1
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Liu J, Wu XL, Zeng YT, Hu ZH, Lu JX. Solid-state NMR studies of amyloids. Structure 2023; 31:230-243. [PMID: 36750098 DOI: 10.1016/j.str.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/10/2022] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Amyloids have special structural properties and are involved in many aspects of biological function. In particular, amyloids are the cause or hallmarks of a group of notorious and incurable neurodegenerative diseases. The extraordinary high molecular weight and aggregation states of amyloids have posed a challenge for researchers studying them. Solid-state NMR (SSNMR) has been extensively applied to study the structures and dynamics of amyloids for the past 20 or more years and brought us tremendous progress in understanding their structure and related diseases. These studies, at the same time, helped to push SSNMR technical developments in sensitivity and resolution. In this review, some interesting research studies and important technical developments are highlighted to give the reader an overview of the current state of this field.
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Affiliation(s)
- Jing Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xia-Lian Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu-Teng Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhi-Heng Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jun-Xia Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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2
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Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 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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3
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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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Matsunaga T, Okabe R, Ishii Y. Efficient solvent suppression with adiabatic inversion for 1H-detected solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2021; 75:365-370. [PMID: 34674106 DOI: 10.1007/s10858-021-00384-8] [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: 08/14/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
This study introduces a conceptually new solvent suppression scheme with adiabatic inversion pulses for 1H-detected multidimensional solid-state NMR (SSNMR) of biomolecules and other systems, which is termed "Solvent suppression of Liquid signal with Adiabatic Pulse" (SLAP). 1H-detected 2D 13C/1H SSNMR data of uniformly 13C- and 15N-labeled GB1 sample using ultra-fast magic angle spinning at a spinning rate of 60 kHz demonstrated that the SLAP scheme showed up to 3.5-fold better solvent suppression performance over a traditional solvent-suppression scheme for SSNMR, MISSISSIPPI (Zhou and Rienstra, J Magn Reson 192:167-172, 2008) with 2/3 of the average RF power.
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Affiliation(s)
- Tatsuya Matsunaga
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryotaro Okabe
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Yoshitaka Ishii
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
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5
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Wickramasinghe A, Xiao Y, Kobayashi N, Wang S, Scherpelz KP, Yamazaki T, Meredith SC, Ishii Y. Sensitivity-Enhanced Solid-State NMR Detection of Structural Differences and Unique Polymorphs in Pico- to Nanomolar Amounts of Brain-Derived and Synthetic 42-Residue Amyloid-β Fibrils. J Am Chem Soc 2021; 143:11462-11472. [PMID: 34308630 PMCID: PMC10279877 DOI: 10.1021/jacs.1c03346] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid-β (Aβ) fibrils in neuritic plaques are a hallmark of Alzheimer's disease (AD). Since the 42-residue Aβ (Aβ42) fibril is the most pathogenic among different Aβ species, its structural characterization is crucial to our understanding of AD. While several polymorphs have been reported for Aβ40, previous studies of Aβ42 fibrils prepared at neutral pH detected essentially only one structure, with an S-shaped β-sheet arrangement (e.g., Xiao et al. Nat. Struct. Mol. Biol. 2015, 22, 499). Herein, we demonstrate the feasibility of characterizing the structure of trace amounts of brain-derived and synthetic amyloid fibrils by sensitivity-enhanced 1H-detected solid-state NMR (SSNMR) under ultrafast magic angle spinning. By taking advantage of the high sensitivity of this technique, we first demonstrate its applicability for the high-throughput screening of trace amounts of selectively 13C- and 15N-labeled Aβ42 fibril prepared with ∼0.01% patient-derived amyloid (ca. 4 pmol) as a seed. The comparison of 2D 13C/1H SSNMR data revealed marked structural differences between AD-derived Aβ42 (∼40 nmol or ∼200 μg) and synthetic fibrils in less than 10 min, confirming the feasibility of assessing the fibril structure from ∼1 pmol of brain amyloid seed in ∼2.5 h. We also present the first structural characterization of synthetic fully protonated Aβ42 fibril by 1H-detected 3D and 4D SSNMR. With procedures assisted by automated assignments, main-chain resonance assignments were completed for trace amounts (∼42 nmol) of a fully protonated amyloid fibril in the 1H-detection approach. The results suggest that this Aβ42 fibril exhibits a novel fold or polymorph structure.
