1
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Free TJ, Talley JP, Hyer CD, Miller CJ, Griffitts JS, Bundy BC. Engineering the Signal Resolution of a Paper-Based Cell-Free Glutamine Biosensor with Genetic Engineering, Metabolic Engineering, and Process Optimization. SENSORS (BASEL, SWITZERLAND) 2024; 24:3073. [PMID: 38793927 PMCID: PMC11124800 DOI: 10.3390/s24103073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Specialized cancer treatments have the potential to exploit glutamine dependence to increase patient survival rates. Glutamine diagnostics capable of tracking a patient's response to treatment would enable a personalized treatment dosage to optimize the tradeoff between treatment success and dangerous side effects. Current clinical glutamine testing requires sophisticated and expensive lab-based tests, which are not broadly available on a frequent, individualized basis. To address the need for a low-cost, portable glutamine diagnostic, this work engineers a cell-free glutamine biosensor to overcome assay background and signal-to-noise limitations evident in previously reported studies. The findings from this work culminate in the development of a shelf-stable, paper-based, colorimetric glutamine test with a high signal strength and a high signal-to-background ratio for dramatically improved signal resolution. While the engineered glutamine test is important progress towards improving the management of cancer and other health conditions, this work also expands the assay development field of the promising cell-free biosensing platform, which can facilitate the low-cost detection of a broad variety of target molecules with high clinical value.
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Affiliation(s)
- Tyler J. Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Joseph P. Talley
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Chad D. Hyer
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Catherine J. Miller
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
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2
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Levin R, Löhr F, Karakoc B, Lichtenecker R, Dötsch V, Bernhard F. E. coli "Stablelabel" S30 lysate for optimized cell-free NMR sample preparation. JOURNAL OF BIOMOLECULAR NMR 2023; 77:131-147. [PMID: 37311907 PMCID: PMC10406690 DOI: 10.1007/s10858-023-00417-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Cell-free (CF) synthesis with highly productive E. coli lysates is a convenient method to produce labeled proteins for NMR studies. Despite reduced metabolic activity in CF lysates, a certain scrambling of supplied isotope labels is still notable. Most problematic are conversions of 15N labels of the amino acids L-Asp, L-Asn, L-Gln, L-Glu and L-Ala, resulting in ambiguous NMR signals as well as in label dilution. Specific inhibitor cocktails suppress most undesired conversion reactions, while limited availability and potential side effects on CF system productivity need to be considered. As alternative route to address NMR label conversion in CF systems, we describe the generation of optimized E. coli lysates with reduced amino acid scrambling activity. Our strategy is based on the proteome blueprint of standardized CF S30 lysates of the E. coli strain A19. Identified lysate enzymes with suspected amino acid scrambling activity were eliminated by engineering corresponding single and cumulative chromosomal mutations in A19. CF lysates prepared from the mutants were analyzed for their CF protein synthesis efficiency and for residual scrambling activity. The A19 derivative "Stablelabel" containing the cumulative mutations asnA, ansA/B, glnA, aspC and ilvE yielded the most useful CF S30 lysates. We demonstrate the optimized NMR spectral complexity of selectively labeled proteins CF synthesized in "Stablelabel" lysates. By taking advantage of ilvE deletion in "Stablelabel", we further exemplify a new strategy for methyl group specific labeling of membrane proteins with the proton pump proteorhodopsin.
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Affiliation(s)
- Roman Levin
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Betül Karakoc
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Roman Lichtenecker
- Institute of Organic Chemistry, University of Vienna, 1090 Vienna, Austria
- MAG-LAB, 1030 Vienna, Austria
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt, Germany
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3
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Cell-free protein synthesis system for bioanalysis: Advances in methods and applications. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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4
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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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5
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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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6
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Lends A, Berbon M, Habenstein B, Nishiyama Y, Loquet A. Protein resonance assignment by solid-state NMR based on 1H-detected 13C double-quantum spectroscopy at fast MAS. JOURNAL OF BIOMOLECULAR NMR 2021; 75:417-427. [PMID: 34813018 DOI: 10.1007/s10858-021-00386-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Solid-state NMR spectroscopy is a powerful technique to study insoluble and non-crystalline proteins and protein complexes at atomic resolution. The development of proton (1H) detection at fast magic-angle spinning (MAS) has considerably increased the analytical capabilities of the technique, enabling the acquisition of 1H-detected fingerprint experiments in few hours. Here an approach based on double-quantum (DQ) 13C spectroscopy, detected on 1H, is proposed for fast MAS regime (> 60 kHz) to perform the sequential assignment of insoluble proteins of small size, without any specific deuteration requirement. By combining two three-dimensional 1H detected experiments correlating a 13C DQ dimension respectively to its intra-residue and sequential 15 N-1H pairs, a sequential walk through DQ (Ca + CO) resonance is obtained. The approach takes advantage of fast MAS to achieve an efficient sensitivity and the addition of a DQ dimension provides spectral features useful for the resonance assignment process.
