi
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Juliane Boger
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Hendrik Schikora
- Scientific Support Unit Machine Physics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Ashley O. Kwok
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA
| | - R. J. Dwayne Miller
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St George Street, Toronto, ON M5S 3H6, Canada
| | - Lars Redecke
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
- Photon Science, Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Eike C. Schulz
- Department for Atomically Resolved Dynamics, Max-Planck-Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
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15
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Klein BA, Tkachuk DG, Terskikh VV, Michaelis VK. Expanding the NMR toolkit for biological solids: oxygen-17 enriched Fmoc-amino acids. NEW J CHEM 2021. [DOI: 10.1039/d1nj02847b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We report the solid-state 17O NMR parameters for five previously uncharacterized N-α-fluoren-9-yl-methoxycarbonyl-O-t-butyl (Fmoc) protected amino acids.
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16
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Proietti N, Di Tullio V, Carsote C, Badea E. 13 C solid-state NMR complemented by ATR-FTIR and micro-DSC to study modern collagen-based material and historical leather. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:840-859. [PMID: 32250473 DOI: 10.1002/mrc.5024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/11/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Ancient vegetable tanned leathers and parchments are very complex materials in which both different manufacturing and deterioration processes make their study and chemical characterisation difficult. In this research, solid-state nuclear magnetic resonance (NMR) spectroscopy was applied to identify different tannin families (condensed and hydrolysable) in historical leather objects such as bookbindings, wall upholsters, footwear and accessories, and military apparel. Furthermore, leather deterioration with special focus on collagen gelatinisation was investigated. A comparison with Fourier transform infrared (FTIR) spectroscopy and micro-differential scanning calorimetry (micro-DSC) was also performed to support the 13 C CP-MAS NMR findings and to point out the advantages and limitations of solid-state NMR in analysing historical and archaeological leathers. A wide database of NMR and FTIR spectra of commercial tannins compounds was also collected in order to characterise historical and archaeological leathers.
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Affiliation(s)
- Noemi Proietti
- "Segre-Capitani" NMR Laboratory, Institute for Biological Systems (ISB-CNR), National Research Council of Italy, Rome, Italy
| | - Valeria Di Tullio
- "Segre-Capitani" NMR Laboratory, Institute for Biological Systems (ISB-CNR), National Research Council of Italy, Rome, Italy
| | - Cristina Carsote
- Center for Research and Physical-Chemical and Biological Investigations, National Museum of Romanian History, Bucharest, Romania
| | - Elena Badea
- Advanced Research for Cultural Heritage Group (ARCH Lab), National Research and Development Institute for Textiles and Leather, ICPI Division, Bucharest, Romania
- Department of Chemistry, Faculty of Sciences, University of Craiova, Craiova, Romania
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17
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El Hariri El Nokab M, van der Wel PC. Use of solid-state NMR spectroscopy for investigating polysaccharide-based hydrogels: A review. Carbohydr Polym 2020; 240:116276. [DOI: 10.1016/j.carbpol.2020.116276] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/22/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022]
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18
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Zhao S, Yang Y, Zhao Y, Li X, Xue Y, Wang S. High-resolution solid-state NMR spectroscopy of hydrated non-crystallized RNA. Chem Commun (Camb) 2019; 55:13991-13994. [PMID: 31687672 DOI: 10.1039/c9cc06552k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We highlight that sufficient hydration of non-crystallized RNA could provide high-resolution solid-state NMR (SSNMR) spectra, with similar spectral quality to the crystallized RNA. This leads to a greatly simplified RNA preparation approach by ethanol precipitation for high-resolution SSNMR studies. It will greatly broaden the scope of SSNMR applications to the characterization of RNAs.
