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Chaloupecká E, Tyrpekl V, Bártová K, Nishiyama Y, Dračínský M. NMR crystallography of amino acids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2024; 130:101921. [PMID: 38422809 DOI: 10.1016/j.ssnmr.2024.101921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
The development of NMR crystallography methods requires a reliable database of chemical shifts measured for systems with known crystal structure. We measured and assigned carbon and hydrogen chemical shifts of twenty solid natural amino acids of known polymorphic structure, meticulously determined using powder X-ray diffraction. We then correlated the experimental data with DFT-calculated isotropic shieldings. The small size of the unit cell of most amino acids allowed for advanced computations using various families of DFT functionals, including generalized gradient approximation (GGA), meta-GGA and hybrid DFT functionals. We tested several combinations of functionals for geometry optimizations and NMR calculations. For carbon shieldings, the widely used GGA functional PBE performed very well, although an improvement could be achieved by adding shielding corrections calculated for isolated molecules using a hybrid functional. For hydrogen nuclei, we observed the best performance for NMR calculations carried out with structures optimized at the hybrid DFT level. The high fidelity of the calculations made it possible to assign additional signals that could not be assigned based on experiments alone, for example signals of two non-equivalent molecules in the unit cell of some of the amino acids.
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Affiliation(s)
- Ema Chaloupecká
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Václav Tyrpekl
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague 2, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic
| | | | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Prague, Czech Republic.
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2
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Tatman BP, Franks WT, Brown SP, Lewandowski JR. Nuclear spin diffusion under fast magic-angle spinning in solid-state NMR. J Chem Phys 2023; 158:2890210. [PMID: 37171196 DOI: 10.1063/5.0142201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
Solid-state nuclear spin diffusion is the coherent and reversible process through which spin order is transferred via dipolar couplings. With the recent increases in magic-angle spinning (MAS) frequencies and magnetic fields becoming routinely applied in solid-state nuclear magnetic resonance, understanding how the increased 1H resolution obtained affects spin diffusion is necessary for interpretation of several common experiments. To investigate the coherent contributions to spin diffusion with fast MAS, we have developed a low-order correlation in Liouville space model based on the work of Dumez et al. (J. Chem. Phys. 33, 224501, 2010). Specifically, we introduce a new method for basis set selection, which accounts for the resonance-offset dependence at fast MAS. Furthermore, we consider the necessity of including chemical shift, both isotropic and anisotropic, in the modeling of spin diffusion. Using this model, we explore how different experimental factors change the nature of spin diffusion. Then, we show case studies to exemplify the issues that arise in using spin diffusion techniques at fast spinning. We show that the efficiency of polarization transfer via spin diffusion occurring within a deuterated and 100% back-exchanged protein sample at 60 kHz MAS is almost entirely dependent on resonance offset. We additionally identify temperature-dependent magnetization transfer in beta-aspartyl L-alanine, which could be explained by the influence of an incoherent relaxation-based nuclear Overhauser effect.
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Affiliation(s)
- Ben P Tatman
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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3
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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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4
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Ahlawat S, Mopidevi SMV, Taware PP, Raran-Kurussi S, Mote KR, Agarwal V. Assignment of aromatic side-chain spins and characterization of their distance restraints at fast MAS. J Struct Biol X 2022; 7:100082. [PMID: 36618437 PMCID: PMC9817166 DOI: 10.1016/j.yjsbx.2022.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/18/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022] Open
Abstract
The assignment of aromatic side-chain spins has always been more challenging than assigning backbone and aliphatic spins. Selective labeling combined with mutagenesis has been the approach for assigning aromatic spins. This manuscript reports a method for assigning aromatic spins in a fully protonated protein by connecting them to the backbone atoms using a low-power TOBSY sequence. The pulse sequence employs residual polarization and sequential acquisitions techniques to record HN- and HC-detected spectra in a single experiment. The unambiguous assignment of aromatic spins also enables the characterization of 1H-1H distance restraints involving aromatic spins. Broadband (RFDR) and selective (BASS-SD) recoupling sequences were used to generate HN-ΗC, HC-HN and HC-HC restraints involving the side-chain proton spins of aromatic residues. This approach has been demonstrated on a fully protonated U-[13C,15N] labeled GB1 sample at 95-100 kHz MAS.
