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Beriashvili D, Zhou J, Liu Y, Folkers GE, Baldus M. Cellular Applications of DNP Solid-State NMR - State of the Art and a Look to the Future. Chemistry 2024; 30:e202400323. [PMID: 38451060 DOI: 10.1002/chem.202400323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Sensitivity enhanced dynamic nuclear polarization solid-state NMR is emerging as a powerful technique for probing the structural properties of conformationally homogenous and heterogenous biomolecular species irrespective of size at atomic resolution within their native environments. Herein we detail advancements that have made acquiring such data, specifically within the confines of intact bacterial and eukaryotic cell a reality and further discuss the type of structural information that can presently be garnered by the technique's exploitation. Subsequently, we discuss bottlenecks that have thus far curbed cellular DNP-ssNMR's broader adoption namely due a lack of sensitivity and spectral resolution. We also explore possible solutions ranging from utilization of new pulse sequences, design of better performing polarizing agents, and application of additional biochemical/ cell biological methodologies.
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Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiaxin Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics, Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands
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2
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Juen F, Glänzer D, Plangger R, Kugler V, Fleischmann J, Stefan E, Case DA, Kovacs H, Dayie TK, Kreutz C. Enhanced TROSY Effect in [2- 19 F, 2- 13 C] Adenosine and ATP Analogs Facilitates NMR Spectroscopy of Very Large Biological RNAs in Solution. Angew Chem Int Ed Engl 2024; 63:e202316273. [PMID: 38185473 PMCID: PMC10922520 DOI: 10.1002/anie.202316273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/28/2023] [Accepted: 12/27/2023] [Indexed: 01/09/2024]
Abstract
Large RNAs are central to cellular functions, but characterizing such RNAs remains challenging by solution NMR. We present two labeling technologies based on [2-19 F, 2-13 C]-adenosine, which allow the incorporation of aromatic 19 F-13 C spin pairs. The labels when coupled with the transverse relaxation optimized spectroscopy (TROSY) enable us to probe RNAs comprising up to 124 nucleotides. With our new [2-19 F, 2-13 C]-adenosine-phosphoramidite, all resonances of the human hepatitis B virus epsilon RNA could be readily assigned. With [2-19 F, 2-13 C]-adenosine triphosphate, the 124 nt pre-miR-17-NPSL1-RNA was produced via in vitro transcription and the TROSY spectrum of this 40 kDa [2-19 F, 2-13 C]-A-labeled RNA featured sharper resonances than the [2-1 H, 2-13 C]-A sample. The mutual cancelation of the chemical-shift-anisotropy and the dipole-dipole-components of TROSY-resonances leads to narrow linewidths over a wide range of molecular weights. With the synthesis of a non-hydrolysable [2-19 F, 2-13 C]-adenosine-triphosphate, we facilitate the probing of co-factor binding in kinase complexes and NMR-based inhibitor binding studies in such systems. Our labels allow a straightforward assignment for larger RNAs via a divide-and-conquer/mutational approach. The new [2-19 F, 2-13 C]-adenosine precursors are a valuable addition to the RNA NMR toolbox and will allow the study of large RNAs/RNA protein complexes in vitro and in cells.
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Affiliation(s)
- Fabian Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - David Glänzer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Valentina Kugler
- Institute of Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Jakob Fleischmann
- Institute of Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Institute of Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020 Innsbruck, Austria
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Theodore Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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3
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Beriashvili D, Yao R, D'Amico F, Krafčíková M, Gurinov A, Safeer A, Cai X, Mulder MPC, Liu Y, Folkers GE, Baldus M. A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity. Chem Sci 2023; 14:9892-9899. [PMID: 37736634 PMCID: PMC10510770 DOI: 10.1039/d3sc02117c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Studying the structural aspects of proteins within sub-cellular compartments is of growing interest. Dynamic nuclear polarization supported solid-state NMR (DNP-ssNMR) is uniquely suited to provide such information, but critically lacks the desired sensitivity and resolution. Here we utilize SNAPol-1, a novel biradical, to conduct DNP-ssNMR at high-magnetic fields (800 MHz/527 GHz) inside HeLa cells and isolated cell nuclei electroporated with [13C,15N] labeled ubiquitin. We report that SNAPol-1 passively diffuses and homogenously distributes within whole cells and cell nuclei providing ubiquitin spectra of high sensitivity and remarkably improved spectral resolution. For cell nuclei, physical enrichment facilitates a further 4-fold decrease in measurement time and provides an exclusive structural view of the nuclear ubiquitin pool. Taken together, these advancements enable atomic interrogation of protein conformational plasticity at atomic resolution and with sub-cellular specificity.
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Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ru Yao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Francesca D'Amico
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Michaela Krafčíková
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Andrei Gurinov
- 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
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Gert E Folkers
- 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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4
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Dai D, Denysenkov V, Bagryanskaya EG, Tormyshev VM, Prisner TF, Kuzhelev AA. 13C Hyperpolarization of Viscous Liquids by Transfer of Solid-Effect 1H Dynamic Nuclear Polarization at High Magnetic Field. J Phys Chem Lett 2023; 14:7059-7064. [PMID: 37526333 DOI: 10.1021/acs.jpclett.3c01732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Dynamic nuclear polarization (DNP) is routinely used as a method for increasing the sensitivity to nuclear magnetic resonance (NMR). Recently, high-field solid-effect DNP in viscous liquids on 1H nuclei was demonstrated using narrow-line polarizing agents. Here we expand the applicability of DNP in viscous media to 13C nuclei. To hyperpolarize 13C nuclei, we combined solid-effect 1H DNP with a subsequent transfer of the 1H polarization to 13C via insensitive nuclei enhanced by polarization transfer (INEPT). We demonstrate this approach using a triarylmethyl radical as a polarizing agent and glycerol-13C3 as an analyte. We achieved 13C enhancement factors of up to 45 at a magnetic field of 9.4 T and room temperature.
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Affiliation(s)
- Danhua Dai
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Max von Laue Str. 7, Frankfurt am Main 60438, Germany
| | - Vasyl Denysenkov
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Max von Laue Str. 7, Frankfurt am Main 60438, Germany
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences (SB RAS), Acad. Lavrentiev Avenue 9, Novosibirsk 630090, Russia
| | - Victor M Tormyshev
- N. N. Vorozhtsov Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences (SB RAS), Acad. Lavrentiev Avenue 9, Novosibirsk 630090, Russia
| | - Thomas F Prisner
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Max von Laue Str. 7, Frankfurt am Main 60438, Germany
| | - Andrei A Kuzhelev
- Goethe University Frankfurt am Main, Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance, Max von Laue Str. 7, Frankfurt am Main 60438, Germany
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5
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Liu J, Wu XL, Zeng YT, Hu ZH, Lu JX. Solid-state NMR studies of amyloids. Structure 2023; 31:230-243. [PMID: 36750098 DOI: 10.1016/j.str.2023.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/10/2022] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Amyloids have special structural properties and are involved in many aspects of biological function. In particular, amyloids are the cause or hallmarks of a group of notorious and incurable neurodegenerative diseases. The extraordinary high molecular weight and aggregation states of amyloids have posed a challenge for researchers studying them. Solid-state NMR (SSNMR) has been extensively applied to study the structures and dynamics of amyloids for the past 20 or more years and brought us tremendous progress in understanding their structure and related diseases. These studies, at the same time, helped to push SSNMR technical developments in sensitivity and resolution. In this review, some interesting research studies and important technical developments are highlighted to give the reader an overview of the current state of this field.