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Affiliation(s)
- Sha Zhao
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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19
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Reese M, George C, Yang C, Jawla S, Grün JT, Schwalbe H, Redfield C, Temkin RJ, Griffin RG. Modular, triple-resonance, transmission line DNP MAS probe for 500 MHz/330 GHz. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 307:106573. [PMID: 31505305 PMCID: PMC6766420 DOI: 10.1016/j.jmr.2019.106573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 06/10/2023]
Abstract
We describe the design and construction of a modular, triple-resonance, fully balanced, DNP-MAS probe based on transmission line technology and its integration into a 500 MHz/330 GHz DNP-NMR spectrometer. A novel quantitative probe design and characterization strategy is developed and employed to achieve optimal sensitivity, RF homogeneity and excellent isolation between channels. The resulting three channel HCN probe has a modular design with each individual, swappable module being equipped with connectorized, transmission line ports. This strategy permits attachment of a mating connector that facilitates accurate impedance measurements at these ports and allows characterization and adjustment (e.g. for balancing or tuning/matching) of each component individually. The RF performance of the probe is excellent; for example, the 13C channel attains a Rabi frequency of 280 kHz for a 3.2 mm rotor. In addition, a frequency tunable 330 GHz gyrotron operating at the second harmonic of the electron cyclotron frequency was developed for DNP applications. Careful alignment of the corrugated waveguide led to minimal loss of the microwave power, and an enhancement factor ε = 180 was achieved for U-13C urea in the glassy matrix at 80 K. We demonstrated the operation of the system with acquisition of multidimensional spectra of cross-linked lysozyme crystals which are insoluble in glycerol-water mixtures used for DNP and samples of RNA.
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Affiliation(s)
- Marcel Reese
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Christy George
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Chen Yang
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Sudheer Jawla
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-Universität Frankfurt, 60438 Frankfurt, Germany
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Richard J Temkin
- Plasma Science and Fusion Center, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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20
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Mehrabi P, Schulz EC, Agthe M, Horrell S, Bourenkov G, von Stetten D, Leimkohl JP, Schikora H, Schneider TR, Pearson AR, Tellkamp F, Miller RJD. Liquid application method for time-resolved analyses by serial synchrotron crystallography. Nat Methods 2019; 16:979-982. [DOI: 10.1038/s41592-019-0553-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 08/06/2019] [Indexed: 01/01/2023]
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21
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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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22
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23
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Hartje LF, Snow CD. Protein crystal based materials for nanoscale applications in medicine and biotechnology. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 11:e1547. [DOI: 10.1002/wnan.1547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/28/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Luke F. Hartje
- Department of Biochemistry and Molecular Biology Colorado State University Fort Collins Colorado
| | - Christopher D. Snow
- Department of Chemical and Biological Engineering Colorado State University Fort Collins Colorado
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24
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Agbaje OBA, Ben Shir I, Zax DB, Schmidt A, Jacob DE. Biomacromolecules within bivalve shells: Is chitin abundant? Acta Biomater 2018; 80:176-187. [PMID: 30217589 DOI: 10.1016/j.actbio.2018.09.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/05/2018] [Accepted: 09/10/2018] [Indexed: 01/09/2023]
Abstract
Bivalve shells are inorganic-organic nanocomposites whose material properties outperform their purely inorganic mineral counterparts. Most typically the inorganic phase is a polymorph of CaCO3, while the organic phase contains biopolymers which have been presumed to be chitin and/or proteins. Identifying the biopolymer phase is therefore a crucial step in improving our understanding of design principles relevant to biominerals. In this work we study seven shells; four are examples of nacroprismatic shells (Alathyria jacksoni, Pinctada maxima, Hyriopsis cumingii and Cucumerunio novaehollandiae), one homogeneous (Arctica islandica), and two are crossed lamellar (Callista kingii, Tridacna gigas). Both intact shells, their organic extracts as isolated after decalcification in acid, and the periostracum overlay have been studied by solid-state CP-MAS NMR, FTIR, SEM and chemical analysis. In none of the shells examined in this work do we find a significant contribution to the organic fraction from chitin or its derivatives despite popular models of bivalve biomineralization which assume abundant chitin in the organic fraction of mollusk bivalve shells. In each of the nacroprismatic extracts the 13C NMR spectra represent similar proteinaceous material, Ala and Gly-rich and primarily organized as β-sheets. A different, yet highly conserved protein was found in the periostracum covering each of the three nacreous shells studied. The Arctica islandica shells with homogeneous microstructure contained proteins which do not appear to be silk-like, while in the crossed lamellar shells we extracted too little organic matter to characterize. STATEMENT OF SIGNIFICANCE: Hydrophobic macromolecules are structural components within the calcareous inorganic matrix of bivalve shells and are responsible for enhanced materials properties of the biominerals. Prevalent models suggest that chitin is such major hydrophobic component. Contrary to that we show that chitin is rare within the hydrophobic biopolymers which primarily consist of proteinaceous matter with structural motifs as silk-like β-sheets, or others yet to be determined. Recognizing that diverse proteinaceous motifs, devoid of abundant chitin, can yield the optimized mechanical properties of bivalve shells is critical both to understand the mechanistic pathways by which they regulate biomineralization and for the design of novel bioinspired materials.
