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Bahri S, Safeer A, Adler A, Smedes H, van Ingen H, Baldus M. 1H-detected characterization of carbon-carbon networks in highly flexible protonated biomolecules using MAS NMR. JOURNAL OF BIOMOLECULAR NMR 2023:10.1007/s10858-023-00415-6. [PMID: 37289305 DOI: 10.1007/s10858-023-00415-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/28/2023] [Indexed: 06/09/2023]
Abstract
In the last three decades, the scope of solid-state NMR has expanded to exploring complex biomolecules, from large protein assemblies to intact cells at atomic-level resolution. This diversity in macromolecules frequently features highly flexible components whose insoluble environment precludes the use of solution NMR to study their structure and interactions. While High-resolution Magic-Angle Spinning (HR-MAS) probes offer the capacity for gradient-based 1H-detected spectroscopy in solids, such probes are not commonly used for routine MAS NMR experiments. As a result, most exploration of the flexible regime entails either 13C-detected experiments, the use of partially perdeuterated systems, or ultra-fast MAS. Here we explore proton-detected pulse schemes probing through-bond 13C-13C networks to study mobile protein sidechains as well as polysaccharides in a broadband manner. We demonstrate the use of such schemes to study a mixture of microtubule-associated protein (MAP) tau and human microtubules (MTs), and the cell wall of the fungus Schizophyllum commune using 2D and 3D spectroscopy, to show its viability for obtaining unambiguous correlations using standard fast-spinning MAS probes at high and ultra-high magnetic fields.
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Affiliation(s)
- Salima Bahri
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Agnes Adler
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hanneke Smedes
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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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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Vasa SK, Rovó P, Giller K, Becker S, Linser R. Access to aliphatic protons as reporters in non-deuterated proteins by solid-state NMR. Phys Chem Chem Phys 2017; 18:8359-63. [PMID: 26686237 DOI: 10.1039/c5cp06601h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Interactions within proteins, with their surrounding, and with other molecules are mediated mostly by hydrogen atoms. In fully protonated, inhomogeneous, or larger proteins, however, aliphatic proton shifts tend to show little dispersion despite fast Magic-Angle Spinning. 3D correlations dispersing aliphatic proton shifts by their better resolved amide N/H shifts can alleviate this problem. Using inverse second-order cross-polarization (iSOCP), we here introduce dedicated and improved means to sensitively link site-specific chemical shift information from aliphatic protons with a backbone amide resolution. Thus, even in cases where protein deuteration is impossible, this approach may enable access to various aspects of protein functions that are reported on by protons.
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Affiliation(s)
- Suresh Kumar Vasa
- Max-Planck Institute for Biophysical Chemistry, Department NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Petra Rovó
- Max-Planck Institute for Biophysical Chemistry, Department NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Karin Giller
- Max-Planck Institute for Biophysical Chemistry, Department NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Stefan Becker
- Max-Planck Institute for Biophysical Chemistry, Department NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Rasmus Linser
- Max-Planck Institute for Biophysical Chemistry, Department NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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Mote KR, Agarwal V, Madhu PK. Five decades of homonuclear dipolar decoupling in solid-state NMR: Status and outlook. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:1-39. [PMID: 27888838 DOI: 10.1016/j.pnmrs.2016.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/11/2016] [Accepted: 08/02/2016] [Indexed: 06/06/2023]
Abstract
It has been slightly more than fifty years since the first homonuclear spin decoupling scheme, Lee-Goldburg decoupling, was proposed for removing homonuclear dipolar interactions in solid-state nuclear magnetic resonance. A family of such schemes has made observation of high-resolution NMR spectra of abundant spins possible in various applications in solid state. This review outlines the strategies used in this field and the future prospects of homonuclear spin decoupling in solid-state NMR.