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Affiliation(s)
- Jing Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xia-Lian Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu-Teng Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhi-Heng Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jun-Xia Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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6
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Porat-Dahlerbruch G, Struppe J, Quinn CM, Gronenborn AM, Polenova T. 19F fast MAS (60-111 kHz) dipolar and scalar based correlation spectroscopy of organic molecules and pharmaceutical formulations. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101831. [PMID: 36182713 DOI: 10.1016/j.ssnmr.2022.101831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
19F magic angle spinning (MAS) NMR spectroscopy is a powerful tool for characterization of fluorinated solids. The recent development of 19F MAS NMR probes, operating at spinning frequencies of 60-111 kHz, enabled analysis of systems spanning from organic molecules to pharmaceutical formulations to biological assemblies, with unprecedented resolution. Herein, we systematically evaluate the benefits of high MAS frequencies (60-111 kHz) for 1D and 2D 19F-detected experiments in two pharmaceuticals, the antimalarial drug mefloquine and a formulation of the cholesterol-lowering drug atorvastatin calcium. We demonstrate that 1H decoupling is essential and that scalar-based, heteronuclear single quantum coherence (HSQC) and heteronuclear multiple quantum coherence (HMQC) correlation experiments become feasible and efficient at the MAS frequency of 100 kHz. This study opens doors for the applications of high frequency 19F MAS NMR to a wide range of problems in chemistry and biology.
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Affiliation(s)
- Gal Porat-Dahlerbruch
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA, 01821, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Angela M Gronenborn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States; Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States; Department of Structural Biology, University of Pittsburgh, School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh, School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA, 15261, United States.
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7
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Cell-free synthesis of amyloid fibrils with infectious properties and amenable to sub-milligram magic-angle spinning NMR analysis. Commun Biol 2022; 5:1202. [DOI: 10.1038/s42003-022-04175-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractStructural investigations of amyloid fibrils often rely on heterologous bacterial overexpression of the protein of interest. Due to their inherent hydrophobicity and tendency to aggregate as inclusion bodies, many amyloid proteins are challenging to express in bacterial systems. Cell-free protein expression is a promising alternative to classical bacterial expression to produce hydrophobic proteins and introduce NMR-active isotopes that can improve and speed up the NMR analysis. Here we implement the cell-free synthesis of the functional amyloid prion HET-s(218-289). We present an interesting case where HET-s(218-289) directly assembles into infectious fibril in the cell-free expression mixture without the requirement of denaturation procedures and purification. By introducing tailored 13C and 15N isotopes or CF3 and 13CH2F labels at strategic amino-acid positions, we demonstrate that cell-free synthesized amyloid fibrils are readily amenable to high-resolution magic-angle spinning NMR at sub-milligram quantity.
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8
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Duan P, Dregni AJ, Hong M. Solid-State NMR 19F- 1H- 15N Correlation Experiments for Resonance Assignment and Distance Measurements of Multifluorinated Proteins. J Phys Chem A 2022; 126:7021-7032. [PMID: 36150071 PMCID: PMC10867861 DOI: 10.1021/acs.jpca.2c05154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several solid-state NMR techniques have been introduced recently to measure nanometer distances involving 19F, whose high gyromagnetic ratio makes it a potent nuclear spin for structural investigation. These solid-state NMR techniques either use 19F correlation with 1H or 13C to obtain qualitative interatomic contacts or use the rotational-echo double-resonance (REDOR) pulse sequence to measure quantitative distances. However, no NMR technique is yet available for disambiguating 1H-19F distances in multiply fluorinated proteins and protein-ligand complexes. Here, we introduce a three-dimensional (3D) 19F-15N-1H correlation experiment that resolves the distances of multiple fluorines to their adjacent amide protons. We show that optimal polarization transfer between 1H and 19F spins is achieved using an out-and-back 1H-19F REDOR sequence. We demonstrate this 3D correlation experiment on the model protein GB1 and apply it to the multidrug-resistance transporter, EmrE, complexed to a tetrafluorinated substrate. This technique should be useful for resolving and assigning distance constraints in multiply fluorinated proteins, leading to significant savings of time and precious samples compared to producing several singly fluorinated samples. Moreover, the method enables structural determination of protein-ligand complexes for ligands that contain multiple fluorines.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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9
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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10
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Jeon J, Blake Wilson C, Yau WM, Thurber KR, Tycko R. Time-resolved solid state NMR of biomolecular processes with millisecond time resolution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 342:107285. [PMID: 35998398 PMCID: PMC9463123 DOI: 10.1016/j.jmr.2022.107285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 05/21/2023]
Abstract
We review recent efforts to develop and apply an experimental approach to the structural characterization of transient intermediate states in biomolecular processes that involve large changes in molecular conformation or assembly state. This approach depends on solid state nuclear magnetic resonance (ssNMR) measurements that are performed at very low temperatures, typically 25-30 K, with signal enhancements from dynamic nuclear polarization (DNP). This approach also involves novel technology for initiating the process of interest, either by rapid mixing of two solutions or by a rapid inverse temperature jump, and for rapid freezing to trap intermediate states. Initiation by rapid mixing or an inverse temperature jump can be accomplished in approximately-one millisecond. Freezing can be accomplished in approximately 100 microseconds. Thus, millisecond time resolution can be achieved. Recent applications to the process by which the biologically essential calcium sensor protein calmodulin forms a complex with one of its target proteins and the process by which the bee venom peptide melittin converts from an unstructured monomeric state to a helical, tetrameric state after a rapid change in pH or temperature are described briefly. Future applications of millisecond time-resolved ssNMR are also discussed briefly.
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Affiliation(s)
- Jaekyun Jeon
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - C Blake Wilson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Kent R Thurber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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11
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Du Y, Su Y. 19F Solid-state NMR characterization of pharmaceutical solids. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 120:101796. [PMID: 35688018 DOI: 10.1016/j.ssnmr.2022.101796] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Solid-state NMR has been increasingly recognized as a high-resolution and versatile spectroscopic tool to characterize drug substances and products. However, the analysis of pharmaceutical materials is often carried out at natural isotopic abundance and a relatively low drug loading in multi-component systems and therefore suffers from challenges of low sensitivity. The fact that fluorinated therapeutics are well represented in pipeline drugs and commercial products offers an excellent opportunity to utilize fluorine as a molecular probe for pharmaceutical analysis. We aim to review recent advancements of 19F magic angle spinning NMR methods in modern drug research and development. Applications to polymorph screening at the micromolar level, structural elucidation, and investigation of molecular interactions at the Ångström to submicron resolution in drug delivery, stability, and quality will be discussed.
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Affiliation(s)
- Yong Du
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, United States
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, United States; Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, IN, 47907, United States; Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, United States; Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT, 06269, United States.