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25
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Martin RW, Kelly JE, Kelz JI. Advances in instrumentation and methodology for solid-state NMR of biological assemblies. J Struct Biol 2018; 206:73-89. [PMID: 30205196 DOI: 10.1016/j.jsb.2018.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 07/08/2018] [Accepted: 09/06/2018] [Indexed: 01/11/2023]
Abstract
Many advances in instrumentation and methodology have furthered the use of solid-state NMR as a technique for determining the structures and studying the dynamics of molecules involved in complex biological assemblies. Solid-state NMR does not require large crystals, has no inherent size limit, and with appropriate isotopic labeling schemes, supports solving one component of a complex assembly at a time. It is complementary to cryo-EM, in that it provides local, atomic-level detail that can be modeled into larger-scale structures. This review focuses on the development of high-field MAS instrumentation and methodology; including probe design, benchmarking strategies, labeling schemes, and experiments that enable the use of quadrupolar nuclei in biomolecular NMR. Current challenges facing solid-state NMR of biological assemblies and new directions in this dynamic research area are also discussed.
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Affiliation(s)
- Rachel W Martin
- Department of Chemistry, University of California, Irvine 92697-2025, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine 92697-3900, United States.
| | - John E Kelly
- Department of Chemistry, University of California, Irvine 92697-2025, United States
| | - Jessica I Kelz
- Department of Chemistry, University of California, Irvine 92697-2025, United States
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26
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Tanaka H, Akutsu H, Yabuta I, Hara M, Sugimoto H, Ikegami T, Watanabe T, Fujiwara T. A novel chitin‐binding mode of the chitin‐binding domain of chitinase A1 from
Bacillus circulans
WL
‐12 revealed by solid‐state
NMR. FEBS Lett 2018; 592:3173-3182. [DOI: 10.1002/1873-3468.13226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Hiroki Tanaka
- Institute for Protein Research Osaka University Suita Japan
| | - Hideo Akutsu
- Institute for Protein Research Osaka University Suita Japan
- Graduate School of Medical Life Science Yokohama City University Tsurumi‐ku Yokohama Japan
| | - Izumi Yabuta
- Institute for Protein Research Osaka University Suita Japan
| | - Masashi Hara
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
| | - Hayuki Sugimoto
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
| | - Takahisa Ikegami
- Institute for Protein Research Osaka University Suita Japan
- Graduate School of Medical Life Science Yokohama City University Tsurumi‐ku Yokohama Japan
| | - Takeshi Watanabe
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
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27
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Yang Y, Wang S. RNA Characterization by Solid-State NMR Spectroscopy. Chemistry 2018; 24:8698-8707. [DOI: 10.1002/chem.201705583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Yufei Yang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
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28
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Opara N, Martiel I, Arnold SA, Braun T, Stahlberg H, Makita M, David C, Padeste C. Direct protein crystallization on ultrathin membranes for diffraction measurements at X-ray free-electron lasers. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717005799] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new era of protein crystallography started when X-ray free-electron lasers (XFELs) came into operation, as these provide an intense source of X-rays that facilitates data collection in the `diffract-before-destroy' regime. In typical experiments, crystals sequentially delivered to the beam are exposed to X-rays and destroyed. Therefore, the novel approach of serial crystallography requires thousands of nearly identical samples. Currently applied sample-delivery methods, in particular liquid jets or drop-on-demand systems, suffer from significant sample consumption of the precious crystalline material. Direct protein microcrystal growth by the vapour diffusion technique inside arrays of nanolitre-sized wells is a method specifically tailored to crystallography at XFELs. The wells, with X-ray transparent Si3N4windows as bottoms, are fabricated in silicon chips. Their reduced dimensions can significantly decrease protein specimen consumption. Arrays provide crystalline samples positioned in an ordered way without the need to handle fragile crystals. The nucleation process inside these microfabricated cavities was optimized to provide high membrane coverage and a quasi-random crystal distribution. Tight sealing of the chips and protection of the crystals from dehydration were achieved, as confirmed by diffraction experiments at a protein crystallography beamline. Finally, the test samples were shown to be suitable for time-resolved measurements at an XFEL at femtosecond resolution.