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Affiliation(s)
- Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
| | - Mélanie Berbon
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Birgit Habenstein
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa, 230-0045, Japan.
- JEOL RESONANCE Inc., 3-1-2 Musashino, Akishima, Tokyo, 196-8558, Japan.
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
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7
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Maleckis A, Herath ID, Otting G. Synthesis of 13C/ 19F/ 2H labeled indoles for use as tryptophan precursors for protein NMR spectroscopy. Org Biomol Chem 2021; 19:5133-5147. [PMID: 34032255 DOI: 10.1039/d1ob00611h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Synthesis of indoles labeled with 13C-1H and 13C-19F spin pairs is described. All syntheses utilize inexpensive carbon-13C dioxide as the 13C isotope source. Ruthenium-mediated ring-closing metathesis is the key step in construction of the 13C containing indole carbocycle. Fluorine is introduced via electrophilic fluorination at the 7-position and via palladium-mediated cross-coupling at the 4-position. Indole and fluoroindoles are viable tryptophan precursors for in vivo protein expression. We show that they are viable also in in vitro protein synthesis using standard E. coli S30 extracts. Incorporation of the synthesized 13C-1H and 13C-19F spin pair labeled tryptophans into proteins enables high-resolution and high-sensitivity nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
| | - Iresha D Herath
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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8
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Pacull EM, Sendker F, Bernhard F, Scheidt HA, Schmidt P, Huster D, Krug U. Integration of Cell-Free Expression and Solid-State NMR to Investigate the Dynamic Properties of Different Sites of the Growth Hormone Secretagogue Receptor. Front Pharmacol 2020; 11:562113. [PMID: 33324203 PMCID: PMC7723455 DOI: 10.3389/fphar.2020.562113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023] Open
Abstract
Cell-free expression represents an attractive method to produce large quantities of selectively labeled protein for NMR applications. Here, cell-free expression was used to label specific regions of the growth hormone secretagogue receptor (GHSR) with NMR-active isotopes. The GHSR is a member of the class A family of G protein-coupled receptors. A cell-free expression system was established to produce the GHSR in the precipitated form. The solubilized receptor was refolded in vitro and reconstituted into DMPC lipid membranes. Methionines, arginines, and histidines were chosen for 13C-labeling as they are representative for the transmembrane domains, the loops and flanking regions of the transmembrane α-helices, and the C-terminus of the receptor, respectively. The dynamics of the isotopically labeled residues was characterized by solid-state NMR measuring motionally averaged 1H-13C dipolar couplings, which were converted into molecular order parameters. Separated local field DIPSHIFT experiments under magic-angle spinning conditions using either varying cross polarization contact times or direct excitation provided order parameters for these residues showing that the C-terminus was the segment with the highest motional amplitude. The loop regions and helix ends as well as the transmembrane regions of the GHSR represent relatively rigid segments in the overall very flexible receptor molecule. Although no site resolution could be achieved in the experiments, the previously reported highly dynamic character of the receptor concluded from uniformly 13C labeled receptor samples could be further specified by this segmental labeling approach, leading to a more diversified understanding of the receptor dynamics under equilibrium conditions.