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12
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Sutherland M, Tran N, Hong M. Clustering of tetrameric influenza M2 peptides in lipid bilayers investigated by 19F solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183909. [PMID: 35276226 DOI: 10.1016/j.bbamem.2022.183909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/08/2022] [Accepted: 03/05/2022] [Indexed: 11/19/2022]
Abstract
The influenza M2 protein forms a drug-targeted tetrameric proton channel to mediate virus uncoating, and carries out membrane scission to enable virus release. While the proton channel function of M2 has been extensively studied, the mechanism by which M2 catalyzes membrane scission is still not well understood. Previous fluorescence and electron microscopy studies indicated that M2 tetramers concentrate at the neck of the budding virus in the host plasma membrane. However, molecular evidence for this clustering is scarce. Here, we use 19F solid-state NMR to investigate M2 clustering in phospholipid bilayers. By mixing equimolar amounts of 4F-Phe47 labeled M2 peptide and CF3-Phe47 labeled M2 peptide and measuring F-CF3 cross peaks in 2D 19F19F correlation spectra, we show that M2 tetramers form nanometer-scale clusters in lipid bilayers. This clustering is stronger in cholesterol-containing membranes and phosphatidylethanolamine (PE) membranes than in cholesterol-free phosphatidylcholine and phosphatidylglycerol membranes. The observed correlation peaks indicate that Phe47 sidechains from different tetramers are less than ~2 nm apart. 1H19F correlation peaks between lipid chain protons and fluorinated Phe47 indicate that Phe47 is more deeply inserted into the lipid bilayer in the presence of cholesterol than in its absence, suggesting that Phe47 preferentially interacts with cholesterol. Static 31P NMR spectra indicate that M2 induces negative Gaussian curvature in the PE membrane. These results suggest that M2 tetramers cluster at cholesterol- and PE-rich regions of cell membranes to cause membrane curvature, which in turn can facilitate membrane scission in the last step of virus budding and release.
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Affiliation(s)
- Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America.
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13
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Elathram N, Ackermann BE, Debelouchina GT. DNP-enhanced solid-state NMR spectroscopy of chromatin polymers. JOURNAL OF MAGNETIC RESONANCE OPEN 2022; 10-11:100057. [PMID: 35707629 PMCID: PMC9191766 DOI: 10.1016/j.jmro.2022.100057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chromatin is a DNA-protein polymer that represents the functional form of the genome. The main building block of chromatin is the nucleosome, a structure that contains 147 base pairs of DNA and two copies each of the histone proteins H2A, H2B, H3 and H4. Previous work has shown that magic angle spinning (MAS) NMR spectroscopy can capture the nucleosome at high resolution although studies have been challenging due to low sensitivity, the presence of dynamic and rigid components, and the complex interaction networks of nucleosomes within the chromatin polymer. Here, we use dynamic nuclear polarization (DNP) to enhance the sensitivity of MAS NMR experiments of nucleosome arrays at 100 K and show that well-resolved 13C-13C MAS NMR correlations can be obtained much more efficiently. We evaluate the effect of temperature on the chemical shifts and linewidths in the spectra and demonstrate that changes are relatively minimal and clustered in regions of histone-DNA or histone-histone contacts. We also compare samples prepared with and without DNA and show that the low temperature 13C-13C correlations exhibit sufficient resolution to detect chemical shift changes and line broadening for residues that form the DNA-histone interface. On the other hand, we show that the measurement of DNP-enhanced 15N-13C histone-histone interactions within the nucleosome core is complicated by the natural 13C abundance network in the sample. Nevertheless, the enhanced sensitivity afforded by DNP can be used to detect long-range correlations between histone residues and DNA. Overall, our experiments demonstrate that DNP-enhanced MAS NMR spectroscopy of chromatin samples yields spectra with high resolution and sensitivity and can be used to capture functionally relevant protein-DNA interactions that have implications for gene regulation and genome organization.
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Affiliation(s)
| | | | - Galia T. Debelouchina
- Corresponding author: Galia Debelouchina, University of California, San Diego, Natural Sciences Building 4322, 9500 Gilman Dr., La Jolla, CA 92093, 858-534-3038,
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14
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Chow WY, De Paëpe G, Hediger S. Biomolecular and Biological Applications of Solid-State NMR with Dynamic Nuclear Polarization Enhancement. Chem Rev 2022; 122:9795-9847. [PMID: 35446555 DOI: 10.1021/acs.chemrev.1c01043] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Solid-state NMR spectroscopy (ssNMR) with magic-angle spinning (MAS) enables the investigation of biological systems within their native context, such as lipid membranes, viral capsid assemblies, and cells. However, such ambitious investigations often suffer from low sensitivity due to the presence of significant amounts of other molecular species, which reduces the effective concentration of the biomolecule or interaction of interest. Certain investigations requiring the detection of very low concentration species remain unfeasible even with increasing experimental time for signal averaging. By applying dynamic nuclear polarization (DNP) to overcome the sensitivity challenge, the experimental time required can be reduced by orders of magnitude, broadening the feasible scope of applications for biological solid-state NMR. In this review, we outline strategies commonly adopted for biological applications of DNP, indicate ongoing challenges, and present a comprehensive overview of biological investigations where MAS-DNP has led to unique insights.
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Affiliation(s)
- Wing Ying Chow
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, Inst. Biol. Struct. IBS, 38044 Grenoble, France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, Interdisciplinary Research Institute of Grenoble (IRIG), Modeling and Exploration of Materials Laboratory (MEM), 38054 Grenoble, France
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15
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Yang D, Gronenborn AM, Chong LT. Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field. J Phys Chem A 2022; 126:2286-2297. [PMID: 35352936 PMCID: PMC9014858 DOI: 10.1021/acs.jpca.2c00255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/15/2022] [Indexed: 12/27/2022]
Abstract
We developed force field parameters for fluorinated, aromatic amino acids enabling molecular dynamics (MD) simulations of fluorinated proteins. These parameters are tailored to the AMBER ff15ipq protein force field and enable the modeling of 4, 5, 6, and 7F-tryptophan, 3F- and 3,5F-tyrosine, and 4F- or 4-CF3-phenylalanine. The parameters include 181 unique atomic charges derived using the implicitly polarized charge (IPolQ) scheme in the presence of SPC/Eb explicit water molecules and 9 unique bond, angle, or torsion terms. Our simulations of benchmark peptides and proteins maintain expected conformational propensities on the μs time scale. In addition, we have developed an open-source Python program to calculate fluorine relaxation rates from MD simulations. The extracted relaxation rates from protein simulations are in good agreement with experimental values determined by 19F NMR. Collectively, our results illustrate the power and robustness of the IPolQ lineage of force fields for modeling the structure and dynamics of fluorine-containing proteins at the atomic level.