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Cataract-associated P23T γD-crystallin retains a native-like fold in amorphous-looking aggregates formed at physiological pH. Nat Commun 2017; 8:15137. [PMID: 28474685 PMCID: PMC5424181 DOI: 10.1038/ncomms15137] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 03/02/2017] [Indexed: 01/14/2023] Open
Abstract
Cataracts cause vision loss through the large-scale aggregation of eye lens proteins as a result of ageing or congenital mutations. The development of new treatments is hindered by uncertainty about the nature of the aggregates and their mechanism of formation. We describe the structure and morphology of aggregates formed by the P23T human γD-crystallin mutant associated with congenital cataracts. At physiological pH, the protein forms aggregates that look amorphous and disordered by electron microscopy, reminiscent of the reported formation of amorphous deposits by other crystallin mutants. Surprisingly, solid-state NMR reveals that these amorphous deposits have a high degree of structural homogeneity at the atomic level and that the aggregated protein retains a native-like conformation, with no evidence for large-scale misfolding. Non-physiological destabilizing conditions used in many in vitro aggregation studies are shown to yield qualitatively different, highly misfolded amyloid-like fibrils. Aggregation of eye lens proteins leads to cataracts, a major cause of blindness. Here the authors use solid state NMR to probe the structure of γD-crystallin eye lens proteins aggregates, which are found to retain a native-like conformation.
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Mandal A, Boatz JC, Wheeler TB, van der Wel PCA. On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR. JOURNAL OF BIOMOLECULAR NMR 2017; 67:165-178. [PMID: 28229262 PMCID: PMC5445385 DOI: 10.1007/s10858-017-0089-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/19/2017] [Indexed: 05/07/2023]
Abstract
A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation. We describe our experience of how custom-made (or commercially available) ultracentrifugal devices can facilitate a simple, fast and reliable sample preparation process. A number of groups have since adopted such tools, in some cases to prepare samples for sedimentation-style MAS NMR experiments. Here we argue for a more widespread adoption of their use for routine MAS NMR sample preparation.
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Affiliation(s)
- Abhishek Mandal
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Jennifer C Boatz
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Travis B Wheeler
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15260, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
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31
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Zheng Q, Li K, Yin X, Li B, Li C, Ma Y, Sun J, Chen D. Corrosion Properties of 34CrMo4 Steel Modified by Shot Peening. SCANNING 2017; 2017:1928198. [PMID: 29430276 PMCID: PMC5752997 DOI: 10.1155/2017/1928198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/30/2017] [Accepted: 10/23/2017] [Indexed: 05/12/2023]
Abstract
A nanocrystalline layer was prepared on the surface of 34CrMo4 steel by time controlling shot peening (SP, i.e., 1, 5, 10, and 20 minutes). Field emission scanning electron microscopy (FESEM), X-ray diffraction (XRD) analysis, and transmission electron microscope (TEM) were applied to analyze the surface, cross-sections, and grain size of the specimens before and after SP. The electrochemical corrosion behavior was used to simulate a liquid under the oil and gas wells environment. It was characterized by the potentiodynamic polarization test and electrochemical impedance spectroscopy (EIS). The analysis results show that the surfaces of the SP samples were very rough and had numerous cracks. A passive film on SP surface was formed by nanocrystalline grains. However, the passive film formed in the initial stage was not dense or uniform, and cracks occurred in the passive film during peening, resulting in a decrease in corrosion resistance.
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Affiliation(s)
- Qiang Zheng
- School of Metallurgy and Materials Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Kejian Li
- School of Metallurgy and Materials Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
- The Center of Material Analysis and Testing, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Xueguo Yin
- School of Metallurgy and Materials Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Bingbing Li
- School of Metallurgy and Materials Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Chunhong Li
- School of Metallurgy and Materials Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
- The Center of Material Analysis and Testing, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Yilong Ma
- School of Metallurgy and Materials Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Jianchun Sun
- School of Metallurgy and Materials Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
| | - Dengming Chen
- School of Metallurgy and Materials Engineering, Chongqing University of Science and Technology, Chongqing 401331, China
- The Center of Material Analysis and Testing, Chongqing University of Science and Technology, Chongqing 401331, China
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32
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Quinn CM, Polenova T. Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q Rev Biophys 2017; 50:e1. [PMID: 28093096 PMCID: PMC5483179 DOI: 10.1017/s0033583516000159] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.