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Affiliation(s)
- Kaustubh R Mote
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India; Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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Mote KR, Madhu PK. Proton-detected solid-state NMR spectroscopy of fully protonated proteins at slow to moderate magic-angle spinning frequencies. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 261:149-56. [PMID: 26580064 DOI: 10.1016/j.jmr.2015.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/11/2015] [Accepted: 10/20/2015] [Indexed: 06/05/2023]
Abstract
(1)H-detection offers a substitute to the sensitivity-starved experiments often used to characterize biomolecular samples using magic-angle spinning solid-state NMR spectroscopy (MAS-ssNMR). To mitigate the effects of the strong (1)H-(1)H dipolar coupled network that would otherwise severely broaden resonances, high MAS frequencies (>40kHz) are often employed. Here, we have explored the alternative of stroboscopic (1)H-detection at moderate MAS frequencies of 5-30kHz using windowed version of supercycled-phase-modulated Lee-Goldburg homonuclear decoupling. We show that improved resolution in the (1)H dimension, comparable to that obtainable at high spinning frequencies of 40-60kHz without homonuclear decoupling, can be obtained in these experiments for fully protonated proteins. Along with detailed analysis of the performance of the method on the standard tri-peptide f-MLF, experiments on micro-crystalline GB1 and amyloid-β aggregates are used to demonstrate the applicability of these pulse-sequences to challenging biomolecular systems. With only two parameters to optimize, broadbanded performance of the homonuclear decoupling sequence, linear dependence of the chemical-shift scaling factor on resonance offset and a straightforward implementation under experimental conditions currently used for many biomolecular studies (viz. spinning frequencies and radio-frequency amplitudes), we expect these experiments to complement the current (13)C-detection based methods in assignments and characterization through chemical-shift mapping.
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Affiliation(s)
- Kaustubh R Mote
- TIFR Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 21 Brundavan Colony, Narsingi, Hyderabad 500075, India.
| | - Perunthiruthy K Madhu
- TIFR Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 21 Brundavan Colony, Narsingi, Hyderabad 500075, India; Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India.
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Paluch P, Pawlak T, Jeziorna A, Trébosc J, Hou G, Vega AJ, Amoureux JP, Dracinsky M, Polenova T, Potrzebowski MJ. Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations. Phys Chem Chem Phys 2015; 17:28789-801. [PMID: 26451400 PMCID: PMC4890705 DOI: 10.1039/c5cp04475h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report a new multidimensional magic angle spinning NMR methodology, which provides an accurate and detailed probe of molecular motions occurring on timescales of nano- to microseconds, in sidechains of proteins. The approach is based on a 3D CPVC-RFDR correlation experiment recorded under fast MAS conditions (ν(R) = 62 kHz), where (13)C-(1)H CPVC dipolar lineshapes are recorded in a chemical shift resolved manner. The power of the technique is demonstrated in model tripeptide Tyr-(d)Ala-Phe and two nanocrystalline proteins, GB1 and LC8. We demonstrate that, through numerical simulations of dipolar lineshapes of aromatic sidechains, their detailed dynamic profile, i.e., the motional modes, is obtained. In GB1 and LC8 the results unequivocally indicate that a number of aromatic residues are dynamic, and using quantum mechanical calculations, we correlate the molecular motions of aromatic groups to their local environment in the crystal lattice. The approach presented here is general and can be readily extended to other biological systems.
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Affiliation(s)
- Piotr Paluch
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.
| | - Tomasz Pawlak
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.
| | - Agata Jeziorna
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.
| | - Julien Trébosc
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS-8181, University Lille North of France, 59652 Villeneuve d'Ascq, France
| | - Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA.
| | - Alexander J Vega
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA.
| | - Jean-Paul Amoureux
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS-8181, University Lille North of France, 59652 Villeneuve d'Ascq, France and Physics Department & Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Martin Dracinsky
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nam. 2, Prague, Czech Republic.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA.
| | - Marek J Potrzebowski
- Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Sienkiewicza 112, PL-90-363 Łodz, Poland.