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Affiliation(s)
- Darian
T. Yang
- Molecular
Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, Pennsylvania 15260, United States
- Department
of Structural Biology, University of Pittsburgh
School of Medicine, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Angela M. Gronenborn
- Department
of Structural Biology, University of Pittsburgh
School of Medicine, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lillian T. Chong
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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16
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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17
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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18
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Duan P, Chen KJ, Wijegunawardena G, Dregni AJ, Wang HK, Wu H, Hong M. Binding Sites of a Positron Emission Tomography Imaging Agent in Alzheimer's β-Amyloid Fibrils Studied Using 19F Solid-State NMR. J Am Chem Soc 2022; 144:1416-1430. [PMID: 35015530 PMCID: PMC8855532 DOI: 10.1021/jacs.1c12056] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amyloid imaging by positron emission tomography (PET) is an important method for diagnosing neurodegenerative disorders such as Alzheimer's disease. Many 11C- and 18F-labeled PET tracers show varying binding capacities, specificities, and affinities for their target proteins. The structural basis of these variations is poorly understood. Here we employ 19F and 13C solid-state NMR to investigate the binding sites of a PET ligand, flutemetamol, to the 40-residue Alzheimer's β-amyloid peptide (Aβ40). Analytical high-performance liquid chromatography and 19F NMR spectra show that flutemetamol binds the current Aβ40 fibril polymorph with a stoichiometry of one ligand per four to five peptides. Half of the ligands are tightly bound while the other half are loosely bound. 13C and 15N chemical shifts indicate that this Aβ40 polymorph has an immobilized N-terminus, a non-β-sheet His14, and a non-β-sheet C-terminus. We measured the proximity of the ligand fluorine to peptide residues using 19F-13C and 19F-1H rotational-echo double-resonance (REDOR) experiments. The spectra show that three segments in the peptide, 12VHH14, 18VFF20, and 39VV40, lie the closest to the ligand. REDOR-constrained docking simulations indicate that these three segments form multiple binding sites, and the ligand orientations and positions at these sites are similar across different Aβ polymorphs. Comparison of the flutemetamol-interacting residues in Aβ40 with the small-molecule binding sites in other amyloid proteins suggest that conjugated aromatic compounds preferentially bind β-sheet surface grooves lined by aromatic, polar, and charged residues. These motifs may explain the specificity of different PET tracers to different amyloid proteins.
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Affiliation(s)
- Pu Duan
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Kelly J. Chen
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Gayani Wijegunawardena
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount St, Wichita, KS 67260, United States
| | - Aurelio J. Dregni
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Harrison K. Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount St, Wichita, KS 67260, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139, United States
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19
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Gronenborn AM. Small, but powerful and attractive: 19F in biomolecular NMR. Structure 2022; 30:6-14. [PMID: 34995480 PMCID: PMC8797020 DOI: 10.1016/j.str.2021.09.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 09/20/2021] [Indexed: 01/09/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool for probing structure, dynamics, folding, and interactions at atomic resolution. While naturally occurring magnetically active isotopes, such as 1H, 13C, or 15N, are most commonly used in biomolecular NMR, with 15N and 13C isotopic labeling routinely employed at the present time, 19F is a very attractive and sensitive alternative nucleus, which offers rich information on biomolecules in solution and in the solid state. This perspective summarizes the unique benefits of solution and solid-state 19F NMR spectroscopy for the study of biological systems. Particular focus is on the most recent studies and on future unique and important potential applications of fluorine NMR methodology.
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20
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Wu T, Chen K, Jiang M, Li A, Peng X, Chen S, Yang Z, Zhou X, Zheng X, Jiang ZX. Hydrofluorocarbons Nanoparticles for 19F MRI-Fluorescence Dual Imaging and Chemo-Photodynamic Therapy. Org Biomol Chem 2022; 20:1299-1305. [DOI: 10.1039/d1ob02392f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synergistic chemotherapy and photodynamic therapy (PDT) may significantly improve cancer therapeutic efficacy, in which fluorinated nanoemulsions are highly advantageous for their ability to deliver oxygen to hypoxic tumors and...
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21
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Ghassemi N, Poulhazan A, Deligey F, Mentink-Vigier F, Marcotte I, Wang T. Solid-State NMR Investigations of Extracellular Matrixes and Cell Walls of Algae, Bacteria, Fungi, and Plants. Chem Rev 2021; 122:10036-10086. [PMID: 34878762 DOI: 10.1021/acs.chemrev.1c00669] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Extracellular matrixes (ECMs), such as the cell walls and biofilms, are important for supporting cell integrity and function and regulating intercellular communication. These biomaterials are also of significant interest to the production of biofuels and the development of antimicrobial treatment. Solid-state nuclear magnetic resonance (ssNMR) and magic-angle spinning-dynamic nuclear polarization (MAS-DNP) are uniquely powerful for understanding the conformational structure, dynamical characteristics, and supramolecular assemblies of carbohydrates and other biomolecules in ECMs. This review highlights the recent high-resolution investigations of intact ECMs and native cells in many organisms spanning across plants, bacteria, fungi, and algae. We spotlight the structural principles identified in ECMs, discuss the current technical limitation and underexplored biochemical topics, and point out the promising opportunities enabled by the recent advances of the rapidly evolving ssNMR technology.
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Affiliation(s)
- Nader Ghassemi
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Alexandre Poulhazan
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal H2X 2J6, Canada
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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22
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Gronenborn AM. Meet the IUPAB councilor - Angela M. Gronenborn. Biophys Rev 2021; 13:835-838. [PMID: 35059003 PMCID: PMC8724357 DOI: 10.1007/s12551-021-00886-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 01/23/2023] Open
Abstract
As an incoming IUPAB Councilor, I have been asked to write a short commentary describing myself and my career in science. Throughout my scientific life, my interests have evolved from initially trying to understand the physical and chemical properties of small molecules toward unraveling biological systems. To that end, I now apply biophysical, biochemical and chemistry tools. Along my journey, I developed and applied nuclear magnetic resonance (NMR) spectroscopy methods to figure out how proteins work at the atomic level and this voyage took me from Germany, where I earned degrees in Physics and Chemistry, to the UK and back to Germany, finally dropping anchor in the USA, where I have led research programs at both the National Institutes of Health and the University of Pittsburgh. I am now the UPMC Rosalind Franklin Professor and Chair of the Department of Structural Biology, University of Pittsburgh School of Medicine, a Professor of Bioengineering, Swanson School of Engineering, and a Professor of Chemistry, Dietrich School of Arts and Sciences, University of Pittsburgh.
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Affiliation(s)
- Angela M. Gronenborn
- Department of Structural Biology, School of Medicine, and Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Biomedical Science Tower 3, Room 1051, 3501 Fifth Avenue, Pittsburgh, PA 15260 USA
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23
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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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24
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Quinn CM, Zadorozhnyi R, Struppe J, Sergeyev IV, Gronenborn AM, Polenova T. Fast 19F Magic-Angle Spinning Nuclear Magnetic Resonance for the Structural Characterization of Active Pharmaceutical Ingredients in Blockbuster Drugs. Anal Chem 2021; 93:13029-13037. [PMID: 34517697 DOI: 10.1021/acs.analchem.1c02917] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fluorinated drugs occupy a large and growing share of the pharmaceutical market. Here, we explore high-frequency, 60 to 111 kHz, 19F magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy for the structural characterization of fluorinated active pharmaceutical ingredients in commercial formulations of seven blockbuster drugs: Celebrex, Cipro, Crestor, Levaquin, Lipitor, Prozac, and Zyvox. 19F signals can be observed in a single scan, and spectra with high signal-to-noise ratios can be acquired in minutes. 19F spectral parameters, such as chemical shifts and line widths, are sensitive to both the nature of the fluorine moiety and the formulation. We anticipate that the fast 19F MAS NMR-based approach presented here will be valuable for the rapid analysis of fluorine-containing drugs in a wide variety of formulations.