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Affiliation(s)
- Caitlin M. Quinn
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
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Nishiyama Y. Fast magic-angle sample spinning solid-state NMR at 60-100kHz for natural abundance samples. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2016; 78:24-36. [PMID: 27400153 DOI: 10.1016/j.ssnmr.2016.06.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
In spite of tremendous progress made in pulse sequence designs and sophisticated hardware developments, methods to improve sensitivity and resolution in solid-state NMR (ssNMR) are still emerging. The rate at which sample is spun at magic angle determines the extent to which sensitivity and resolution of NMR spectra are improved. To this end, the prime objective of this article is to give a comprehensive theoretical and experimental framework of fast magic angle spinning (MAS) technique. The engineering design of fast MAS rotors based on spinning rate, sample volume, and sensitivity is presented in detail. Besides, the benefits of fast MAS citing the recent progress in methodology, especially for natural abundance samples are also highlighted. The effect of the MAS rate on (1)H resolution, which is a key to the success of the (1)H inverse detection methods, is described by a simple mathematical factor named as the homogeneity factor k. A comparison between various (1)H inverse detection methods is also presented. Moreover, methods to reduce the number of spinning sidebands (SSBs) for the systems with huge anisotropies in combination with (1)H inverse detection at fast MAS are discussed.
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Affiliation(s)
- Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 186-8558, Japan.
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Dörner K, Martin-Garcia JM, Kupitz C, Gong Z, Mallet TC, Chen L, Wachter RM, Fromme P. Characterization of Protein Nanocrystals Based on the Reversibility of Crystallization. CRYSTAL GROWTH & DESIGN 2016; 16:3838-3845. [PMID: 29056873 PMCID: PMC5649632 DOI: 10.1021/acs.cgd.6b00384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A new approach is described to screen for protein nanocrystals based on the reversibility of crystallization. Methods to characterize nanocrystals are in strong need to facilitate sample preparation for serial femtosecond X-ray nanocrystallography (SFX). SFX enables protein structure determination by collecting X-ray diffraction from nano- and microcrystals using a free electron laser. This technique is especially valuable for challenging proteins as for example membrane proteins and is in general a powerful method to overcome the radiation damage problem and to perform time-resolved structure analysis. Nanocrystal growth cannot be monitored with common methods used in protein crystallography, as the resolution of bright field microscopy is not sufficient. A high-performance method to screen for nanocrystals is second order nonlinear imaging of chiral crystals (SONICC). However, the high cost prevents its use in every laboratory, and some protein nanocrystals may be "invisible" to SONICC. In this work using a crystallization robot and a common imaging system precipitation comprised of nanocrystals and precipitation caused by aggregated protein can be distinguished.
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Affiliation(s)
- Katerina Dörner
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Jose M Martin-Garcia
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, United States
| | - Christopher Kupitz
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Zhen Gong
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - T Conn Mallet
- Life Science, Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, Texas 77381, United States
| | - Liqing Chen
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Rebekka M Wachter
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Membrane Proteins in Infectious Diseases (MPID), Arizona State University, Box 871604, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, PO Box 875001, Tempe, Arizona 85287, United States
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Hisao GS, Harland MA, Brown RA, Berthold DA, Wilson TE, Rienstra CM. An efficient method and device for transfer of semisolid materials into solid-state NMR spectroscopy rotors. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:172-6. [PMID: 26905816 PMCID: PMC4818695 DOI: 10.1016/j.jmr.2016.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 01/17/2016] [Indexed: 05/23/2023]
Abstract
The study of mass-limited biological samples by magic angle spinning (MAS) solid-state NMR spectroscopy critically relies upon the high-yield transfer of material from a biological preparation into the MAS rotor. This issue is particularly important for maintaining biological activity and hydration of semi-solid samples such as membrane proteins in lipid bilayers, pharmaceutical formulations, microcrystalline proteins and protein fibrils. Here we present protocols and designs for rotor-packing devices specifically suited for packing hydrated samples into Pencil-style 1.6 mm, 3.2 mm standard, and 3.2 mm limited speed MAS rotors. The devices are modular and therefore readily adaptable to other rotor and/or ultracentrifugation tube geometries.