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Polenova T, Gupta R, Goldbourt A. Magic angle spinning NMR spectroscopy: a versatile technique for structural and dynamic analysis of solid-phase systems. Anal Chem 2015; 87:5458-69. [PMID: 25794311 PMCID: PMC4890703 DOI: 10.1021/ac504288u] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Magic Angle Spinning (MAS) NMR spectroscopy is a powerful method for analysis of a broad range of systems, including inorganic materials, pharmaceuticals, and biomacromolecules. The recent developments in MAS NMR instrumentation and methodologies opened new vistas to atomic-level characterization of a plethora of chemical environments previously inaccessible to analysis, with unprecedented sensitivity and resolution.
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Affiliation(s)
- Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Rupal Gupta
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Amir Goldbourt
- School of Chemistry, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
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Dannatt HRW, Taylor GF, Varga K, Higman VA, Pfeil MP, Asilmovska L, Judge PJ, Watts A. ¹³C- and ¹H-detection under fast MAS for the study of poorly available proteins: application to sub-milligram quantities of a 7 trans-membrane protein. JOURNAL OF BIOMOLECULAR NMR 2015; 62:17-23. [PMID: 25701262 DOI: 10.1007/s10858-015-9911-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/14/2015] [Indexed: 06/04/2023]
Abstract
We demonstrate that (13)C-detected spectra recorded using fast (60 kHz) magic angle spinning on sub-milligram (<10 μmol) quantities of a protonated 7 trans-membrane helix protein (bacteriorhodopsin) in its native lipid environment are comparable in sensitivity and resolution to those recorded using 15-fold larger sample volumes with conventional solid state NMR methodology. We demonstrate the utility of proton-detected measurements which yield narrow (1)H linewidths under these conditions, and that no structural alterations are observed. We propose that these methods will prove useful to gain structural information on membrane proteins with poor availability, which can be studied in their native lipid environments.
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Affiliation(s)
- Hugh R W Dannatt
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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Wang S, Parthasarathy S, Nishiyama Y, Endo Y, Nemoto T, Yamauchi K, Asakura T, Takeda M, Terauchi T, Kainosho M, Ishii Y. Nano-mole scale side-chain signal assignment by 1H-detected protein solid-state NMR by ultra-fast magic-angle spinning and stereo-array isotope labeling. PLoS One 2015; 10:e0122714. [PMID: 25856081 PMCID: PMC4391754 DOI: 10.1371/journal.pone.0122714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 02/14/2015] [Indexed: 11/19/2022] Open
Abstract
We present a general approach in 1H-detected 13C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. et al., Nature 440, 52-57, 2006]. First, we demonstrate that 1H indirect detection improves the sensitivity and resolution of 13C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. 1H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by 1H-detected 2D 1H/13C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over 13C-detected 2D 1H/13C SSNMR and 1D 13C CPMAS, demonstrating that 2D 1H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D 13C detection for the first time. High 1H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A 1H-detected 3D 13C/13C/1H experiment on SAIL-ubiquitin provided nearly complete 1H and 13C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.
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Affiliation(s)
- Songlin Wang
- Department of Chemistry and University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Sudhakar Parthasarathy
- Department of Chemistry and University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., Akishima, Tokyo, Japan
- RIKEN CLST-JEOL collaboration center, RIKEN, Yokohama, Kanagawa, Japan
| | - Yuki Endo
- JEOL RESONANCE Inc., Akishima, Tokyo, Japan
| | | | - Kazuo Yamauchi
- School of Science and Technology, Nazarbayev University, Astana, Kazakhstan
- Nuclear Magnetic Resonance Core Lab., King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Mitsuhiro Takeda
- Structural Biology Research Center, Graduate School of Science, Furocho, Chikusa-ku, Nagoya University, Nagoya, Japan 464–8601
| | - Tsutomu Terauchi
- SAIL Technologies Co., Inc., Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Masatsune Kainosho
- Structural Biology Research Center, Graduate School of Science, Furocho, Chikusa-ku, Nagoya University, Nagoya, Japan 464–8601
- Center for Priority Areas, Tokyo Metropolitan University, Tokyo, Japan
| | - Yoshitaka Ishii
- Department of Chemistry and University of Illinois at Chicago, Chicago, Illinois, United States of America
- Center for Structural Biology, University of Illinois at Chicago, Chicago, Illinois, United States of America
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