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Affiliation(s)
- Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Roman Zadorozhnyi
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
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25
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Guo C, Fritz MP, Struppe J, Wegner S, Stringer J, Sergeyev IV, Quinn CM, Gronenborn AM, Polenova T. Fast 19F Magic Angle Spinning NMR Crystallography for Structural Characterization of Fluorine-Containing Pharmaceutical Compounds. Anal Chem 2021; 93:8210-8218. [PMID: 34080855 DOI: 10.1021/acs.analchem.1c00784] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fluorine-containing compounds comprise 20 to 30 percent of all commercial drugs, and the proportion of fluorinated pharmaceuticals is rapidly growing. While magic angle spinning (MAS) NMR spectroscopy is a popular technique for analysis of solid pharmaceutical compounds, fluorine has been underutilized as a structural probe so far. Here, we report a fast (40-60 kHz) MAS 19F NMR approach for structural characterization of fluorine-containing crystalline pharmaceutical compounds at natural abundance, using the antimalarial fluorine-containing drug mefloquine as an example. We demonstrate the utility of 2D 19F-13C and 19F-19F dipolar-coupling-based correlation experiments for 19F and 13C resonance frequency assignment, which permit identification of crystallographically inequivalent sites. The efficiency of 19F-13C cross-polarization and the effect of 1H and 19F decoupling on spectral resolution and sensitivity were evaluated in a broad range of experimental conditions. We further demonstrate a protocol for measuring accurate interfluorine distances based on 1D DANTE-RFDR experiments combined with multispin numerical simulations.
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Affiliation(s)
- Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Matthew P Fritz
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | | | - John Stringer
- PhoenixNMR, 510 E. 5th Street, Loveland, Colorado 80537, United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
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26
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Phạm TTT, Rainey JK. On-cell nuclear magnetic resonance spectroscopy to probe cell surface interactions. Biochem Cell Biol 2021; 99:683-692. [PMID: 33945753 DOI: 10.1139/bcb-2021-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy allows determination of atomic-level information about intermolecular interactions, molecular structure, and molecular dynamics in the cellular environment. This may be broadly divided into studies focused on obtaining detailed molecular information in the intracellular context ("in-cell") or those focused on characterizing molecules or events at the cell surface ("on-cell"). In this review, we outline some key NMR techniques applied for on-cell NMR studies through both solution-state and solid-state NMR and survey studies that have used these techniques to uncover key information. We particularly focus on application of on-cell NMR spectroscopy to characterize ligand interactions with cell surface membrane proteins such as G-protein coupled receptors (GPCRs), receptor tyrosine kinases, etc. These techniques allow for quantification of binding affinities, competitive binding assays, delineation of portions of ligands involved in binding, ligand bound-state conformational determination, evaluation of receptor structuring and dynamics, and inference of distance constraints characteristic of the ligand-receptor bound state. Excitingly, it is possible to avoid the barriers of production and purification of membrane proteins while obtaining directly physiologically-relevant information through on-cell NMR. We also provide a briefer survey of the applicability of on-cell NMR approaches to other classes of cell surface molecule.
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Affiliation(s)
- Trần Thanh Tâm Phạm
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Nova Scotia, Canada;
| | - Jan K Rainey
- Dalhousie University, 3688, Department of Biochemistry & Molecular Biology, Halifax, Canada;
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27
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Sergeyev IV, Quinn CM, Struppe J, Gronenborn A, Polenova T. Competing Transfer Pathways in Direct and Indirect Dynamic Nuclear Polarization MAS NMR Experiments on HIV-1 Capsid Assemblies: Implications for Sensitivity and Resolution. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:239-249. [PMID: 34136885 PMCID: PMC8203495 DOI: 10.5194/mr-2-239-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/23/2021] [Indexed: 04/25/2023]
Abstract
Dynamic nuclear polarization-enhanced (DNP) magic angle spinning (MAS) NMR of biological systems is a rapidly growing field. Large signal enhancements make the technique particularly attractive for signal-limited cases, such as studies of complex biological assemblies or at natural isotopic abundance. However, spectral resolution is considerably reduced compared to ambient-temperature non-DNP spectra. Herein, we report a systematic investigation into sensitivity and resolution of 1D and 2D 13C-detected DNP MAS NMR experiments on HIV-1 CA tubular assemblies. We show that the magnitude and sign of signal enhancement as well as the homogeneous line width are strongly dependent on the biradical concentration, the dominant polarization transfer pathway, and the enhancement buildup time. Our findings provide guidance for optimal choice of sample preparation and experimental conditions in DNP experiments.
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Affiliation(s)
- Ivan V. Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Caitlin M. Quinn
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, MA 01821, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware,
Newark, DE 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of
Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth
Avenue, Pittsburgh, PA 15261, United States
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28
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Wilbourne M, Zhang P. Visualizing HIV-1 Capsid and Its Interactions with Antivirals and Host Factors. Viruses 2021; 13:246. [PMID: 33557422 PMCID: PMC7914784 DOI: 10.3390/v13020246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 02/03/2023] Open
Abstract
Understanding of the construction and function of the HIV capsid has advanced considerably in the last decade. This is due in large part to the development of more sophisticated structural techniques, particularly cryo-electron microscopy (cryoEM) and cryo-electron tomography (cryoET). The capsid is known to be a pleomorphic fullerene cone comprised of capsid protein monomers arranged into 200-250 hexamers and 12 pentamers. The latter of these induce high curvature necessary to close the cone at both ends. CryoEM/cryoET, NMR, and X-ray crystallography have collectively described these interactions to atomic or near-atomic resolutions. Further, these techniques have helped to clarify the role the HIV capsid plays in several parts of the viral life cycle, from reverse transcription to nuclear entry and integration into the host chromosome. This includes visualizing the capsid bound to host factors. Multiple proteins have been shown to interact with the capsid. Cyclophilin A, nucleoporins, and CPSF6 promote viral infectivity, while MxB and Trim5α diminish the viral infectivity. Finally, structural insights into the intra- and intermolecular interactions that govern capsid function have enabled development of small molecules, peptides, and truncated proteins to disrupt or stabilize the capsid to inhibit HIV replication. The most promising of these, GS6207, is now in clinical trial.
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Affiliation(s)
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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29
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Nevzorov AA, Marek A, Milikisiyants S, Smirnov AI. Characterization of photonic band resonators for DNP NMR of thin film samples at 7 T magnetic field. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 323:106893. [PMID: 33418455 PMCID: PMC8362290 DOI: 10.1016/j.jmr.2020.106893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Polarization of nuclear spins via Dynamic Nuclear Polarization (DNP) relies on generating sufficiently high mm-wave B1e fields over the sample, which could be achieved by developing suitable resonance structures. Recently, we have introduced one-dimensional photonic band gap (1D PBG) resonators for DNP and reported on prototype devices operating at ca. 200 GHz electron resonance frequency. Here we systematically compare the performance of five (5) PBG resonators constructed from various alternating dielectric layers by monitoring the DNP effect on natural-abundance 13C spins in synthetic diamond microparticles embedded into a commercial polyester-based lapping film of just 3 mil (76 μm) thickness. An odd-numbered configuration of dielectric layers for 1D PBG resonator was introduced to achieve further B1e enhancements. Among the PBG configurations tested, combinations of high-ε perovskite LiTaO3 together with AlN as well as AlN with optical quartz wafers have resulted in ca. 40 to over 50- fold gains in the average mm-wave power over the sample vs. the mirror-only configuration. The results are rationalized in terms of the electromagnetic energy distribution inside the resonators obtained analytically and from COMSOL simulations. It was found that average of B1e2 over the sample strongly depends on the arrangement of the dielectric layers that are the closest to the sample, which favors odd-numbered PBG resonator configurations for their use in DNP.