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Affiliation(s)
- Grant S Hisao
- University of Illinois at Urbana-Champaign, Department of Chemistry, 600 South Mathews Avenue, Urbana, IL 61801, USA.
| | - Michael A Harland
- University of Illinois at Urbana-Champaign, School of Chemical Sciences Machine Shop, 505 South Matthews Ave., Urbana, IL 61801, USA.
| | - Robert A Brown
- University of Illinois at Urbana-Champaign, School of Chemical Sciences Machine Shop, 505 South Matthews Ave., Urbana, IL 61801, USA
| | - Deborah A Berthold
- University of Illinois at Urbana-Champaign, Department of Chemistry, 600 South Mathews Avenue, Urbana, IL 61801, USA.
| | - Thomas E Wilson
- University of Illinois at Urbana-Champaign, School of Chemical Sciences Machine Shop, 505 South Matthews Ave., Urbana, IL 61801, USA.
| | - Chad M Rienstra
- University of Illinois at Urbana-Champaign, Department of Chemistry, 600 South Mathews Avenue, Urbana, IL 61801, USA; University of Illinois at Urbana-Champaign, Department of Biochemistry, Center for Biophysics and Quantitative Biology, 600 South Mathews Avenue, Urbana, IL 61801, USA.
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36
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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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37
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:9162-85. [PMID: 26136394 PMCID: PMC4943876 DOI: 10.1002/anie.201410653] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 01/26/2015] [Indexed: 11/07/2022]
Abstract
In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi-author interdisciplinary Review presents a state-of-the-art description of the primary approaches that were considered. Topics discussed included the future of ultrahigh-field NMR systems, emerging NMR detection technologies, new approaches to nuclear hyperpolarization, and progress in sample preparation. All of these are orthogonal efforts, whose gains could multiply and thereby enhance the sensitivity of solid- and liquid-state experiments. While substantial advances have been made in all these areas, numerous challenges remain in the quest of endowing NMR spectroscopy with the sensitivity that has characterized forms of spectroscopies based on electrical or optical measurements. These challenges, and the ways by which scientists and engineers are striving to solve them, are also addressed.
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Affiliation(s)
- Jan-Henrik Ardenkjaer-Larsen
- GE Healthcare, Broendby, Denmark; Department of Electrical Engineering, Technical University of Denmark, Danish Research Centre for Magnetic Resonance, Copenhagen University Hospital Hvidovre (Denmark)
| | - Gregory S Boebinger
- U.S. National High Magnetic Field Lab, Florida State University, Tallahassee, FL 32310 (USA)
| | - Arnaud Comment
- Institute of Physics of Biological Systems, Ecole Polytechnique Fédérale de Lausanne, Lausanne (Switzerland)
| | - Simon Duckett
- Department of Chemistry, University of York, Heslington, York, YO10 5DD (UK)
| | - Arthur S Edison
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610 (USA)
| | | | | | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Lab, MIT, Cambridge, MA 02139-4703 (USA)
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, College Station (USA)
| | - Hidaeki Maeda
- Riken Center for Life Science Technologies, Yokohama, Kanagawa (Japan)
| | - Giacomo Parigi
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | - Thomas Prisner
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Enrico Ravera
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy)
| | | | - Shimon Vega
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel)
| | - Andrew Webb
- Department of Radiology, C. J. Gorter Center for High Field MRI, Leiden University Medical Center (The Netherlands)
| | - Claudio Luchinat
- CERM and Department of Chemistry, University of Florence, Sesto Fiorentino (Italy).
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).
| | - Lucio Frydman
- Chemical Physics Department, Weizmann Institute of Science, Rehovot (Israel).
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38
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Hansen SK, Bertelsen K, Paaske B, Nielsen NC, Vosegaard T. Solid-state NMR methods for oriented membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:48-85. [PMID: 26282196 DOI: 10.1016/j.pnmrs.2015.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.
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Affiliation(s)
- Sara K Hansen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Berit Paaske
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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39
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Ardenkjaer-Larsen JH, Boebinger GS, Comment A, Duckett S, Edison AS, Engelke F, Griesinger C, Griffin RG, Hilty C, Maeda H, Parigi G, Prisner T, Ravera E, van Bentum J, Vega S, Webb A, Luchinat C, Schwalbe H, Frydman L. Neue Ansätze zur Empfindlichkeitssteigerung in der biomolekularen NMR-Spektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410653] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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40
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Brown LS, Ladizhansky V. Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy. Protein Sci 2015; 24:1333-46. [PMID: 25973959 DOI: 10.1002/pro.2700] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022]
Abstract
Membrane proteins play many critical roles in cells, mediating flow of material and information across cell membranes. They have evolved to perform these functions in the environment of a cell membrane, whose physicochemical properties are often different from those of common cell membrane mimetics used for structure determination. As a result, membrane proteins are difficult to study by traditional methods of structural biology, and they are significantly underrepresented in the protein structure databank. Solid-state Nuclear Magnetic Resonance (SSNMR) has long been considered as an attractive alternative because it allows for studies of membrane proteins in both native-like membranes composed of synthetic lipids and in cell membranes. Over the past decade, SSNMR has been rapidly developing into a major structural method, and a growing number of membrane protein structures obtained by this technique highlights its potential. Here we discuss membrane protein sample requirements, review recent progress in SSNMR methodologies, and describe recent advances in characterizing membrane proteins in the environment of a cellular membrane.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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41
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Ravera E, Schubeis T, Martelli T, Fragai M, Parigi G, Luchinat C. NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:60-70. [PMID: 25797005 DOI: 10.1016/j.jmr.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/06/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tobias Schubeis
- Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tommaso Martelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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42
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Xue Y, Skrynnikov NR. Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics. Protein Sci 2015; 23:488-507. [PMID: 24452989 DOI: 10.1002/pro.2433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 01/06/2014] [Accepted: 01/18/2014] [Indexed: 11/07/2022]
Abstract
Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for (15) N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields.