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Chávez M, Ernst M. Interaction frames in solid-state NMR: A case study for chemical-shift-selective irradiation schemes. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101834. [PMID: 36327552 DOI: 10.1016/j.ssnmr.2022.101834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Interaction frames play an important role in describing and understanding experimental schemes in magnetic resonance. They are often used to eliminate dominating parts of the spin Hamiltonian, e.g., the Zeeman Hamiltonian in the usual (Zeeman) rotating frame, or the radio-frequency-field (rf) Hamiltonian to describe the efficiency of decoupling or recoupling sequences. Going into an interaction frame can also make parts of a time-dependent Hamiltonian time independent like the rf-field Hamiltonian in the usual (Zeeman) rotating frame. Eliminating the dominant term often allows a better understanding of the details of the spin dynamics. Going into an interaction frame can also reduces the energy-level splitting in the Hamiltonian leading to a faster convergence of perturbation expansions, average Hamiltonian, or Floquet theory. Often, there is no obvious choice of the interaction frame to use but some can be more convenient than others. Using the example of frequency-selective dipolar recoupling, we discuss the differences, advantages, and disadvantages of different choices of interaction frames. They always include the complete radio-frequency Hamiltonian but can also contain the chemical shifts of the spins and may or may not contain the effective fields over one cycle of the pulse sequence.
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Affiliation(s)
- Matías Chávez
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Matthias Ernst
- Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.
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Ahlawat S, Mote KR, Raran-Kurussi S, Agarwal V. Mechanism of selective polarization exchange amongst chemically similar and distinct protons during weak rf irradiation at fast magic angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 340:107236. [PMID: 35609347 DOI: 10.1016/j.jmr.2022.107236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/16/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Band Selective Spectral Spin-Diffusion (BASS-SD) is a method to obtain selective 1H-1H contacts between chemically similar protons within a distance range of 5-6 Å in fully protonated proteins. BASS-SD combines low-amplitude proton spinlock radio frequency (rf) pulses with fast MAS frequency to enable selective polarization exchange in fully protonated molecules. The selectivity of transfer is dictated by the bandwidth of the spinlock pulse and has been used to observe selective HN-HN, Hα-Ηα and Hmethyl-Hmethyl correlations. These proton-proton spatial contacts are similar to those observed in perdeuterated samples and serve as useful structural restraints towards de novo protein structure determination. This study employs bimodal Floquet theory to derive the first- and second-order effective Hamiltonians necessary to understand the spin dynamics during BASS-SD. Analytical calculations combined with numerical simulations delineate two different mechanisms for polarization transfer amongst the proton spins. The BASS-SD recoupling condition has been reoptimized to observe selective correlations between chemically different protons (e.g., HN-Hα) while retaining the spatial contacts between chemically similar protons (e.g., HN-HN). The new BASS-SD condition is integrated with simultaneous and sequential acquisition approaches to generate four different types of structural restraints (HN-HN, Hα-Ηα, HN-Hα, Hα-HN) in one experiment. The approach has been demonstrated on microcrystalline U-[13C,15N] labeled GB1 protein at ∼ 95-100 kHz MAS.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Sreejith Raran-Kurussi
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Sy. No. 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District, Hyderabad 500 046, India.
