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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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2
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Xu Y, Tijssen KCH, Bomans PHH, Akiva A, Friedrich H, Kentgens APM, Sommerdijk NAJM. Microscopic structure of the polymer-induced liquid precursor for calcium carbonate. Nat Commun 2018; 9:2582. [PMID: 29968713 PMCID: PMC6030133 DOI: 10.1038/s41467-018-05006-w] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 06/06/2018] [Indexed: 11/17/2022] Open
Abstract
Many biomineral crystals form complex non-equilibrium shapes, often via transient amorphous precursors. Also in vitro crystals can be grown with non-equilibrium morphologies, such as thin films or nanorods. In many cases this involves charged polymeric additives that form a polymer-induced liquid precursor (PILP). Here, we investigate the CaCO3 based PILP process with a variety of techniques including cryoTEM and NMR. The initial products are 30-50 nm amorphous calcium carbonate (ACC) nanoparticles with ~2 nm nanoparticulate texture. We show the polymers strongly interact with ACC in the early stages, and become excluded during crystallization, with no liquid-liquid phase separation detected during the process. Our results suggest that "PILP" is actually a polymer-driven assembly of ACC clusters, and that its liquid-like behavior at the macroscopic level is due to the small size and surface properties of the assemblies. We propose that a similar biopolymer-stabilized nanogranular phase may be active in biomineralization.
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Affiliation(s)
- Yifei Xu
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Koen C H Tijssen
- Solid-state NMR Group, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Paul H H Bomans
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Anat Akiva
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Heiner Friedrich
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Arno P M Kentgens
- Solid-state NMR Group, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Nico A J M Sommerdijk
- Department of Chemical Engineering and Chemistry, Laboratory of Materials and Interface Chemistry and Centre for Multiscale Electron Microscopy, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
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On the Helical Structure of Guanosine 5'-Monophosphate Formed at pH 5: Is It Left- or Right-Handed? J Nucleic Acids 2017; 2017:6798759. [PMID: 29230324 PMCID: PMC5688352 DOI: 10.1155/2017/6798759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/11/2017] [Indexed: 11/26/2022] Open
Abstract
Early X-ray fiber diffraction studies have established that the spontaneous gel formation of guanosine 5′-monophosphate (5′-GMP) under slightly acidic conditions (e.g., pH 5) results from self-assembly of 5′-GMP into a helical structure in which hydrogen-bonded guanine bases form a continuous helix with 15 nucleotides per 4 turns. For more than five decades, the sense of this helix is believed to be left-handed. Using multinuclear solid-state NMR and IR spectroscopic methods, we have finally determined the long-missing structural details of this helix. First, we found that this 5′-GMP helix is right-handed containing exclusive C3′-endo sugar puckers. Second, we showed that the central channel of this helix is free of Na+ ions, which is in sharp contrast to the helix formed by 5′-GMP at pH 8 where the central channel is filled with Na+ ions.
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Lee GH, Oh SY, Yeo KJ, Ferdous T, Cho M, Paik Y. Solid-state 31P NMR investigation on the status of guanine nucleotides in paclitaxel-stabilized microtubules. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:330-336. [PMID: 25808514 DOI: 10.1002/mrc.4183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 08/20/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
Microtubule dynamics is a target for many chemotherapeutic drugs. In order to understand the biochemical effects of paclitaxel on the GTPase activity of tubulin, the status of guanine nucleotides in microtubules was investigated by (31)P cross-polarization magic angle spinning (CPMAS) NMR. Microtubules were freshly prepared in vitro in the presence of paclitaxel and then lyophilized in sucrose buffer for solid-state NMR experiments. A (31)P CPMAS NMR spectrum with the SNR of 25 was successfully acquired from the lyophilized microtubule sample. The broadness of the (31)P spectral lines in the spectrum indicates that the molecular environments around the guanine nucleotides inside tubulin may not be as crystalline as reported by many diffraction studies. Deconvolution of the spectrum into four spectral components was carried out in comparison with the (31)P NMR spectra obtained from five control samples. The spectral analysis suggested that about 13% of the nucleotides were present as GTP and 37% as GDP in the β-tubulin (E-site) of the microtubules. It was found that most of the GDPs were present as GDP-Pi complex in the microtubules, which seems to be one of the effects of paclitaxel binding.
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Affiliation(s)
- Ga Hyang Lee
- Daegu Center, Korea Basic Science Institute, 80 Daehakro, Bukgu, Daegu, 702-701, Korea; Ochang Center, Korea Basic Science Institute, 162 Yeongudanjiro, Ochangeup, Cheongwongun, Chungcheongbukdo, 363-883, Korea
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Abstract
Recent applications of solid-state NMR spectroscopy to studies of nucleic acids and their components.