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Affiliation(s)
- Emelyne M Pacull
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Franziska Sendker
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Peter Schmidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Ulrike Krug
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
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9
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Morató A, Elena-Real CA, Popovic M, Fournet A, Zhang K, Allemand F, Sibille N, Urbanek A, Bernadó P. Robust Cell-Free Expression of Sub-Pathological and Pathological Huntingtin Exon-1 for NMR Studies. General Approaches for the Isotopic Labeling of Low-Complexity Proteins. Biomolecules 2020; 10:E1458. [PMID: 33086646 PMCID: PMC7603387 DOI: 10.3390/biom10101458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/07/2020] [Accepted: 10/16/2020] [Indexed: 12/23/2022] Open
Abstract
The high-resolution structural study of huntingtin exon-1 (HttEx1) has long been hampered by its intrinsic properties. In addition to being prone to aggregate, HttEx1 contains low-complexity regions (LCRs) and is intrinsically disordered, ruling out several standard structural biology approaches. Here, we use a cell-free (CF) protein expression system to robustly and rapidly synthesize (sub-) pathological HttEx1. The open nature of the CF reaction allows the application of different isotopic labeling schemes, making HttEx1 amenable for nuclear magnetic resonance studies. While uniform and selective labeling facilitate the sequential assignment of HttEx1, combining CF expression with nonsense suppression allows the site-specific incorporation of a single labeled residue, making possible the detailed investigation of the LCRs. To optimize CF suppression yields, we analyze the expression and suppression kinetics, revealing that high concentrations of loaded suppressor tRNA have a negative impact on the final reaction yield. The optimized CF protein expression and suppression system is very versatile and well suited to produce challenging proteins with LCRs in order to enable the characterization of their structure and dynamics.
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Affiliation(s)
| | | | | | | | | | | | | | - Annika Urbanek
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France; (A.M.); (C.A.E.-R.); (M.P.); (A.F.); (K.Z.); (F.A.); (N.S.)
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier. 29 rue de Navacelles, 34090 Montpellier, France; (A.M.); (C.A.E.-R.); (M.P.); (A.F.); (K.Z.); (F.A.); (N.S.)
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10
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Jirasko V, Lakomek N, Penzel S, Fogeron M, Bartenschlager R, Meier BH, Böckmann A. Proton-Detected Solid-State NMR of the Cell-Free Synthesized α-Helical Transmembrane Protein NS4B from Hepatitis C Virus. Chembiochem 2020; 21:1453-1460. [PMID: 31850615 PMCID: PMC7318649 DOI: 10.1002/cbic.201900765] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Indexed: 01/01/2023]
Abstract
Proton-detected 100 kHz magic-angle-spinning (MAS) solid-state NMR is an emerging analysis method for proteins with only hundreds of microgram quantities, and thus allows structural investigation of eukaryotic membrane proteins. This is the case for the cell-free synthesized hepatitis C virus (HCV) nonstructural membrane protein 4B (NS4B). We demonstrate NS4B sample optimization using fast reconstitution schemes that enable lipid-environment screening directly by NMR. 2D spectra and relaxation properties guide the choice of the best sample preparation to record 2D 1 H-detected 1 H,15 N and 3D 1 H,13 C,15 N correlation experiments with linewidths and sensitivity suitable to initiate sequential assignments. Amino-acid-selectively labeled NS4B can be readily obtained using cell-free synthesis, opening the door to combinatorial labeling approaches which should enable structural studies.
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Affiliation(s)
- Vlastimil Jirasko
- ETH ZürichPhysical ChemistryVladimir-Prelog Weg 28093ZürichSwitzerland
| | | | - Susanne Penzel
- ETH ZürichPhysical ChemistryVladimir-Prelog Weg 28093ZürichSwitzerland
| | - Marie‐Laure Fogeron
- Institut de Biologie et Chimie des ProteinesMMSBLabex EcofectUMR 5086 CNRSUniversité de Lyon7 passage du Vercors69367LyonFrance
| | - Ralf Bartenschlager
- Department of Infectious DiseasesMolecular VirologyHeidelberg UniversityIm Neuenheimer Feld 34569120HeidelbergGermany
- Division of Virus-Associated Carcinogenesis (Germany)Cancer Research Center (DKFZ)Im Neuenheimer Feld 24269120HeidelbergGermany
| | - Beat H. Meier
- ETH ZürichPhysical ChemistryVladimir-Prelog Weg 28093ZürichSwitzerland
| | - Anja Böckmann
- Institut de Biologie et Chimie des ProteinesMMSBLabex EcofectUMR 5086 CNRSUniversité de Lyon7 passage du Vercors69367LyonFrance
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11
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Kojima R, Uchiya K, Manshio H, Masuda K. Cell-free synthesis of functionally active HSPB5. Cell Stress Chaperones 2020; 25:287-301. [PMID: 31960264 PMCID: PMC7058722 DOI: 10.1007/s12192-020-01073-5] [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: 09/04/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 10/25/2022] Open
Abstract
Human αB-crystallin (HSPB5) is frequently modified post-translationally by UV radiation, oxidation, and age-associated processes, which complicates functional analyses of the protein using natural sources. Thus, determining the biological function of HSPB5 at the molecular structure level requires unmodified protein. Here, we employed an Escherichia coli cell-free protein synthesis system to prepare unmodified, functionally active human HSPB5. An S30 extract prepared from E. coli strain BL21 (DE3) was used for HSPB5 synthesis. The efficacy of protein synthesis was assessed by monitoring influencing factors, such as the concentrations of Mg2+ and other reaction mixture constituents, and by evaluating batch and/or dialysis synthesis systems. Chaperone-like activity of synthesized HSPB5 was assayed using alcohol dehydrogenase (ADH) under thermal stress. The amount of HSPB5 synthesized using the cell-free system depended significantly on the concentration of Mg2+ in the reaction mixture. Use of condensed S30 extract and increased levels of amino acids promoted HSPB5 production. Compared with the batch system, HSPB5 synthesis was markedly increased using the dialysis system. The construction vector played a critical role in regulating the efficacy of protein synthesis. HSPB5 synthesized using the cell-free system had a native molecular mass, as determined by mass spectrometry analysis. The co-presence of synthesized HSPB5 suppressed heat-associated denaturation of ADH. Human HSPB5 synthesized using the cell-free system thus retains functional activity as a molecular chaperone.