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Affiliation(s)
- Ayesha Wickramasinghe
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yiling Xiao
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Naohiro Kobayashi
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Songlin Wang
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Kathryn P. Scherpelz
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Toshio Yamazaki
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Stephen C. Meredith
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- NMR Division, RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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6
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Matsunaga T, Matsuda I, Yamazaki T, Ishii Y. Decoherence optimized tilted-angle cross polarization: A novel concept for sensitivity-enhanced solid-state NMR using ultra-fast magic angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 322:106857. [PMID: 33227675 DOI: 10.1016/j.jmr.2020.106857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Ultra-fast magic-angle spinning (UFMAS) at a MAS rate (ωR/2π) of 60 kHz or higher has dramatically improved the resolution and sensitivity of solid-state NMR (SSNMR). However, limited polarization transfer efficiency using cross-polarization (CP) between 1H and rare spins such as 13C still restricts the sensitivity and multi-dimensional applications of SSNMR using UFMAS. We propose a novel approach, which we call decoherence-optimized tilted-angle CP (DOTA CP), to improve CP efficiency with prolonged lifetime of 1H coherence in the spin-locked condition and efficient band-selective polarization transfer by incorporating off-resonance irradiation to 1H spins. 13C CP-MAS at ωR/2π of 70-90 kHz suggested that DOTA CP notably outperformed traditional adiabatic CP, a de-facto-standard CP scheme over the past decade, in sensitivity for the aliphatic-region spectra of 13C-labeled GB1 protein and N-formyl-Met-Leu-Phe samples by up to 1.4- and 1.2-fold, respectively. 1H-detected 2D 1H/13C SSNMR for the GB1 sample indicated the effectiveness of this approach in various multidimensional applications.
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Affiliation(s)
- Tatsuya Matsunaga
- NMR Division, the RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Isamu Matsuda
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.
| | - Toshio Yamazaki
- NMR Division, the RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yoshitaka Ishii
- NMR Division, the RIKEN SPring-8 Center, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.
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7
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Li M, Meng F, Tsutsumi Y, Amoureux JP, Xu W, Lu X, Zhang F, Su Y. Understanding Molecular Interactions in Rafoxanide–Povidone Amorphous Solid Dispersions from Ultrafast Magic Angle Spinning NMR. Mol Pharm 2020; 17:2196-2207. [DOI: 10.1021/acs.molpharmaceut.0c00317] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mingyue Li
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Fan Meng
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | - Jean-Paul Amoureux
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR 8181-UCCS Unit of Catalysis and Chemistry of Solids, F-59000 Lille, France
- Bruker Biospin, 34 Rue de l’Industrie, F-67166 Wissembourg, France
- Riken NMR Science and Development Division, Yokohama, 230-0045 Kanagawa Japan
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Xingyu Lu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Feng Zhang
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
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8
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Venkatesh A, Hung I, Boteju KC, Sadow AD, Gor'kov PL, Gan Z, Rossini AJ. Suppressing 1H Spin Diffusion in Fast MAS Proton Detected Heteronuclear Correlation Solid-State NMR Experiments. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 105:101636. [PMID: 31816590 DOI: 10.1016/j.ssnmr.2019.101636] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
Fast magic angle spinning (MAS) and indirect detection by high gyromagnetic ratio (γ) nuclei such as proton or fluorine are increasingly utilized to obtain 2D heteronuclear correlation (HETCOR) solid-state NMR spectra of spin-1/2 nuclei by using cross polarization (CP) for coherence transfer. However, one major drawback of CP HETCOR pulse sequences is that 1H spin diffusion during the back X→1H CP transfer step may result in relayed correlations. This problem is particularly pronounced for the indirect detection of very low-γ nuclei such as 89Y, 103Rh, 109Ag and 183W where long contact times on the order of 10-30 ms are necessary for optimal CP transfer. Here we propose two methods that eliminate relayed correlations and allow more reliable distance information to be obtained from 2D HETCOR NMR spectra. The first method uses Lee-Goldburg (LG) CP during the X→1H back-transfer step to suppress 1H spin diffusion. We determine LG conditions compatible with fast MAS frequencies (νrot) of 40-95 kHz and show that 1H spin diffusion can be efficiently suppressed at low effective radiofrequency (RF) fields (ν1,eff ≪ 0.5νrot) and also at high effective RF fields (ν1,eff ≫ 2νrot). We describe modified Hartmann-Hahn LG-CP match conditions compatible with fast MAS and suitable for indirect detection of moderate-γ nuclei such as 13C, and low-γ nuclei such as 89Y. The second method uses D-RINEPT (dipolar refocused insensitive nuclei enhanced by polarization transfer) during the X→1H back-transfer step of the HETCOR pulse sequence. The effectiveness of these methods for acquiring HETCOR spectra with reduced relayed signal intensities is demonstrated with 1H{13C} HETCOR NMR experiments on l-histidine⋅HCl⋅H2O and 1H{89Y} HETCOR NMR experiments on an organometallic yttrium complex.