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7
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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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8
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Duong NT, Agarwal V, Nishiyama Y. Separating an overlapped 1H peak and identifying its 1H- 1H correlations with the use of single-channel 1H solid-state NMR at fast MAS. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 117:101774. [PMID: 35051807 DOI: 10.1016/j.ssnmr.2022.101774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Fast magic-angle spinning (≥60 kHz) technique has enabled the acquisition of high-resolution 1H NMR spectra of solid materials. However, the spectral interpretation is still difficult because the 1H peaks are overlapped due to the narrow chemical shift range and broad linewidths. An additional 13C or 14N or 1H dimension possibly addresses the issues of overlapped proton resonances, but it leads to the elongated experimental time. Herein, we introduce a single-channel 1H experiment to separate the overlapped 1H peak and identify its spatially proximal 1H-1H correlations. This sequence combines selective excitation, selective 1H-1H polarization transfer by selective recoupling of protons (SERP), and broadband 1H recoupling by back-to-back (BABA) recoupling sequences. The concept for 1H separation is based on (i) the selective excitation of a well-resolved 1H peak and (ii) the selective dipolar polarization transfer from this isolated 1H peak to one of the 1H peaks in the overlapped/poor resolution region by SERP and (iii) the detection of 1H-1H correlations from these two 1H peaks to other neighboring 1Hs by BABA. We demonstrated the applicability of this approach to identify overlapped peaks on two molecules, β-L-aspartyl-l-alanine and Pioglitazone.HCl. The sequence allows the clear observation of 1H-1H correlations from an overlapped 1H peak without an additional heteronuclear dimension and ensures efficient polarization transfers that leads to twelve fold reduction in experimental time compared to 14N edited experiments. The limitation and the conditions of applicability for this approach are discussed in detail.
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Affiliation(s)
- Nghia Tuan Duong
- Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa, 230-0045, Japan
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, Sy. No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad, 500 107, India
| | - Yusuke Nishiyama
- Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa, 230-0045, Japan; JEOL RESONANCE Inc., Akishima, Tokyo, 196-8558, Japan.
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9
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Liang L, Ji Y, Chen K, Gao P, Zhao Z, Hou G. Solid-State NMR Dipolar and Chemical Shift Anisotropy Recoupling Techniques for Structural and Dynamical Studies in Biological Systems. Chem Rev 2022; 122:9880-9942. [PMID: 35006680 DOI: 10.1021/acs.chemrev.1c00779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the development of NMR methodology and technology during the past decades, solid-state NMR (ssNMR) has become a particularly important tool for investigating structure and dynamics at atomic scale in biological systems, where the recoupling techniques play pivotal roles in modern high-resolution MAS NMR. In this review, following a brief introduction on the basic theory of recoupling in ssNMR, we highlight the recent advances in dipolar and chemical shift anisotropy recoupling methods, as well as their applications in structural determination and dynamical characterization at multiple time scales (i.e., fast-, intermediate-, and slow-motion). The performances of these prevalent recoupling techniques are compared and discussed in multiple aspects, together with the representative applications in biomolecules. Given the recent emerging advances in NMR technology, new challenges for recoupling methodology development and potential opportunities for biological systems are also discussed.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, 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, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Ji
- State Key Laboratory of Catalysis, 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, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuizhi Chen
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
| | - Pan Gao
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, 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, Dalian 116023, China
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10
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Yan Z, Zhang R. Rapid Structural Analysis of Minute Quantities of Organic Solids by Exhausting 1H Polarization in Solid-State NMR Spectroscopy Under Fast Magic Angle Spinning. J Phys Chem Lett 2021; 12:12067-12074. [PMID: 34910488 DOI: 10.1021/acs.jpclett.1c03672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Solid-state nuclear magnetic resonance (NMR) often suffers from significant limitations due to the inherent low signal sensitivity when low-γ nuclei are involved. Herein, we report an elegant solid-state NMR approach for rapid structural analysis of minute amounts of organic solids. By encoding staggered chemical shift evolution in the indirect dimension and staggered acquisition in the 1H dimension, a proton-detected homonuclear 1H/1H and heteronuclear 13C/1H chemical shift correlation (HETCOR) spectrum can be obtained simultaneously in a single experiment at a fast magic-angle-spinning (MAS) condition with barely increasing the experimental time. We further show that during the conventional 1H-detected HETCOR experimental time, multiple homonuclear 1H/1H correlation spectra can be recorded in addition to the HETCOR spectrum, enabling the determination of 1H-1H distances. We establish that abundant 1H polarization can be efficiently manipulated and fully utilized in proton-detected solid-state NMR spectroscopy for extraction of more critical structural information and thus reduction of the total experimental time.