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Affiliation(s)
- Ryoji Kojima
- Laboratory of Analytical Pharmacology, Meijo University, Nagoya, 468-8503, Japan.
| | - Keiichi Uchiya
- Laboratory of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya, 468-8503, Japan
| | - Hiroyuki Manshio
- Laboratory of Analytical Pharmacology, Meijo University, Nagoya, 468-8503, Japan
| | - Kastuyoshi Masuda
- Suntory Institute for Bioorganic Research, 1-1 Wakayamadai, Shimamoto, Osaka, 618-8503, Japan
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12
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Kasai T, Ono S, Koshiba S, Yamamoto M, Tanaka T, Ikeda S, Kigawa T. Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra. JOURNAL OF BIOMOLECULAR NMR 2020; 74:125-137. [PMID: 32002710 PMCID: PMC7080692 DOI: 10.1007/s10858-019-00295-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Signal overlapping is a major bottleneck for protein NMR analysis. We propose a new method, stable-isotope-assisted parameter extraction (SiPex), to resolve overlapping signals by a combination of amino-acid selective isotope labeling (AASIL) and tensor decomposition. The basic idea of Sipex is that overlapping signals can be decomposed with the help of intensity patterns derived from quantitative fractional AASIL, which also provides amino-acid information. In SiPex, spectra for protein characterization, such as 15N relaxation measurements, are assembled with those for amino-acid information to form a four-order tensor, where the intensity patterns from AASIL contribute to high decomposition performance even if the signals share similar chemical shift values or characterization profiles, such as relaxation curves. The loading vectors of each decomposed component, corresponding to an amide group, represent both the amino-acid and relaxation information. This information link provides an alternative protein analysis method that does not require "assignments" in a general sense; i.e., chemical shift determinations, since the amino-acid information for some of the residues allows unambiguous assignment according to the dual selective labeling. SiPex can also decompose signals in time-domain raw data without Fourier transform, even in non-uniformly sampled data without spectral reconstruction. These features of SiPex should expand biological NMR applications by overcoming their overlapping and assignment problems.
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Affiliation(s)
- Takuma Kasai
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan.
- PRESTO, JST, Kawaguchi, Japan.
| | - Shunsuke Ono
- PRESTO, JST, Kawaguchi, Japan
- School of Computing, Tokyo Institute of Technology, Yokohama, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Toshiyuki Tanaka
- Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto, Japan
| | - Shiro Ikeda
- Department of Statistical Inference and Mathematics, The Institute of Statistical Mathematics, Tachikawa, Japan
| | - Takanori Kigawa
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan.
- School of Computing, Tokyo Institute of Technology, Yokohama, Japan.