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Affiliation(s)
- Amrit Venkatesh
- US DOE Ames Laboratory, Ames, IA, USA, 50011; Iowa State University, Department of Chemistry, Ames, IA, USA, 50011
| | - Ivan Hung
- National High Magnetic Field Laboratory (NHMFL), Tallahassee, FL, USA, 32310
| | - Kasuni C Boteju
- US DOE Ames Laboratory, Ames, IA, USA, 50011; Iowa State University, Department of Chemistry, Ames, IA, USA, 50011
| | - Aaron D Sadow
- US DOE Ames Laboratory, Ames, IA, USA, 50011; Iowa State University, Department of Chemistry, Ames, IA, USA, 50011
| | - Peter L Gor'kov
- National High Magnetic Field Laboratory (NHMFL), Tallahassee, FL, USA, 32310
| | - Zhehong Gan
- National High Magnetic Field Laboratory (NHMFL), Tallahassee, FL, USA, 32310
| | - Aaron J Rossini
- US DOE Ames Laboratory, Ames, IA, USA, 50011; Iowa State University, Department of Chemistry, Ames, IA, USA, 50011.
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9
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Struppe J, Quinn CM, Sarkar S, Gronenborn AM, Polenova T. Ultrafast 1H MAS NMR Crystallography for Natural Abundance Pharmaceutical Compounds. Mol Pharm 2020; 17:674-682. [PMID: 31891271 DOI: 10.1021/acs.molpharmaceut.9b01157] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Magic angle spinning (MAS) NMR is a powerful method for the study of pharmaceutical compounds, and probes with spinning frequencies above 100 kHz enable an atomic-resolution analysis of sub-micromole quantities of fully protonated solids. Here, we present an ultrafast NMR crystallography approach for structural characterization of organic solids at MAS frequencies of 100-111 kHz. We assess the efficiency of 1H-detected experiments in the solid state and demonstrate the utility of 2D and 3D homo- and heteronuclear correlation spectra for resonance assignments. These experiments are demonstrated for an amino acid, U-13C,15N-histidine, and also for the significantly larger, natural product Posaconazole, an antifungal compound investigated at natural abundance. Our results illustrate the power for characterizing organic molecules, enabled by exploiting the increased 1H resolution and sensitivity at MAS frequencies above 100 kHz.
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Affiliation(s)
- Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sucharita Sarkar
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Angela M Gronenborn
- Department of Structural Biology , University of Pittsburgh School of Medicine , Pittsburgh , Pennsylvania 15260 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , Pittsburgh , Pennsylvania 15260 , United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , Pittsburgh , Pennsylvania 15260 , United States
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10
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Lu X, Tsutsumi Y, Huang C, Xu W, Byrn SR, Templeton AC, Buevich AV, Amoureux JP, Su Y. Molecular packing of pharmaceuticals analyzed with paramagnetic relaxation enhancement and ultrafast magic angle pinning NMR. Phys Chem Chem Phys 2020; 22:13160-13170. [DOI: 10.1039/d0cp02049d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Probing molecular details of fluorinated pharmaceutical compounds at a faster acquisition utilizing paramagnetic relaxation enhancement and better resolution from ultrafast magic angle spinning (νrot = 110 kHz) and high magnetic field (B0 = 18.8 T).