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Affiliation(s)
- Zhiwei Yan
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Molecular Science and Engineering (MoSE), South China University of Technology, Guangzhou, 510640, P. R. China
| | - Rongchun Zhang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Molecular Science and Engineering (MoSE), South China University of Technology, Guangzhou, 510640, P. R. China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, 510640, P. R. China
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11
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Lusky OS, Meir M, Goldbourt A. Characterizing hydrogen bonds in intact RNA from MS2 bacteriophage using magic angle spinning NMR. BIOPHYSICAL REPORTS 2021; 1:100027. [PMID: 36425459 PMCID: PMC9680805 DOI: 10.1016/j.bpr.2021.100027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/23/2021] [Indexed: 05/14/2023]
Abstract
RNA is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step toward understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide basepairs, and it defines the positions and shapes of functional stem-loops, internal loops, bulges, and other functional and structural elements. In this work, we present a methodology for studying large intact RNA biomolecules using homonuclear 15N solid-state NMR spectroscopy. We show that proton-driven spin-diffusion experiments with long mixing times, up to 16 s, improved by the incorporation of multiple rotor-synchronous 1H inversion pulses (termed radio-frequency dipolar recoupling pulses), reveal key hydrogen-bond contacts. In the full-length RNA isolated from MS2 phage, we observed strong and dominant contributions of guanine-cytosine Watson-Crick basepairs, and beyond these common interactions, we observe a significant contribution of the guanine-uracil wobble basepairs. Moreover, we can differentiate basepaired and non-basepaired nitrogen atoms. Using the improved technique facilitates characterization of hydrogen-bond types in intact large-scale RNA using solid-state NMR. It can be highly useful to guide secondary structure prediction techniques and possibly structure determination methods.
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Affiliation(s)
| | - Moran Meir
- School of Molecular Cell Biology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Amir Goldbourt
- School of Chemistry, Faculty of Exact Sciences
- Corresponding author
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12
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Reif B. Deuteration for High-Resolution Detection of Protons in Protein Magic Angle Spinning (MAS) Solid-State NMR. Chem Rev 2021; 122:10019-10035. [PMID: 34870415 DOI: 10.1021/acs.chemrev.1c00681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton detection developed in the last 20 years as the method of choice to study biomolecules in the solid state. In perdeuterated proteins, proton dipolar interactions are strongly attenuated, which allows yielding of high-resolution proton spectra. Perdeuteration and backsubstitution of exchangeable protons is essential if samples are rotated with MAS rotation frequencies below 60 kHz. Protonated samples can be investigated directly without spin dilution using proton detection methods in case the MAS frequency exceeds 110 kHz. This review summarizes labeling strategies and the spectroscopic methods to perform experiments that yield assignments, quantitative information on structure, and dynamics using perdeuterated samples. Techniques for solvent suppression, H/D exchange, and deuterium spectroscopy are discussed. Finally, experimental and theoretical results that allow estimation of the sensitivity of proton detected experiments as a function of the MAS frequency and the external B0 field in a perdeuterated environment are compiled.
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Affiliation(s)
- Bernd Reif
- Bayerisches NMR Zentrum (BNMRZ) at the Department of Chemistry, Technische Universität München (TUM), Lichtenbergstr. 4, 85747 Garching, Germany.,Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Institute of Structural Biology (STB), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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13
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Shcherbakov AA, Medeiros-Silva J, Tran N, Gelenter MD, Hong M. From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR. Chem Rev 2021; 122:9848-9879. [PMID: 34694769 DOI: 10.1021/acs.chemrev.1c00662] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Internuclear distances represent one of the main structural constraints in molecular structure determination using solid-state NMR spectroscopy, complementing chemical shifts and orientational restraints. Although a large number of magic-angle-spinning (MAS) NMR techniques have been available for distance measurements, traditional 13C and 15N NMR experiments are inherently limited to distances of a few angstroms due to the low gyromagnetic ratios of these nuclei. Recent development of fast MAS triple-resonance 19F and 1H NMR probes has stimulated the design of MAS NMR experiments that measure distances in the 1-2 nm range with high sensitivity. This review describes the principles and applications of these multiplexed multidimensional correlation distance NMR experiments, with an emphasis on 19F- and 1H-based distance experiments. Representative applications of these long-distance NMR methods to biological macromolecules as well as small molecules are reviewed.