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Affiliation(s)
- Martin Dračínský
- Institute of Organic Chemistry and Biochemistry
- Prague
- Czech Republic
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6
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Johnson R, Fleming AM, Burrows CJ, White HS. Effect of an Electrolyte Cation on Detecting DNA Damage with the Latch Constriction of α-Hemolysin. J Phys Chem Lett 2014; 5:3781-3786. [PMID: 25400876 PMCID: PMC4226304 DOI: 10.1021/jz502030e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 10/14/2014] [Indexed: 05/30/2023]
Abstract
The effect of an electrolyte cation on the unzipping of furan-containing double-stranded DNA in an α-hemolysin (αHL) nanopore is described. The current through an open αHL channel increases in proportion to the ion mobility. However, the ionic current measured during residence of a DNA duplex inside of the protein pore shows a more complex dependence on the choice of cation, indicating that the current measured during DNA residence in the pore is modulated by the specific interactions of the cations with the DNA and/or αHL. The residence time (stability) of the DNA duplex inside of the pore prior to unzipping is also highly dependent on the cation, in striking contrast to the small variation in duplex stability (as measured by the melting temperature) in bulk electrolyte solution. A missing base in DNA can be detected in the latch region of αHL with optimal current resolution in RbCl, while optimal time resolution is possible in LiCl.
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Gao ZF, Gao JB, Zhou LY, Zhang Y, Si JC, Luo HQ, Li NB. Rapid assembly of ssDNA on gold electrode surfaces at low pH and high salt concentration conditions. RSC Adv 2013. [DOI: 10.1039/c3ra40810h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Perras FA, Korobkov I, Bryce DL. 23Na double-rotation NMR of sodium nucleotides leads to the discovery of a new dCMP hendecahydrate. Phys Chem Chem Phys 2012; 14:4677-81. [PMID: 22389051 DOI: 10.1039/c2cp40273d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Obtaining definitive information concerning the coordination environment of sodium ions which balance the negative charges found in nucleotides is a challenging task. We show that high resolution 1D and 2D (23)Na NMR spectra of sodium nucleotides obtained in the solid state with the use of double-rotation (DOR) provide valuable structural information. Sensitive spin diffusion homonuclear correlation experiments are used to establish the relative proximities of various pairs of crystallographically distinct Na sites and to assign the spectral resonances. Additionally, the DOR sidebands are simulated to obtain coordination information which is complementary to that obtained using multiple-quantum magic-angle spinning NMR spectra. These experiments led us to discover a new hendecahydrate of deoxycytidine monophosphate (dCMP), the structure of which is confirmed via single-crystal X-ray diffraction. This hydrate crystallizes reproducibly when deuterated water is used exclusively in the preparation process.
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Affiliation(s)
- Frédéric A Perras
- Department of Chemistry and Centre for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Private, Ottawa, Ontario, Canada
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Wu G, Zhu J. NMR studies of alkali metal ions in organic and biological solids. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 61:1-70. [PMID: 22340207 DOI: 10.1016/j.pnmrs.2011.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 05/31/2011] [Indexed: 05/31/2023]
Affiliation(s)
- Gang Wu
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada.
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Li Z, Niu T, Zhang Z, Feng G, Bi S. Effect of monovalent cations (Li+, Na+, K+, Cs+) on self-assembly of thiol-modified double-stranded and single-stranded DNA on gold electrode. Analyst 2012; 137:1680-91. [DOI: 10.1039/c2an15716k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Kwan ICM, Delley RJ, Hodgson DRW, Wu G. Single atom modification leads to enhanced nucleotide self-assembly: the role of cation bridging. Chem Commun (Camb) 2011; 47:3882-4. [PMID: 21336356 DOI: 10.1039/c0cc05654e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report that the ability of disodium 5'-deoxy-5'-thioguanosine-5'-monophosphate, Na(2)(5'-GSMP), to self-associate into a helical G-quadruplex structure in aqueous solution at pH 8 is significantly higher than that of disodium guanosine-5'-monophosphate, Na(2)(5'-GMP), which supports our earlier hypothesis regarding the importance of cation bridging.
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Affiliation(s)
- Irene C M Kwan
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, Canada K7L 3N6
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Cesare Marincola F, Virno A, Randazzo A, Mocci F, Saba G, Lai A. Competitive binding exchange between alkali metal ions (K+, Rb+, and Cs+) and Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2: a 23Na and 1H NMR study. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47:1036-1042. [PMID: 19757406 DOI: 10.1002/mrc.2509] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A comparative study of the competitive cation exchange between the alkali metal ions K+, Rb+, and Cs+ and the Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2 was performed in aqueous solution by a combined use of the 23Na and 1H NMR spectroscopy. The titration data confirm the different binding affinities of these ions for the G-quadruplex and, in particular, major differences in the behavior of Cs+ as compared to the other ions were found. Accordingly, Cs+ competes with Na+ only for the binding sites at the quadruplex surface (primarily phosphate groups), while K+ and Rb+ are also able to replace sodium ions located inside the quadruplex. Furthermore, the 1H NMR results relative to the CsCl titration evidence a close approach of Cs+ ions to the phosphate groups in the narrow groove of [d(G4T4G4)]2. Based on a three-site exchange model, the 23Na NMR relaxation data lead to an estimate of the relative binding affinity of Cs+ versus Na+ for the quadruplex surface of 0.5 at 298 K. Comparing this value to those reported in the literature for the surface of the G-quadruplex formed by 5'-guanosinemonophosphate and for the surface of double-helical DNA suggests that topology factors may have an important influence on the cation affinity for the phosphate groups on DNA.
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Affiliation(s)
- Flaminia Cesare Marincola
- Dipartimento di Scienze Chimiche, Università di Cagliari, Cittadella Universitaria di Monserrato, S.S. 554 (bivio per Sestu), I-09042, Monserrato, Cagliari, Italy.
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