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Affiliation(s)
- Alexander A Nevzorov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
| | - Antonin Marek
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Sergey Milikisiyants
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States
| | - Alex I Smirnov
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204, United States.
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30
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Structure and dynamics of the drug-bound bacterial transporter EmrE in lipid bilayers. Nat Commun 2021; 12:172. [PMID: 33420032 PMCID: PMC7794478 DOI: 10.1038/s41467-020-20468-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/01/2020] [Indexed: 01/29/2023] Open
Abstract
The dimeric transporter, EmrE, effluxes polyaromatic cationic drugs in a proton-coupled manner to confer multidrug resistance in bacteria. Although the protein is known to adopt an antiparallel asymmetric topology, its high-resolution drug-bound structure is so far unknown, limiting our understanding of the molecular basis of promiscuous transport. Here we report an experimental structure of drug-bound EmrE in phospholipid bilayers, determined using 19F and 1H solid-state NMR and a fluorinated substrate, tetra(4-fluorophenyl) phosphonium (F4-TPP+). The drug-binding site, constrained by 214 protein-substrate distances, is dominated by aromatic residues such as W63 and Y60, but is sufficiently spacious for the tetrahedral drug to reorient at physiological temperature. F4-TPP+ lies closer to the proton-binding residue E14 in subunit A than in subunit B, explaining the asymmetric protonation of the protein. The structure gives insight into the molecular mechanism of multidrug recognition by EmrE and establishes the basis for future design of substrate inhibitors to combat antibiotic resistance.
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31
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Heiliger J, Matzel T, Çetiner EC, Schwalbe H, Kuenze G, Corzilius B. Site-specific dynamic nuclear polarization in a Gd(III)-labeled protein. Phys Chem Chem Phys 2020; 22:25455-25466. [PMID: 33103678 DOI: 10.1039/d0cp05021k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dynamic nuclear polarization (DNP) of a biomolecule tagged with a polarizing agent has the potential to not only increase NMR sensitivity but also to provide specificity towards the tagging site. Although the general concept has been often discussed, the observation of true site-specific DNP and its dependence on the electron-nuclear distance has been elusive. Here, we demonstrate site-specific DNP in a uniformly isotope-labeled ubiquitin. By recombinant expression of three different ubiquitin point mutants (F4C, A28C, and G75C) post-translationally modified with a Gd3+-chelator tag, localized metal-ion DNP of 13C and 15N is investigated. Effects counteracting the site-specificity of DNP such as nuclear spin-lattice relaxation and proton-driven spin diffusion have been attenuated by perdeuteration of the protein. Particularly for 15N, large DNP enhancement factors on the order of 100 and above as well as localized effects within side-chain resonances differently distributed over the protein are observed. By analyzing the experimental DNP built-up dynamics combined with structural modeling of Gd3+-tags in ubiquitin supported by paramagnetic relaxation enhancement (PRE) in solution, we provide, for the first time, quantitative information on the distance dependence of the initial DNP transfer. We show that the direct 15N DNP transfer rate indeed linearly depends on the square of the hyperfine interaction between the electron and the nucleus following Fermi's golden rule, however, below a certain distance cutoff paramagnetic signal bleaching may dramatically skew the correlation.
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Affiliation(s)
- Jörg Heiliger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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32
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The Potential of 19F NMR Application in GPCR Biased Drug Discovery. Trends Pharmacol Sci 2020; 42:19-30. [PMID: 33250272 DOI: 10.1016/j.tips.2020.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/16/2020] [Accepted: 11/02/2020] [Indexed: 01/14/2023]
Abstract
Although structure-based virtual drug discovery is revolutionizing the conventional high-throughput cell-based screening system, its limitation is obvious, together with other critical challenges. In particular, the resolved static snapshots fail to represent a full free-energy landscape due to homogenization in structural determination processing. The loss of conformational heterogeneity and related functional diversity emphasize the necessity of developing an approach that can fill this space. In this regard, NMR holds undeniable potential. However, outstanding questions regarding the NMR application remain. This review summarizes the limitations of current drug discovery and explores the potential of 19F NMR in establishing a conformation-guided drug screening system, advancing the cell- and structure-based discovery strategy for G protein-coupled receptor (GPCR) biased drug screening.
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33
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Nußbaumer F, Plangger R, Roeck M, Kreutz C. Aromatic
19
F–
13
C TROSY—[
19
F,
13
C]‐Pyrimidine Labeling for NMR Spectroscopy of RNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Felix Nußbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Manuel Roeck
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI) University of Innsbruck Innrain 80/82 6020 Innsbruck Austria
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34
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Nußbaumer F, Plangger R, Roeck M, Kreutz C. Aromatic 19 F- 13 C TROSY-[ 19 F, 13 C]-Pyrimidine Labeling for NMR Spectroscopy of RNA. Angew Chem Int Ed Engl 2020; 59:17062-17069. [PMID: 32558232 PMCID: PMC7540360 DOI: 10.1002/anie.202006577] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 12/22/2022]
Abstract
We present the access to [5-19 F, 5-13 C]-uridine and -cytidine phosphoramidites for the production of site-specifically modified RNAs up to 65 nucleotides (nts). The amidites were used to introduce [5-19 F, 5-13 C]-pyrimidine labels into five RNAs-the 30 nt human immunodeficiency virus trans activation response (HIV TAR) 2 RNA, the 61 nt human hepatitis B virus ϵ (hHBV ϵ) RNA, the 49 nt SAM VI riboswitch aptamer domain from B. angulatum, the 29 nt apical stem loop of the pre-microRNA (miRNA) 21 and the 59 nt full length pre-miRNA 21. The main stimulus to introduce the aromatic 19 F-13 C-spin topology into RNA comes from a work of Boeszoermenyi et al., in which the dipole-dipole interaction and the chemical shift anisotropy relaxation mechanisms cancel each other leading to advantageous TROSY properties shown for aromatic protein sidechains. This aromatic 13 C-19 F labeling scheme is now transferred to RNA. We provide a protocol for the resonance assignment by solid phase synthesis based on diluted [5-19 F, 5-13 C]/[5-19 F] pyrimidine labeling. For the 61 nt hHBV ϵ we find a beneficial 19 F-13 C TROSY enhancement, which should be even more pronounced in larger RNAs and will facilitate the NMR studies of larger RNAs. The [19 F, 13 C]-labeling of the SAM VI aptamer domain and the pre-miRNA 21 further opens the possibility to use the biorthogonal stable isotope reporter nuclei in in vivo NMR to observe ligand binding and microRNA processing in a biological relevant setting.