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Affiliation(s)
| | | | | | - Wei Xu
- MRL, Merck & Co., Inc
- Kenilworth
- USA
| | - Stephen R. Byrn
- Department of Industrial and Physical Pharmacy
- College of Pharmacy
- Purdue University
- Indiana 47907
- USA
| | | | | | | | - Yongchao Su
- MRL, Merck & Co., Inc
- Kenilworth
- USA
- Department of Industrial and Physical Pharmacy
- College of Pharmacy
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11
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Wang S, Gopinath T, Veglia G. Improving the quality of oriented membrane protein spectra using heat-compensated separated local field experiments. JOURNAL OF BIOMOLECULAR NMR 2019; 73:617-624. [PMID: 31463642 PMCID: PMC6861693 DOI: 10.1007/s10858-019-00273-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/21/2019] [Indexed: 05/03/2023]
Abstract
Oriented sample solid-state NMR (OS-ssNMR) spectroscopy is a powerful technique to determine the topology of membrane proteins in oriented lipid bilayers. Separated local field (SLF) experiments are central to this technique as they provide first-order orientational restraints, i.e., dipolar couplings and anisotropic chemical shifts. Despite the use of low-E (or E-free) probes, the heat generated during the execution of 2D and 3D SLF pulse sequences causes sizeable line-shape distortions. Here, we propose a new heat-compensated SE-SAMPI4 (hcSE-SAMPI4) pulse sequence that holds the temperature constant for the duration of the experiment. This modification of the SE-SAMPI4 results in sharper and more intense resonances without line-shape distortions. The spectral improvements are even more apparent when paramagnetic relaxation agents are used to speed up data collection. We tested the hcSE-SAMPI4 pulse sequence on a single-span membrane protein, sarcolipin (SLN), reconstituted in magnetically aligned lipid bicelles. In addition to eliminating peak distortions, the hcSE-SAMPI4 experiment increased the average signal-to-noise ratio by 20% with respect to the original SE-SAMPI4.
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Affiliation(s)
- Songlin Wang
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - T Gopinath
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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12
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Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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13
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Potnuru LR, Ramanathan KV. Polarization inversion applied to proton MAS-NMR spectroscopy - Methylene and methine free proton NMR spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 296:181-187. [PMID: 30292003 DOI: 10.1016/j.jmr.2018.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/22/2018] [Accepted: 09/22/2018] [Indexed: 06/08/2023]
Abstract
Polarization-inversion (PI) has been applied to proton magic angle spinning (MAS) NMR spectra recorded under fast MAS conditions. The combination of cross-polarization (CP) from carbon to proton and subsequent polarization-inversion produces strong oscillatory behavior in the proton signal intensities at high MAS speeds of 60 kHz. It is observed that by a suitable choice of the polarization-inversion time, a proton spectrum free of methylene and methine protons can be obtained. Such a spectrum, on the one hand, increases the resolution of the crowded proton spectrum and on the other hand provides exclusively chemical shifts of protons such as NH, OH and SH which might otherwise overlap with carbon attached protons. The oscillations observed during PI can also be used to estimate the dipolar coupling between proton and carbon by Fourier transformation of data acquired at equally incremented time periods. The utility of the above ideas has been demonstrated on a set of molecules with both 13C labeled and 13C in natural abundance.
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Affiliation(s)
- Lokeswara Rao Potnuru
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India; Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - K V Ramanathan
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India.
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14
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Wi S, Schurko RW, Frydman L. Broadband adiabatic inversion cross-polarization phenomena in the NMR of rotating solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 94:31-53. [PMID: 30125798 DOI: 10.1016/j.ssnmr.2018.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
We explore the use of cross-polarization magic-angle spinning (CPMAS) methods incorporating an adiabatic frequency sweep in a standard Hartman-Hahn CPMAS pulse scheme, to achieve signal enhancements in solid-state NMR spectra of rare spins under fast MAS spinning rates, including spin-1/2, integer spin, and half-integer spin nuclides. These experiments, dubbed Broadband Adiabatic INversion Cross-Polarization Magic-Angle Spinning (BRAIN-CPMAS) experiments, involve an adiabatic inversion pulse on the S-channel of a rare spin nuclide while simultaneously applying a conventional spin-locking pulse on the I-channel (1H). The signal enhancement imparted by this CP scheme on the S-spin is broadbanded, while employing low RF field strengths on both I- and S-channels. A feature demanded by these BRAIN-CPMAS methods is to impose a selective adiabatic frequency sweep over a single MAS spinning centerband or sideband, to avoid interference between the MAS modulation and sweeps over multiple sidebands. Upon implementing this swept-CP method, a number of MAS-driven processes happen, including broadband zero- and double-quantum CP transfers, and MAS-driven rotary-resonance phenomena. When this CP method is applied to integer and half-integer quadrupolar nuclei at very fast MAS spinning rates, a favorable double-quantum CP condition is found that can be easily achieved, and avoids the level-crossings among various ms energy levels that complicate quadrupolar CPMAS NMR experiments along lines first shown by Alex Vega. An additional CP mechanism was found in the 1H-2H case, involving static-like zero-quantum CP modes driven by a quadrupole-modulated RF-dipolar zero-order recoupling under MAS. All these phenomena were examined using average Hamiltonian theory, numerical simulations, and experiments on model compounds. Sensitivity-enhanced, distortion-free CP over wide bandwidths were predicted and observed for S = 1/2 and for S = 1 (2H) under fast MAS rates. BRAIN-CPMAS also delivered undistorted central transition NMR spectra of half-integer quadrupolar nuclei, while utilizing low RF field strengths that avoid complex level-crossing effects under high MAS rates.