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Affiliation(s)
- Yi Xue
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana, 47907-2084, USA
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Helliwell JR, Brink A, Kaenket S, Starkey VL, Tanley SWM. X-ray diffraction in temporally and spatially resolved biomolecular science. Faraday Discuss 2015; 177:429-41. [PMID: 25605312 DOI: 10.1039/c4fd00166d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why is this? The X-ray laser now gives us femtosecond (fs) duration pulses, typically 10 fs up to ∼50 fs. Their use is attractive for the fastest time-resolved protein crystallography studies. It has been proposed that single molecules could even be studied with the advantage of being able to measure X-ray diffraction from a 'crystal lattice free' single molecule, with or without temporal resolved structural changes. This is altogether very challenging R&D. So as to assist this effort we have undertaken studies of metal clusters that bind to proteins, both 'fresh' and after repeated X-ray irradiation to assess their X-ray-photo-dynamics, namely Ta6Br12, K2PtI6 and K2PtBr6 bound to a test protein, hen egg white lysozyme. These metal complexes have the major advantage of being very recognisable shapes (pseudo spherical or octahedral) and thereby offer a start to (probably very difficult) single molecule electron density map interpretations, both static and dynamic. A further approach is to investigate the X-ray laser beam diffraction strength of a well scattering nano-cluster; an example from nature being the iron containing ferritin. Electron crystallography and single particle electron microscopy imaging offers alternatives to X-ray structural studies; our structural studies of crustacyanin, a 320 kDa protein carotenoid complex, can be extended either by electron based techniques or with the X-ray laser representing a fascinating range of options. General outlook remarks concerning X-ray, electron and neutron macromolecular crystallography as well as 'NMR crystallography' conclude the article.
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Barbet-Massin E, Pell AJ, Retel JS, Andreas LB, Jaudzems K, Franks WT, Nieuwkoop AJ, Hiller M, Higman V, Guerry P, Bertarello A, Knight MJ, Felletti M, Le Marchand T, Kotelovica S, Akopjana I, Tars K, Stoppini M, Bellotti V, Bolognesi M, Ricagno S, Chou JJ, Griffin RG, Oschkinat H, Lesage A, Emsley L, Herrmann T, Pintacuda G. Rapid proton-detected NMR assignment for proteins with fast magic angle spinning. J Am Chem Soc 2014; 136:12489-97. [PMID: 25102442 PMCID: PMC4156866 DOI: 10.1021/ja507382j] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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Using a set of six 1H-detected
triple-resonance NMR
experiments, we establish a method for sequence-specific backbone
resonance assignment of magic angle spinning (MAS) nuclear magnetic
resonance (NMR) spectra of 5–30 kDa proteins. The approach
relies on perdeuteration, amide 2H/1H exchange,
high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling
the use of automated analysis. The method is validated with five examples
of proteins in different condensed states, including two microcrystalline
proteins, a sedimented virus capsid, and two membrane-embedded systems.
In comparison to contemporary 13C/15N-based
methods, this approach facilitates and accelerates the MAS NMR assignment
process, shortening the spectral acquisition times and enabling the
use of unsupervised state-of-the-art computational data analysis protocols
originally developed for solution NMR.