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Affiliation(s)
- Felix Nußbaumer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Manuel Roeck
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
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35
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Boeszoermenyi A, Ogórek B, Jain A, Arthanari H, Wagner G. The precious fluorine on the ring: fluorine NMR for biological systems. JOURNAL OF BIOMOLECULAR NMR 2020; 74:365-379. [PMID: 32651751 PMCID: PMC7539674 DOI: 10.1007/s10858-020-00331-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/29/2020] [Indexed: 05/08/2023]
Abstract
The fluorine-19 nucleus was recognized early to harbor exceptional properties for NMR spectroscopy. With 100% natural abundance, a high gyromagnetic ratio (83% sensitivity compared to 1H), a chemical shift that is extremely sensitive to its surroundings and near total absence in biological systems, it was destined to become a favored NMR probe, decorating small and large molecules. However, after early excitement, where uptake of fluorinated aromatic amino acids was explored in a series of animal studies, 19F-NMR lost popularity, especially in large molecular weight systems, due to chemical shift anisotropy (CSA) induced line broadening at high magnetic fields. Recently, two orthogonal approaches, (i) CF3 labeling and (ii) aromatic 19F-13C labeling leveraging the TROSY (Transverse Relaxation Optimized Spectroscopy) effect have been successfully applied to study large biomolecular systems. In this perspective, we will discuss the fascinating early work with fluorinated aromatic amino acids, which reveals the enormous potential of these non-natural amino acids in biological NMR and the potential of 19F-NMR to characterize protein and nucleic acid structure, function and dynamics in the light of recent developments. Finally, we explore how fluorine NMR might be exploited to implement small molecule or fragment screens that resemble physiological conditions and discuss the opportunity to follow the fate of small molecules in living cells.
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Affiliation(s)
- Andras Boeszoermenyi
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
| | - Barbara Ogórek
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and, Harvard Medical School, Boston, MA, 02115, USA
| | - Akshay Jain
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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36
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Viger-Gravel J, Paruzzo FM, Cazaux C, Jabbour R, Leleu A, Canini F, Florian P, Ronzon F, Gajan D, Lesage A. Atomic-Scale Description of Interfaces between Antigen and Aluminum-Based Adjuvants Used in Vaccines by Dynamic Nuclear Polarization (DNP) Enhanced NMR Spectroscopy. Chemistry 2020; 26:8976-8982. [PMID: 32428253 DOI: 10.1002/chem.202001141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Indexed: 11/05/2022]
Abstract
The addition of aluminum-based adjuvants in vaccines enhances the immune response to antigens. The strength of antigen adsorption on adjuvant gels is known to modulate vaccine efficacy. However, a detailed understanding of the mechanisms of interaction between aluminum gels and antigens is still missing. Herein, a new analytical approach based on dynamic nuclear polarization (DNP) enhanced NMR spectroscopy under magic angle spinning (MAS) is implemented to provide a molecular description of the antigen-adjuvant interface. This approach is demonstrated on hepatitis B surface antigen particles in combination with three aluminum gels obtained from different suppliers. Both noncovalent and covalent interactions between the phospholipids of the antigen particles and the surface of the aluminum gels are identified by using MAS DNP NMR 27 Al and 31 P correlation experiments. Although covalent interactions were detected for only one of the formulations, dipolar recoupling rotational echo adiabatic passage double resonance (REAPDOR) experiments reveal significant differences in the strength of weak interactions.
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Affiliation(s)
- Jasmine Viger-Gravel
- Centre de résonance magnétique à très hauts champs (CRMN), FRE 2034 CNRS, Université Claude Bernard Lyon-1, ENS-Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques Batochime, École Polytechnique Fédérale de Lausanne (EPFL), 1530, Lausanne, Switzerland
| | - Corine Cazaux
- Sanofi Pasteur, 1541 av. Marcel Mérieux, 69280, Marcy l'Étoile, France
| | - Ribal Jabbour
- Centre de résonance magnétique à très hauts champs (CRMN), FRE 2034 CNRS, Université Claude Bernard Lyon-1, ENS-Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Amandine Leleu
- Sanofi Pasteur, 1541 av. Marcel Mérieux, 69280, Marcy l'Étoile, France
| | - Françoise Canini
- Sanofi Pasteur, 1541 av. Marcel Mérieux, 69280, Marcy l'Étoile, France
| | - Pierre Florian
- CNRS, UPR3079 CEMHTI, 1D ave de la Recherche Scientifique, 45100, Orléans, France
| | - Frédéric Ronzon
- Sanofi Pasteur, 1541 av. Marcel Mérieux, 69280, Marcy l'Étoile, France
| | - David Gajan
- Centre de résonance magnétique à très hauts champs (CRMN), FRE 2034 CNRS, Université Claude Bernard Lyon-1, ENS-Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Anne Lesage
- Centre de résonance magnétique à très hauts champs (CRMN), FRE 2034 CNRS, Université Claude Bernard Lyon-1, ENS-Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
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37
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Chakraborty A, Deligey F, Quach J, Mentink-Vigier F, Wang P, Wang T. Biomolecular complex viewed by dynamic nuclear polarization solid-state NMR spectroscopy. Biochem Soc Trans 2020; 48:1089-1099. [PMID: 32379300 PMCID: PMC7565284 DOI: 10.1042/bst20191084] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 01/07/2023]
Abstract
Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing technique magic-angle spinning dynamic nuclear polarization (MAS-DNP) have substantially expanded the territory of ssNMR investigations and enabled the detection of polymer interfaces in a cellular environment. This article highlights the emerging MAS-DNP approaches and their applications to the analysis of biomolecular composites and intact cells to determine the folding pathway and ligand binding of proteins, the structural polymorphism of low-populated biopolymers, as well as the physical interactions between carbohydrates, proteins, and lignin. These structural features provide an atomic-level understanding of many cellular processes, promoting the development of better biomaterials and inhibitors. It is anticipated that the capabilities of MAS-DNP in biomolecular and biomaterial research will be further enlarged by the rapid development of instrumentation and methodology.
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Affiliation(s)
- Arnab Chakraborty
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Fabien Deligey
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jenny Quach
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Ping Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Tuo Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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38
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Lu X, Huang C, Li M, Skomski D, Xu W, Yu L, Byrn SR, Templeton AC, Su Y. Molecular Mechanism of Crystalline-to-Amorphous Conversion of Pharmaceutical Solids from 19F Magic Angle Spinning NMR. J Phys Chem B 2020; 124:5271-5283. [PMID: 32378905 DOI: 10.1021/acs.jpcb.0c02131] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Crystalline and amorphous materials usually possess distinct physicochemical properties due to major variations in long-range and local molecular packings. Enhanced fundamental knowledge of the molecular details of crystalline-to-amorphous interconversions is necessary to correlate the intermolecular structure to material properties and functions. While crystal structures can be readily obtained by X-ray crystallography, the microstructure of amorphous materials has rarely been explored due to a lack of high-resolution techniques capable of probing local molecular structures. Moreover, there is increasing interest in understanding the molecular nature of amorphous solids in pharmaceutical sciences due to the widespread utilization of amorphous active pharmaceutical ingredients (APIs) in pharmaceutical development for solubility and bioavailability enhancement. In this study, we explore multidimensional 13C and 19F magic angle spinning (MAS) NMR spectroscopy to study the molecular packing of amorphous posaconazole (POSA) in conjunction with the crystalline counterpart. Utilizing methods integrating homonuclear and heteronuclear 1H, 13C, and 19F correlation spectroscopy and atomic 19F-to-13C distance measurements, we identified the major differences in molecular packing between crystalline and amorphous POSA. The intermolecular "head-to-head" interaction along the molecule's major axis, as well as the "head-to-tail" molecular packing perpendicular to the major axis in POSA crystals, was recapitulated by MAS NMR. Furthermore, critical intermolecular distances in the crystal lattice were determined. Most importantly, the head-to-tail contact of two neighboring molecules was found to be preserved in amorphous POSA, suggesting localized molecular order, whereas crucial interactions for head-to-head packing are absent in the amorphous form resulting in long-range disorder. Our study, likely one of the first documented examples, provides molecular-level structural details to understand the molecular mechanism of crystalline-to-amorphous conversion of fluorine-containing drug substances occurring in drug processing and development and establish a high-resolution experimental protocol for investigating amorphous materials.