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13
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Urbanek A, Elena-Real CA, Popovic M, Morató A, Fournet A, Allemand F, Delbecq S, Sibille N, Bernadó P. Site-Specific Isotopic Labeling (SSIL): Access to High-Resolution Structural and Dynamic Information in Low-Complexity Proteins. Chembiochem 2019; 21:769-775. [PMID: 31697025 DOI: 10.1002/cbic.201900583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/05/2019] [Indexed: 12/17/2022]
Abstract
Remarkable technical progress in the area of structural biology has paved the way to study previously inaccessible targets. For example, large protein complexes can now be easily investigated by cryo-electron microscopy, and modern high-field NMR magnets have challenged the limits of high-resolution characterization of proteins in solution. However, the structural and dynamic characteristics of certain proteins with important functions still cannot be probed by conventional methods. These proteins in question contain low-complexity regions (LCRs), compositionally biased sequences where only a limited number of amino acids is repeated multiple times, which hamper their characterization. This Concept article describes a site-specific isotopic labeling (SSIL) strategy, which combines nonsense suppression and cell-free protein synthesis to overcome these limitations. An overview on how poly-glutamine tracts were made amenable to high-resolution structural studies is used to illustrate the usefulness of SSIL. Furthermore, we discuss the potential of this methodology to give further insights into the roles of LCRs in human pathologies and liquid-liquid phase separation, as well as the challenges that must be addressed in the future for the popularization of SSIL.
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Affiliation(s)
- Annika Urbanek
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090, Montpellier, France
| | - Carlos A Elena-Real
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090, Montpellier, France
| | - Matija Popovic
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090, Montpellier, France
| | - Anna Morató
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090, Montpellier, France
| | - Aurélie Fournet
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090, Montpellier, France
| | - Frédéric Allemand
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090, Montpellier, France
| | - Stephane Delbecq
- Laboratoire de Biologie Cellulaire et Moléculaire, (LBCM-EA4558 Vaccination Antiparasitaire), UFR Pharmacie, Université de Montpellier, 15, Av. Charles Flahault, BP 14491, 34000, Montpellier, France
| | - Nathalie Sibille
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090, Montpellier, France
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, Université de Montpellier, 29, rue de Navacelles, 34090, Montpellier, France
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Löhr F, Gebel J, Henrich E, Hein C, Dötsch V. Towards complete polypeptide backbone NH assignment via combinatorial labeling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 302:50-63. [PMID: 30959416 DOI: 10.1016/j.jmr.2019.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Combinatorial selective isotope labeling is a valuable tool to facilitate polypeptide backbone resonance assignment in cases of low sensitivity or extensive chemical shift degeneracy. It involves recording of 15N-HSQC and 2D HN-projections of triple-resonance spectra on a limited set of samples containing different combinations of labeled and unlabeled amino acid types. Using labeling schemes in which the three backbone heteronuclei (amide nitrogen, α-carbon and carbonyl carbon) are enriched in 15N or 13C isotopes - individually as well as simultaneously - usually yields abundant amino-acid type information of consecutive residues i and i - 1. Although this results in a large number of anchor points that can be used in the sequential assignment process, for most amide signals the exact positioning of the corresponding residue the polypeptide sequence still relies on matching intra- and interresidual 13C chemical shifts obtained from 3D spectra. An obvious way to obtain more sequence-specific assignments directly with combinatorial labeling would be to increase the number of samples. This is, however, undesirable because of increased sample preparation efforts and costs. Irrespective of the number of samples, unambiguous assignments cannot be accomplished for i - 1/i pairs that are not unique in the sequence. Here we show that the ambiguity for non-unique pairs can be resolved by including information about the labeling state of residues i + 1 and i - 2. Application to a 35-residue peptide resulted in complete assignments of all detectable signals in the 15N HSQC which, due to its repetitive sequence and 13C chemical shift degeneracies, was difficult to achieve by other means. For a medium-sized protein (165 residues, rotational correlation time 8.2 ns) the improved protocol allowed the extent of backbone amide assignment to be expanded to 88% solely using a suite of 2D 1H-15N correlated spectra.