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Affiliation(s)
- Emeline Barbet-Massin
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 69100 Villeurbanne, France
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Zurawel AA, Walsh DJ, Fortier SM, Chidawanyika T, Sengupta S, Zilm K, Supattapone S. Prion nucleation site unmasked by transient interaction with phospholipid cofactor. Biochemistry 2014; 53:68-76. [PMID: 24328062 DOI: 10.1021/bi4014825] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Infectious mammalian prions can be formed de novo from purified recombinant prion protein (PrP) substrate through a pathway that requires the sequential addition of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) and RNA cofactor molecules. Recent studies show that the initial interaction between PrP and POPG causes widespread and persistent conformational changes to form an insoluble intermediate species, termed PrP(Int1). Here, we characterize the mechanism and functional consequences of the interaction between POPG and PrP. Negative-stain electron microscopy of PrP(Int1) revealed the presence of amorphous aggregates. Pull-down and photoaffinity label experiments indicate that POPG induces the formation of a PrP(C) polybasic-domain-binding neoepitope within PrP(Int1). The ongoing presence of POPG is not required to maintain PrP(Int1) structure, as indicated by the absence of stoichiometric levels of POPG in solid-state NMR measurements of PrP(Int1). Together, these results show that a transient interaction with POPG cofactor unmasks a PrP(C) binding site, leading to PrP(Int1) aggregation.
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Affiliation(s)
- Ashley A Zurawel
- Departments of Biochemistry and ‡Medicine, Geisel School of Medicine at Dartmouth , Hanover, New Hampshire 03755, United States
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Fragai M, Luchinat C, Martelli T, Ravera E, Sagi I, Solomonov I, Udi Y. SSNMR of biosilica-entrapped enzymes permits an easy assessment of preservation of native conformation in atomic detail. Chem Commun (Camb) 2014; 50:421-3. [DOI: 10.1039/c3cc46896h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Yamamoto K, Caporini MA, Im S, Waskell L, Ramamoorthy A. Shortening spin-lattice relaxation using a copper-chelated lipid at low-temperatures - A magic angle spinning solid-state NMR study on a membrane-bound protein. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 237:175-181. [PMID: 24246881 PMCID: PMC3868731 DOI: 10.1016/j.jmr.2013.10.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/19/2013] [Accepted: 10/24/2013] [Indexed: 05/21/2023]
Abstract
Inherent low sensitivity of NMR spectroscopy has been a major disadvantage, especially to study biomolecules like membrane proteins. Recent studies have successfully demonstrated the advantages of performing solid-state NMR experiments at very low and ultralow temperatures to enhance the sensitivity. However, the long spin-lattice relaxation time, T1, at very low temperatures is a major limitation. To overcome this difficulty, we demonstrate the use of a copper-chelated lipid for magic angle spinning solid-state NMR measurements on cytochrome-b5 reconstituted in multilamellar vesicles. Our results on multilamellar vesicles containing as small as 0.5mol% of a copper-chelated lipid can significantly shorten T1 of protons, which can be used to considerably reduce the data collection time or to enhance the signal-to-noise ratio. We also monitored the effect of slow cooling on the resolution and sensitivity of (13)C and (15)N signals from the protein and (13)C signals from lipids.
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Affiliation(s)
- Kazutoshi Yamamoto
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States
| | - Marc A Caporini
- Bruker BioSpin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Sangchoul Im
- Department of Anesthesiology, University of Michigan, VA Medical Center, Ann Arbor, MI, United States
| | - Lucy Waskell
- Department of Anesthesiology, University of Michigan, VA Medical Center, Ann Arbor, MI, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States.
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Ferella L, Luchinat C, Ravera E, Rosato A. SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR. JOURNAL OF BIOMOLECULAR NMR 2013; 57:319-26. [PMID: 24243317 DOI: 10.1007/s10858-013-9795-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 11/11/2013] [Indexed: 05/09/2023]
Abstract
We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity--obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device--into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment.
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Affiliation(s)
- Lucio Ferella
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
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Fragai M, Luchinat C, Parigi G, Ravera E. Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 57:155-66. [PMID: 23990200 DOI: 10.1007/s10858-013-9776-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/23/2013] [Indexed: 05/09/2023]
Abstract
Great theoretical and methodological advances are pushing the limits of resolution and sensitivity in solid state NMR (SSNMR). However, sample preparation remains a critical issue for the success of an experiment. The factors affecting spectral quality in SSNMR samples are discussed, examining cases encountered in the literature and presenting new experimental data. A discussion on resolution and sensitivity in sedimented solutes is framed in this context.
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Affiliation(s)
- Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
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