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Affiliation(s)
- Sungsool Wi
- National High Magnetic Field Laboratory, Tallahassee, FL, 32304, USA.
| | - Robert W Schurko
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, NPB 3P4, Canada
| | - Lucio Frydman
- National High Magnetic Field Laboratory, Tallahassee, FL, 32304, USA; Department of Chemical and Biological Physics, Weizmann Institute of Sciences, Rehovot, 76100, Israel.
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15
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Potnuru LR, Yarava JR, Pahari B, Ramanathan K. Use of reverse cross-polarization for editing solid–state proton NMR spectra. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.04.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Paluch P, Pawlak T, Ławniczak K, Trébosc J, Lafon O, Amoureux JP, Potrzebowski MJ. Simple and Robust Study of Backbone Dynamics of Crystalline Proteins Employing 1H- 15N Dipolar Coupling Dispersion. J Phys Chem B 2018; 122:8146-8156. [PMID: 30070484 DOI: 10.1021/acs.jpcb.8b04557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new solid-state multidimensional NMR approach based on the cross-polarization with variable-contact pulse sequence [ Paluch , P. ; Pawlak , T. ; Amoureux , J.-P. ; Potrzebowski , M. J. J. Magn. Reson. 233 , 2013 , 56 ], with 1H inverse detection and very fast magic angle spinning (νR = 60 kHz), dedicated to the measurement of local molecular motions of 1H-15N vectors. The introduced three-dimensional experiments, 1H-15N-1H and hCA(N)H, are particularly useful for the study of molecular dynamics of proteins and other complex structures. The applicability and power of this methodology have been revealed by employing as a model sample the GB-1 small protein doped with Na2CuEDTA. The results clearly prove that the dispersion of 1H-15N dipolar coupling constants well correlates with higher order structure of the protein. Our approach complements the conventional studies and offers a fast and reasonably simple method.
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Affiliation(s)
- Piotr Paluch
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland
| | - Karol Ławniczak
- Department of Theoretical Physics, Faculty of Physics and Applied Informatics , University of Łódź , Pomorska 149/153 , PL-90236 Łódź , Poland
| | - Julien Trébosc
- Unit of Catalysis and Chemistry of Solids (UCCS) , Univ. Lille, UMR 8181 , F-59000 Lille , France
| | - Olivier Lafon
- Unit of Catalysis and Chemistry of Solids (UCCS) , Univ. Lille, UMR 8181 , F-59000 Lille , France
| | - Jean-Paul Amoureux
- Unit of Catalysis and Chemistry of Solids (UCCS) , Univ. Lille, UMR 8181 , F-59000 Lille , France.,Bruker France , 34 rue de l'Industrie , F-67166 Wissembourg , France
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies , Polish Academy of Sciences , Sienkiewicza 112 , PL-90363 Łódź , Poland
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17
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Gupta R, Polenova T. Magic angle spinning NMR spectroscopy guided atomistic characterization of structure and dynamics in HIV-1 protein assemblies. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2017.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Ishii Y, Wickramasinghe A, Matsuda I, Endo Y, Ishii Y, Nishiyama Y, Nemoto T, Kamihara T. Progress in proton-detected solid-state NMR (SSNMR): Super-fast 2D SSNMR collection for nano-mole-scale proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 286:99-109. [PMID: 29223566 PMCID: PMC6387629 DOI: 10.1016/j.jmr.2017.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 05/22/2023]
Abstract