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Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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Duong NT, Aoyama Y, Kawamoto K, Yamazaki T, Nishiyama Y. Structure Solution of Nano-Crystalline Small Molecules Using MicroED and Solid-State NMR Dipolar-Based Experiments. Molecules 2021; 26:molecules26154652. [PMID: 34361806 PMCID: PMC8347922 DOI: 10.3390/molecules26154652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022] Open
Abstract
Three-dimensional electron diffraction crystallography (microED) can solve structures of sub-micrometer crystals, which are too small for single crystal X-ray crystallography. However, R factors for the microED-based structures are generally high because of dynamic scattering. That means R factor may not be reliable provided that kinetic analysis is used. Consequently, there remains ambiguity to locate hydrogens and to assign nuclei with close atomic numbers, like carbon, nitrogen, and oxygen. Herein, we employed microED and ssNMR dipolar-based experiments together with spin dynamics numerical simulations. The NMR dipolar-based experiments were 1H-14N phase-modulated rotational-echo saturation-pulse double-resonance (PM-S-RESPDOR) and 1H-1H selective recoupling of proton (SERP) experiments. The former examined the dephasing effect of a specific 1H resonance under multiple 1H-14N dipolar couplings. The latter examined the selective polarization transfer between a 1H-1H pair. The structure was solved by microED and then validated by evaluating the agreement between experimental and calculated dipolar-based NMR results. As the measurements were performed on 1H and 14N, the method can be employed for natural abundance samples. Furthermore, the whole validation procedure was conducted at 293 K unlike widely used chemical shift calculation at 0 K using the GIPAW method. This combined method was demonstrated on monoclinic l-histidine.
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Affiliation(s)
- Nghia Tuan Duong
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
| | | | | | - Toshio Yamazaki
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan;
- JEOL RESONANCE Inc., Akishima, Tokyo 196-8558, Japan
- Correspondence:
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Potnuru LR, Duong NT, Sasank B, Raran-Kurussi S, Nishiyama Y, Agarwal V. Selective 1H- 1H recoupling via symmetry sequences in fully protonated samples at fast magic angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 328:107004. [PMID: 34049237 DOI: 10.1016/j.jmr.2021.107004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 05/08/2023]
Abstract
Proton-detected solid-state NMR at fast Magic Angle Spinning (MAS) is becoming the norm to characterize molecules. Routinely 1H-1H and 1H-X dipolar couplings are used to characterize the structure and dynamics of molecules. Selective proton recoupling techniques are emerging as a method for structural characterization via estimation of qualitative and quantitative distances. In the present study, we demonstrate through numerical simulations and experiments that the well-characterized CNvn sequences can also be tailored for selective recoupling of proton spins by employing C elements of the type (β)Φ(4β)Φ+π(3β)Φ. Herein, several CNvn sequences were examined through numerical simulations and experiments. C614 recoupling sequence with a modified POST-element ((β)Φ(4β)Φ+π(3β)Φ) shows selective polarization transfer efficiencies on the order of 40-50% between various proton spin pairs in fully protonated samples at rf amplitudes ranging from 0.3 to 0.8 times the MAS frequency. These selective recoupling sequences have been labeled as frequency-selective-CNvn sequences. The extent of selectivity, polarization transfer efficiency and the feasibility of experimentally measuring proton-proton distances in fully protonated samples are explored here. The development of efficient and robust selective 1H-1H recoupling experiments is required to structurally characterize molecules without artificial isotope enrichment or the need for diffracting crystals.
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Affiliation(s)
- Lokeswara Rao Potnuru
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, Sy. No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
| | - Nghia Tuan Duong
- Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Budaraju Sasank
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, Sy. No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India; Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali 140306, India
| | - Sreejith Raran-Kurussi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, Sy. No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
| | - Yusuke Nishiyama
- Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan; JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558, Japan.
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, Sy. No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India.
