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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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2
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Lu X, Li M, Huang C, Lowinger MB, Xu W, Yu L, Byrn SR, Templeton AC, Su Y. Atomic-Level Drug Substance and Polymer Interaction in Posaconazole Amorphous Solid Dispersion from Solid-State NMR. Mol Pharm 2020; 17:2585-2598. [DOI: 10.1021/acs.molpharmaceut.0c00268] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xingyu Lu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Mingyue Li
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Chengbin Huang
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Michael B. Lowinger
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Lian Yu
- School of Pharmacy and Department of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53705, United States
| | - Stephen R. Byrn
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, Indiana 47907, United States
| | - Allen C. Templeton
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Yongchao Su
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, Indiana 47907, United States
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, Texas 78712, United States
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Loy BA, Lesser AB, Staveness D, Billingsley KL, Cegelski L, Wender PA. Toward a biorelevant structure of protein kinase C bound modulators: design, synthesis, and evaluation of labeled bryostatin analogues for analysis with rotational echo double resonance NMR spectroscopy. J Am Chem Soc 2015; 137:3678-85. [PMID: 25710634 DOI: 10.1021/jacs.5b00886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein kinase C (PKC) modulators are currently of great importance in preclinical and clinical studies directed at cancer, immunotherapy, HIV eradication, and Alzheimer's disease. However, the bound conformation of PKC modulators in a membrane environment is not known. Rotational echo double resonance (REDOR) NMR spectroscopy could uniquely address this challenge. However, REDOR NMR requires strategically labeled, high affinity ligands to determine interlabel distances from which the conformation of the bound ligand in the PKC-ligand complex could be identified. Here we report the first computer-guided design and syntheses of three bryostatin analogues strategically labeled for REDOR NMR analysis. Extensive computer analyses of energetically accessible analogue conformations suggested preferred labeling sites for the identification of the PKC-bound conformers. Significantly, three labeled analogues were synthesized, and, as required for REDOR analysis, all proved highly potent with PKC affinities (∼1 nM) on par with bryostatin. These potent and strategically labeled bryostatin analogues are new structural leads and provide the necessary starting point for projected efforts to determine the PKC-bound conformation of such analogues in a membrane environment, as needed to design new PKC modulators and understand PKC-ligand-membrane structure and dynamics.
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Affiliation(s)
- Brian A Loy
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Adam B Lesser
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Daryl Staveness
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Kelvin L Billingsley
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Lynette Cegelski
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Paul A Wender
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
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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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5
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Tkachenko AN, Mykhailiuk PK, Radchenko DS, Babii O, Afonin S, Ulrich AS, Komarov IV. Design and Synthesis of a Monofluoro-Substituted Aromatic Amino Acid as a Conformationally Restricted19F NMR Label for Membrane-Bound Peptides. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301737] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Kong X, Deng H, Yan F, Kim J, Swisher JA, Smit B, Yaghi OM, Reimer JA. Mapping of Functional Groups in Metal-Organic Frameworks. Science 2013; 341:882-5. [DOI: 10.1126/science.1238339] [Citation(s) in RCA: 360] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We determined the heterogeneous mesoscale spatial apportionment of functional groups in a series of multivariate metal-organic frameworks (MTV-MOF-5) containing BDC (1,4-benzenedicarboxylate) linkers with different functional groups—B (BDC-NH2), E (BDC-NO2), F [(BDC-(CH3)2], H [BDC-(OC3H5)2], and I [BDC-(OC7H7)2]—using solid-state nuclear magnetic resonance measurements combined with molecular simulations. Our analysis reveals that these methods discern between random (EF), alternating (EI and EHI), and various cluster (BF) forms of functional group apportionments. This combined synthetic, characterization, and computational approach predicts the adsorptive properties of crystalline MTV-MOF systems. This methodology, developed in the context of ordered frameworks, is a first step in resolving the more general problem of spatial disorder in other ordered materials, including mesoporous materials, functionalized polymers, and defect distributions within crystalline solids.
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Affiliation(s)
- Xueqian Kong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Environmental Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hexiang Deng
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Fangyong Yan
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jihan Kim
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joseph A. Swisher
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Berend Smit
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Omar M. Yaghi
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- NanoCentury KAIST Institute and Graduate School of Energy, Environment, Water, and Sustainability (World Class University), Daejeon 305-701, Republic of Korea
| | - Jeffrey A. Reimer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
- Environmental Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Luthra SA, Utz M, Gorman EM, Pikal MJ, Munson EJ, Lubach JW. Carbon–Deuterium Rotational-Echo Double-Resonance NMR Spectroscopy of Lyophilized Aspartame Formulations. J Pharm Sci 2012; 101:283-90. [DOI: 10.1002/jps.22769] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/28/2011] [Accepted: 09/02/2011] [Indexed: 11/08/2022]
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8
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Matsuoka S, Inoue M. Application of REDOR NMR in natural product chemistry. Chem Commun (Camb) 2009:5664-75. [DOI: 10.1039/b910230b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Barhate NB, Barhate RN, Cekan P, Drobny G, Sigurdsson ST. A nonafluoro nucleoside as a sensitive 19f NMR probe of nucleic acid conformation. Org Lett 2008; 10:2745-7. [PMID: 18533676 DOI: 10.1021/ol800872a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A nucleoside carrying a perfluorinated tert-butyl group ( 4) was prepared by a Sonogashira coupling of 5-iodo-2'-deoxyuridine with 4,4,4-trifluoro-3,3-bis(trifluoromethyl)-1-butyne in nearly quantitative yield and subsequently incorporated into DNA oligomers. Thermal denaturation studies showed that 4 had a negligible effect on duplex stability when compared to thymidine. Transition from single strand to duplex was monitored by (19)F NMR spectroscopy at micromolar concentrations of oligomers, demonstrating the sensitivity of 4 as an NMR reporter nucleoside.