Proton-detected solid-state NMR (SSNMR) spectroscopy has attracted much attention due to its excellent sensitivity and effectiveness in the analysis of trace amounts of amyloid proteins and other important biological systems. In this perspective article, we present the recent sensitivity limit of 1H-detected SSNMR using "ultra-fast" magic-angle spinning (MAS) at a spinning rate (νR) of 80-100 kHz. It was demonstrated that the high sensitivity of 1H-detected SSNMR at νR of 100 kHz and fast recycling using the paramagnetic-assisted condensed data collection (PACC) approach permitted "super-fast" collection of 1H-detected 2D protein SSNMR. A 1H-detected 2D 1H-15N correlation SSNMR spectrum for ∼27 nmol of a uniformly 13C- and 15N-labeled GB1 protein sample in microcrystalline form was acquired in only 9 s with 50% non-uniform sampling and short recycle delays of 100 ms. Additional data suggests that it is now feasible to detect as little as 1 nmol of the protein in 5.9 h by 1H-detected 2D 1H-15N SSNMR at a nominal signal-to-noise ratio of five. The demonstrated sensitivity is comparable to that of modern solution protein NMR. Moreover, this article summarizes the influence of ultra-fast MAS and 1H-detection on the spectral resolution and sensitivity of protein SSNMR. Recent progress in signal assignment and structural elucidation by 1H-detected protein SSNMR is outlined with both theoretical and experimental aspects.
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Affiliation(s)
- Yoshitaka Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, Kanagawa 226-8503, Japan; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States; The RIKEN Center for Life Science Technologies (CLST), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Ayesha Wickramasinghe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, Kanagawa 226-8503, Japan; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States; The RIKEN Center for Life Science Technologies (CLST), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Isamu Matsuda
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama, Kanagawa 226-8503, Japan; Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Yuki Endo
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Yuji Ishii
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan; RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Nemoto
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
| | - Takayuki Kamihara
- The RIKEN Center for Life Science Technologies (CLST), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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19
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Struppe J, Quinn CM, Lu M, Wang M, Hou G, Lu X, Kraus J, Andreas LB, Stanek J, Lalli D, Lesage A, Pintacuda G, Maas W, Gronenborn AM, Polenova T. Expanding the horizons for structural analysis of fully protonated protein assemblies by NMR spectroscopy at MAS frequencies above 100 kHz. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:117-125. [PMID: 28732673 PMCID: PMC5824719 DOI: 10.1016/j.ssnmr.2017.07.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/28/2017] [Accepted: 07/02/2017] [Indexed: 05/20/2023]
Abstract
The recent breakthroughs in NMR probe technologies resulted in the development of MAS NMR probes with rotation frequencies exceeding 100 kHz. Herein, we explore dramatic increases in sensitivity and resolution observed at MAS frequencies of 110-111 kHz in a novel 0.7 mm HCND probe that enable structural analysis of fully protonated biological systems. Proton- detected 2D and 3D correlation spectroscopy under such conditions requires only 0.1-0.5 mg of sample and a fraction of time compared to conventional 13C-detected experiments. We discuss the performance of several proton- and heteronuclear- (13C-,15N-) based correlation experiments in terms of sensitivity and resolution, using a model microcrystalline fMLF tripeptide. We demonstrate the applications of ultrafast MAS to a large, fully protonated protein assembly of the 231-residue HIV-1 CA capsid protein. Resonance assignments of protons and heteronuclei, as well as 1H-15N dipolar and 1HN CSA tensors are readily obtained from the high sensitivity and resolution proton-detected 3D experiments. The approach demonstrated here is expected to enable the determination of atomic-resolution structures of large protein assemblies, inaccessible by current methodologies.
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Affiliation(s)
- Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States.