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Affiliation(s)
- Xingyu Lu
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Chengbin Huang
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Mingyue Li
- Pharmaceutical Sciences, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Daniel Skomski
- 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, West Lafayette, 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, West Lafayette, 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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39
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Shcherbakov AA, Roos M, Kwon B, Hong M. Two-dimensional 19F- 13C correlation NMR for 19F resonance assignment of fluorinated proteins. JOURNAL OF BIOMOLECULAR NMR 2020; 74:193-204. [PMID: 32088840 PMCID: PMC7445029 DOI: 10.1007/s10858-020-00306-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/13/2020] [Indexed: 05/09/2023]
Abstract
19F solid-state NMR is an excellent approach for measuring long-range distances for structure determination and for studying molecular motion. For multi-fluorinated proteins, assignment of 19F chemical shifts has been traditionally carried out using mutagenesis. Here we show 2D 19F-13C correlation experiments that allow efficient assignment of the 19F chemical shifts. We have compared several rotational-echo double-resonance-based pulse sequences and 19F-13C cross polarization (CP) for 2D 19F-13C correlation. We found that direct transferred-echo double-resonance (TEDOR) transfer from 19F to 13C and vice versa outperforms out-and-back coherence transfer schemes. 19F detection gives twofold higher sensitivity over 13C detection for the 2D correlation experiment. At MAS frequencies of 25-35 kHz, double-quantum 19F-13C CP has higher coherence transfer efficiencies than zero-quantum CP. The most efficient TEDOR transfer experiment has higher sensitivity than the most efficient double-quantum CP experiment. We demonstrate these 2D 19F-13C correlation experiments on the model compounds t-Boc-4F-phenylalanine and GB1. Application of the 2D 19F-13C TEDOR correlation experiment to the tetrameric influenza BM2 transmembrane peptide shows intermolecular 13C-19F cross peaks that indicate that the BM2 tetramers cluster in the lipid bilayer in an antiparallel fashion. This clustering may be relevant for the virus budding function of this protein.
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Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Matthias Roos
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA.
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40
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Gennaro A, Karabanov A, Potapov A, Köckenberger W. Heteronuclear DNP of 1H and 19F nuclei using BDPA as a polarizing agent. Phys Chem Chem Phys 2020; 22:7803-7816. [DOI: 10.1039/d0cp00892c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study reveals heteronuclear-thermal mixing – a novel mechanism of dynamic nuclear polarization in a system with 1H and 19F nuclei.
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Affiliation(s)
- Antonio Gennaro
- School of Physics and Astronomy
- University of Nottingham
- Nottingham
- UK
| | | | - Alexey Potapov
- School of Physics and Astronomy
- University of Nottingham
- Nottingham
- UK
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Venkatesh A, Luan X, Perras FA, Hung I, Huang W, Rossini AJ. t1-Noise eliminated dipolar heteronuclear multiple-quantum coherence solid-state NMR spectroscopy. Phys Chem Chem Phys 2020; 22:20815-20828. [DOI: 10.1039/d0cp03511d] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
t1-Noise eliminated (TONE) heteronuclear multiple quantum correlation (HMQC) solid-state nuclear magnetic resonance pulse sequences improve the sensitivity of 2D 1H{X} heteronuclear correlation experiments with X = 17O, 25Mg, 27Al and 35Cl.
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Affiliation(s)
- Amrit Venkatesh
- Department of Chemistry
- Iowa State University
- Ames
- USA
- US DOE Ames Laboratory
| | - Xuechen Luan
- Department of Chemistry
- Iowa State University
- Ames
- USA
| | | | - Ivan Hung
- National High Magnetic Field Laboratory (NHMFL)
- Tallahassee
- USA
| | - Wenyu Huang
- Department of Chemistry
- Iowa State University
- Ames
- USA
- US DOE Ames Laboratory
| | - Aaron J. Rossini
- Department of Chemistry
- Iowa State University
- Ames
- USA
- US DOE Ames Laboratory
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Fritz M, Kraus J, Quinn CM, Yap GPA, Struppe J, Sergeyev IV, Gronenborn AM, Polenova T. Measurement of Accurate Interfluorine Distances in Crystalline Organic Solids: A High-Frequency Magic Angle Spinning NMR Approach. J Phys Chem B 2019; 123:10680-10690. [PMID: 31682453 DOI: 10.1021/acs.jpcb.9b08919] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Long-range interatomic distance restraints are critical for the determination of molecular structures by NMR spectroscopy, both in solution and in the solid state. Fluorine is a powerful NMR probe in a wide variety of contexts, owing to its favorable magnetic properties, ease of incorporation into biological molecules, and ubiquitous use in synthetic organic molecules designed for diverse applications. Because of the large gyromagnetic ratio of the 100% naturally abundant 19F isotope, interfluorine distances as long as 20 Å are accessible in magic-angle spinning (MAS) dipolar recoupling experiments. Herein, we present an approach for the determination of accurate interfluorine distances in multispin systems, using the finite pulse radio frequency driven recoupling (fpRFDR) at high MAS frequencies of 40-60 kHz. We use a series of crystalline "molecular ruler" solids, difluorobenzoic acids and 7F-L-tryptophan, for which the intra- and intermolecular interfluorine distances are known. We describe the optimal experimental conditions for accurate distance determinations, including the choice of a phase cycle, the relative advantages of selective inversion one-dimensional versus two-dimensional correlation experiments, and the appropriate numerical simulation protocols. An optimal strategy for the analysis of RFDR exchange curves in organic solids with extended spin interaction networks is presented, which, even in the absence of crystal structures, can be potentially incorporated into NMR structure determination.
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Affiliation(s)
- Matthew Fritz
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Jodi Kraus
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Jochem Struppe
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation , 15 Fortune Drive , Billerica , Massachusetts 01821 , United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States.,Department of Structural Biology , University of Pittsburgh School of Medicine , 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Pittsburgh Center for HIV Protein Interactions , University of Pittsburgh School of Medicine , 1051 Biomedical Science Tower 3, 3501 Fifth Avenue , Pittsburgh , Pennsylvania 15261 , United States
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