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Affiliation(s)
- Nivrutti B Barhate
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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11
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Dürr UHN, Grage SL, Witter R, Ulrich AS. Solid state 19F NMR parameters of fluorine-labeled amino acids. Part I: aromatic substituents. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 191:7-15. [PMID: 18155936 DOI: 10.1016/j.jmr.2007.11.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 10/30/2007] [Accepted: 11/21/2007] [Indexed: 05/25/2023]
Abstract
Structural parameters of peptides and proteins in biomembranes can be directly measured by solid state NMR of selectively labeled amino acids. The 19F nucleus is a promising label to overcome the low sensitivity of 2H, 13C or 15N, and to serve as a background-free reporter group in biological compounds. To make the advantages of solid state 19F NMR fully available for structural studies of polypeptides, we have systematically measured the chemical shift anisotropies and relaxation properties of the most relevant aromatic and aliphatic 19F-labeled amino acids. In this first part of two consecutive contributions, six different 19F-substituents on representative aromatic side chains were characterized as polycrystalline powders by static and MAS experiments. The data are also compared with results on the same amino acids incorporated in synthetic peptides. The spectra show a wide variety of lineshapes, from which the principal values of the CSA tensors were extracted. In addition, temperature-dependent T(1) and T(2) relaxation times were determined by 19F NMR in the solid state, and isotropic chemical shifts and scalar couplings were obtained in solution.
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Affiliation(s)
- Ulrich H N Dürr
- Max-Planck-Institute for Biophysical Chemistry, Department of NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany
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Graesser DT, Wylie BJ, Nieuwkoop AJ, Franks WT, Rienstra CM. Long-range 19F-15N distance measurements in highly-13C, 15N-enriched solid proteins with 19F-dephased REDOR shift (FRESH) spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S129-S134. [PMID: 18157807 DOI: 10.1002/mrc.2126] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We present a novel rotational-echo double resonance (REDOR) method for detection of multiple (19)F-(15)N distances in solid proteins. The method is applicable to protein samples containing a single (19)F label, in addition to high levels of (13)C and (15)N enrichment. REDOR dephasing pulses are applied on the (19)F channel during an indirect constant time chemical shift evolution period on (15)N, and polarization is then transferred to (13)C for detection, with high-power (1)H decoupling throughout the sequence. This four-channel experiment reports site-specifically on (19)F-(15)N distances, with highly accurate determinations of approximately 5 A distances and detection of correlations arising from internuclear distances of at least 8 A. We demonstrate the method on the well-characterized 56-residue model protein GB1, where the sole tryptophan residue (Trp-43) has been labeled with 5-(19)F-Trp, in a bacterial growth medium also including (13)C-glucose and (15)N ammonium chloride. In GB1, 11 distances are determined, all agreeing within 20% of the X-ray structure distances. We envision the experiment will be utilized to measure quantitative long-range distances for protein structure determination.
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Affiliation(s)
- Daniel T Graesser
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 68101, USA
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Hennig M, Scott LG, Sperling E, Bermel W, Williamson JR. Synthesis of 5-fluoropyrimidine nucleotides as sensitive NMR probes of RNA structure. J Am Chem Soc 2007; 129:14911-21. [PMID: 17990877 DOI: 10.1021/ja073825i] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymatic synthesis methods for the fluorinated 5'-triphosphate analogues 5F-UTP and 5F-CTP have been developed to facilitate 19F-labeling of RNAs for biophysical studies. HIV-2 TAR RNAs were synthesized using these analogues by in vitro transcription reactions using T7 RNA polymerase. The uniform incorporation of 5F-U or 5F-C analogues into HIV-2 TAR RNA transcripts does not significantly alter the RNA structure or thermodynamic stability. Fluorine observed homonuclear 19F-19F and heteronuclear 19F-1H NOE experiments providing selective distance information are presented and discussed. The availability of efficient synthesis of 5F-UTP, and for the first time, 5F-CTP, will facilitate the use of 5F-labeled RNAs in structural, ligand binding, and dynamic studies of RNAs using the advantages of 19F-labeling.
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Affiliation(s)
- Mirko Hennig
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 173 Ashley Avenue, P.O. Box 250509, Charleston, South Carolina 29425, USA.
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