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Manman Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Mingzhang Wang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Jodi Kraus
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Loren B Andreas
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Jan Stanek
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Daniela Lalli
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Anne Lesage
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280 CNRS / Ecole Normale Supérieure de Lyon, 5 rue de la Doua, 69100, Villeurbanne, Lyon, France
| | - Werner Maas
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, United States
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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20
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Malon M, Pandey MK, Nishiyama Y. Revealing the Local Proton Network through Three-Dimensional 13C/ 1H Double-Quantum/ 1H Single-Quantum and 1H Double-Quantum/ 13C/ 1H Single-Quantum Correlation Fast Magic-Angle Spinning Solid-State NMR Spectroscopy at Natural Abundance. J Phys Chem B 2017; 121:8123-8131. [PMID: 28782953 DOI: 10.1021/acs.jpcb.7b06203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
1H double quantum (DQ)/1H single quantum (SQ) correlation solid-state NMR spectroscopy is widely used to obtain internuclear 1H-1H proximities, especially at fast magic-angle spinning (MAS) rate (>60 kHz). However, to date, 1H signals are not well-resolved because of intense 1H-1H homonuclear dipolar interactions even at the attainable maximum MAS frequencies of ∼100 kHz and/or under 1H-1H homonuclear dipolar decoupling irradiations. Here we introduce novel three-dimensional (3D) experiments to resolve the 1H DQ/1H SQ correlation peaks using the additional 13C dimension. Although the low natural abundance of 13C (1.1%) significantly reduces the sensitivities, the 1H indirect measurements alleviate this issue and make this experiment possible even in naturally abundant samples. The two different implementations of 13C/1H DQ/1H SQ correlations and 1H DQ/13C/1H SQ correlations are discussed and demonstrated using l-histidine·HCl·H2O at natural abundance to reveal the local 1H-1H networks near each 13C. In addition, the complete 1H resonance assignments are achieved from a single 3D 13C/1H DQ/1H SQ experiment. We have also demonstrated the applicability of our proposed method on a biologically relevant molecule, capsaicin.
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Affiliation(s)
- Michal Malon
- RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan.,JEOL RESONANCE Inc., Akishima, Tokyo 196-8558, Japan
| | - Manoj Kumar Pandey
- Department of Chemistry, Indian Institute of Technology Ropar , Rupnagar, Punjab 140001, India
| | - Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan.,JEOL RESONANCE Inc., Akishima, Tokyo 196-8558, Japan
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21
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Pindelska E, Sokal A, Kolodziejski W. Pharmaceutical cocrystals, salts and polymorphs: Advanced characterization techniques. Adv Drug Deliv Rev 2017; 117:111-146. [PMID: 28931472 DOI: 10.1016/j.addr.2017.09.014] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/21/2017] [Accepted: 09/14/2017] [Indexed: 12/11/2022]
Abstract
The main goal of a novel drug development is to obtain it with optimal physiochemical, pharmaceutical and biological properties. Pharmaceutical companies and scientists modify active pharmaceutical ingredients (APIs), which often are cocrystals, salts or carefully selected polymorphs, to improve the properties of a parent drug. To find the best form of a drug, various advanced characterization methods should be used. In this review, we have described such analytical methods, dedicated to solid drug forms. Thus, diffraction, spectroscopic, thermal and also pharmaceutical characterization methods are discussed. They all are necessary to study a solid API in its intrinsic complexity from bulk down to the molecular level, gain information on its structure, properties, purity and possible transformations, and make the characterization efficient, comprehensive and complete. Furthermore, these methods can be used to monitor and investigate physical processes, involved in the drug development, in situ and in real time. The main aim of this paper is to gather information on the current advancements in the analytical methods and highlight their pharmaceutical relevance.
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22
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Rajput L, Banik M, Yarava JR, Joseph S, Pandey MK, Nishiyama Y, Desiraju GR. Exploring the salt-cocrystal continuum with solid-state NMR using natural-abundance samples: implications for crystal engineering. IUCRJ 2017; 4:466-475. [PMID: 28875033 PMCID: PMC5571809 DOI: 10.1107/s205225251700687x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/08/2017] [Indexed: 05/14/2023]
Abstract
There has been significant recent interest in differentiating multicomponent solid forms, such as salts and cocrystals, and, where appropriate, in determining the position of the proton in the X-H⋯A-YX-⋯H-A+-Y continuum in these systems, owing to the direct relationship of this property to the clinical, regulatory and legal requirements for an active pharmaceutical ingredient (API). In the present study, solid forms of simple cocrystals/salts were investigated by high-field (700 MHz) solid-state NMR (ssNMR) using samples with naturally abundant 15N nuclei. Four model compounds in a series of prototypical salt/cocrystal/continuum systems exhibiting {PyN⋯H-O-}/{PyN+-H⋯O-} hydrogen bonds (Py is pyridine) were selected and prepared. The crystal structures were determined at both low and room temperature using X-ray diffraction. The H-atom positions were determined by measuring the 15N-1H distances through 15N-1H dipolar interactions using two-dimensional inversely proton-detected cross polarization with variable contact-time (invCP-VC) 1H→15N→1H experiments at ultrafast (νR ≥ 60-70 kHz) magic angle spinning (MAS) frequency. It is observed that this method is sensitive enough to determine the proton position even in a continuum where an ambiguity of terminology for the solid form often arises. This work, while carried out on simple systems, has implications in the pharmaceutical industry where the salt/cocrystal/continuum condition of APIs is considered seriously.