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Nakai T. Perturbation Approach for NMR Signals with Infinite-Order Corrections and Its Application to Solid-State MAS INADEQUATE Spectra Exhibiting Auto-Correlation Peaks due to Chemically-Equivalent Spin Pairs: Analogy to Renormalization Theory. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshihito Nakai
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo 196-8558, Japan
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17
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Ji Y, Liang L, Bao X, Hou G. Recent progress in dipolar recoupling techniques under fast MAS in solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 112:101711. [PMID: 33508579 DOI: 10.1016/j.ssnmr.2020.101711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
With the recent advances in NMR hardware and probe design technology, magic-angle spinning (MAS) rates over 100 kHz are accessible now, even on commercial solid NMR probes. Under such fast MAS conditions, excellent spectral resolution has been achieved by efficient suppression of anisotropic interactions, which also opens an avenue to the proton-detected NMR experiments in solids. Numerous methods have been developed to take full advantage of fast MAS during the last decades. Among them, dipolar recoupling techniques under fast MAS play vital roles in the determination of the molecular structure and dynamics, and are also key elements in multi-dimensional correlation NMR experiments. Herein, we review the dipolar recoupling techniques, especially those developed in the past two decades for fast-to-ultrafast MAS conditions. A major focus for our discussion is the ratio of RF field strength (in frequency) to MAS frequency, ν1/νr, in different pulse sequences, which determines whether these dipolar recoupling techniques are suitable for NMR experiments under fast MAS conditions. Systematic comparisons are made among both heteronuclear and homonuclear dipolar recoupling schemes. In addition, the schemes developed specially for proton-detection NMR experiments under ultrafast MAS conditions are highlighted as well.
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Affiliation(s)
- Yi Ji
- State Key Laboratory of Catalysis, 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, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lixin Liang
- State Key Laboratory of Catalysis, 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, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinhe Bao
- State Key Laboratory of Catalysis, 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, Dalian, 116023, China
| | - Guangjin Hou
- State Key Laboratory of Catalysis, 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, Dalian, 116023, China.
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Potnuru LR, Duong NT, Ahlawat S, Raran-Kurussi S, Ernst M, Nishiyama Y, Agarwal V. Accuracy of 1H- 1H distances measured using frequency selective recoupling and fast magic-angle spinning. J Chem Phys 2020; 153:084202. [PMID: 32872876 DOI: 10.1063/5.0019717] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Selective recoupling of protons (SERP) is a method to selectively and quantitatively measure magnetic dipole-dipole interaction between protons and, in turn, the proton-proton distance in solid-state samples at fast magic-angle spinning. We present a bimodal operator-based Floquet approach to describe the numerically optimized SERP recoupling sequence. The description calculates the allowed terms in the first-order effective Hamiltonian, explains the origin of selectivity during recoupling, and shows how different terms are modulated as a function of the radio frequency amplitude and the phase of the sequence. Analytical and numerical simulations have been used to evaluate the effect of higher-order terms and offsets on the polarization transfer efficiency and quantitative distance measurement. The experimentally measured 1H-1H distances on a fully protonated thymol sample are ∼10%-15% shorter than those reported from diffraction studies. A semi-quantitative model combined with extensive numerical simulations is used to rationalize the effect of the third-spin and the role of different parameters in the experimentally observed shorter distances. Measurements at high magnetic fields improve the match between experimental and diffraction distances. The measurement of 1H-1H couplings at offsets different from the SERP-offset has also been explored. Experiments were also performed on a perdeuterated ubiquitin sample to demonstrate the feasibility of simultaneously measuring multiple quantitative distances and to evaluate the accuracy of the measured distance in the absence of multispin effects. The estimation of proton-proton distances provides a boost to structural characterization of small pharmaceuticals and biomolecules, given that the positions of protons are generally not well defined in x-ray structures.
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Affiliation(s)
- Lokeswara Rao Potnuru
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
| | - Nghia Tuan Duong
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Sahil Ahlawat
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
| | - Sreejith Raran-Kurussi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
| | - Matthias Ernst
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Yusuke Nishiyama
- NMR Science and Development Division, RIKEN SPring-8 Center, and Nano-Crystallography Unit, RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa 230-0045, Japan
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P, Gopanpally, Ranga Reddy District, Hyderabad 500 107, India
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