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Affiliation(s)
- Lalit Rajput
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560 012, India
| | - Manas Banik
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560 012, India
| | | | - Sumy Joseph
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560 012, India
| | - Manoj Kumar Pandey
- RIKEN CLST–JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan
- Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, India
| | - Yusuke Nishiyama
- RIKEN CLST–JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan
| | - Gautam R. Desiraju
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, 560 012, India
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23
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Zhang R, Duong NT, Nishiyama Y, Ramamoorthy A. 3D Double-Quantum/Double-Quantum Exchange Spectroscopy of Protons under 100 kHz Magic Angle Spinning. J Phys Chem B 2017; 121:5944-5952. [DOI: 10.1021/acs.jpcb.7b03480] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rongchun Zhang
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Nghia Tuan Duong
- RIKEN
CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Yusuke Nishiyama
- RIKEN
CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- JEOL Resonance Inc., Musashino, Akishima, Tokyo 196-8558, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics
and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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24
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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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25
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Oikawa T, Okumura M, Kimura T, Nishiyama Y. Solid-state NMR meets electron diffraction: determination of crystalline polymorphs of small organic microcrystalline samples. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2017; 73:219-228. [PMID: 28257016 DOI: 10.1107/s2053229617003084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/24/2017] [Indexed: 01/24/2023]
Abstract
A combination of solid-state NMR (ssNMR) and electron diffraction (ED) has been used to determine the crystalline polymorphs in small-organic microcrystalline molecules. Although 13C cross-polarization magic angle spinning (CPMAS) is a widely used method for determining crystalline polymorphs, even in a mixture, it sometimes fails if the molecular conformations are similar. On the other hand, ED can, in principle, differentiate crystalline forms with different lattice parameters, even when they have very similar molecular conformations. However, its application is usually limited to inorganic molecules only. This is because the ED measurements of organic molecules are very challenging due to degradation of the sample by electron irradiation. We overcame these difficulties by the use of 1H double-quantum/single-quantum correlation experiments at very fast magic angle spinning, together with ED observations under mild electron irradiation. The experiments were demonstrated on L-histidine samples in L-histidine·HCl·H2O, orthorhombic L-histidine and monoclinic L-histidine.
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Affiliation(s)
| | - Manabu Okumura
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Tsunehisa Kimura
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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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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Pandey MK, Yarava JR, Zhang R, Ramamoorthy A, Nishiyama Y. Proton-detected 3D (15)N/(1)H/(1)H isotropic/anisotropic/isotropic chemical shift correlation solid-state NMR at 70kHz MAS. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2016; 76-77:1-6. [PMID: 27017575 PMCID: PMC4903906 DOI: 10.1016/j.ssnmr.2016.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/18/2016] [Accepted: 03/01/2016] [Indexed: 05/15/2023]
Abstract
Chemical shift anisotropy (CSA) tensors offer a wealth of information for structural and dynamics studies of a variety of chemical and biological systems. In particular, CSA of amide protons can provide piercing insights into hydrogen-bonding interactions that vary with the backbone conformation of a protein and dynamics. However, the narrow span of amide proton resonances makes it very difficult to measure (1)H CSAs of proteins even by using the recently proposed 2D (1)H/(1)H anisotropic/isotropic chemical shift (CSA/CS) correlation technique. Such difficulties due to overlapping proton resonances can in general be overcome by utilizing the broad span of isotropic chemical shifts of low-gamma nuclei like (15)N. In this context, we demonstrate a proton-detected 3D (15)N/(1)H/(1)H CS/CSA/CS correlation experiment at fast MAS frequency (70kHz) to measure (1)H CSA values of unresolved amide protons of N-acetyl-(15)N-l-valyl-(15)N-l-leucine (NAVL).
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Affiliation(s)
- Manoj Kumar Pandey
- RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | | | - Rongchun Zhang
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Yusuke Nishiyama
- RIKEN CLST-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
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