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Affiliation(s)
- Frank Löhr
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jakob Gebel
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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15
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Kögler LM, Stichel J, Kaiser A, Beck-Sickinger AG. Cell-Free Expression and Photo-Crosslinking of the Human Neuropeptide Y 2 Receptor. Front Pharmacol 2019; 10:176. [PMID: 30881304 PMCID: PMC6405639 DOI: 10.3389/fphar.2019.00176] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/11/2019] [Indexed: 12/15/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent a large family of different proteins, which are involved in physiological processes throughout the entire body. Furthermore, they represent important drug targets. For rational drug design, it is important to get further insights into the binding mode of endogenous ligands as well as of therapeutic agents at the respective target receptors. However, structural investigations usually require homogenous, solubilized and functional receptors, which is still challenging. Cell-free expression methods have emerged in the last years and many different proteins are successfully expressed, including hydrophobic membrane proteins like GPCRs. In this work, an Escherichia coli based cell-free expression system was used to express the neuropeptide Y2 receptor (Y2R) for structural investigations. This GPCR was expressed in two different variants, a C-terminal enhanced green fluorescent fusion protein and a cysteine deficient variant. In order to obtain soluble receptors, the expression was performed in the presence of mild detergents, either Brij-35 or Brij-58, which led to high amounts of soluble receptor. Furthermore, the influence of temperature, pH value and additives on protein expression and solubilization was tested. For functional and structural investigations, the receptors were expressed at 37°C, pH 7.4 in the presence of 1 mM oxidized and 5 mM reduced glutathione. The expressed receptors were purified by ligand affinity chromatography and functionality of Y2R_cysteine_deficient was verified by a homogenous binding assay. Finally, photo-crosslinking studies were performed between cell-free expressed Y2R_cysteine_deficient and a neuropeptide Y (NPY) analog bearing the photoactive, unnatural amino acid p-benzoyl-phenylalanine at position 27 and biotin at position 22 for purification. After enzymatic digestion, fragments of crosslinked receptor were identified by mass spectrometry. Our findings demonstrate that, in contrast to Y1R, NPY position 27 remains flexible when bound to Y2R. These results are in agreement with the suggested binding mode of NPY at Y2R.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Anette Kaiser
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
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16
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Lacabanne D, Fogeron ML, Wiegand T, Cadalbert R, Meier BH, Böckmann A. Protein sample preparation for solid-state NMR investigations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 110:20-33. [PMID: 30803692 DOI: 10.1016/j.pnmrs.2019.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
Preparation of a protein sample for solid-state NMR is in many aspects similar to solution-state NMR approaches, mainly with respect to the need for stable isotope labeling. But the possibility of using solid-state NMR to investigate membrane proteins in (native) lipids adds the important requirement of adapted membrane-reconstitution schemes. Also, dynamic nuclear polarization and paramagnetic NMR in solids need specific schemes using metal ions and radicals. Sample sedimentation has enabled structural investigations of objects inaccessible to other structural techniques, but rotor filling using sedimentation has become increasingly complex with smaller and smaller rotors, as needed for higher and higher magic-angle spinning (MAS) frequencies. Furthermore, solid-state NMR can investigate very large proteins and their complexes without the concomitant increase in line widths, motivating the use of selective labeling and unlabeling strategies, as well as segmental labeling, to decongest spectra. The possibility of investigating sub-milligram amounts of protein today using advanced fast MAS techniques enables alternative protein synthesis schemes such as cell-free expression. Here we review these specific aspects of solid-state NMR sample preparation.
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Affiliation(s)
- Denis Lacabanne
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France; Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Beat H Meier
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS/Université de Lyon, 69367 Lyon, France.
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17
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Graether SP. Troubleshooting Guide to Expressing Intrinsically Disordered Proteins for Use in NMR Experiments. Front Mol Biosci 2019; 5:118. [PMID: 30713842 PMCID: PMC6345686 DOI: 10.3389/fmolb.2018.00118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/23/2018] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) represent a structural class of proteins that do not have a well-defined, 3D fold in solution, and often have little secondary structure. To characterize their function and molecular mechanism, it is helpful to examine their structure using nuclear magnetic resonance (NMR), which can report on properties, such as residual structure (at both the secondary and tertiary levels), ligand binding affinity, and the effect of ligand binding on IDP structure, all on a per residue basis. This brief review reports on the common problems and decisions that are involved when preparing a disordered protein for NMR studies. The paper covers gene design, expression host choice, protein purification, and the initial NMR experiments that are performed. While many of these steps are essentially identical to those for ordered proteins, a few key differences are highlighted, including the extreme sensitivity of IDPs to proteolytic cleavage, the ability to use denaturing conditions without having to refold the protein, the optimal chromatographic system choice, and the challenges of quantifying an IDP. After successful purification, characterization by NMR can be done using the standard 15N-heteronuclear single quantum coherence (15N-HSQC) experiment, or the newer CON series of experiments that are superior for disordered proteins.
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Affiliation(s)
- Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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Henrich E, Löhr F, Mezhyrova J, Laguerre A, Bernhard F, Dötsch V. Synthetic Biology-Based Solution NMR Studies on Membrane Proteins in Lipid Environments. Methods Enzymol 2018; 614:143-185. [PMID: 30611423 DOI: 10.1016/bs.mie.2018.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although membrane proteins are in the focus of biochemical research for many decades the general knowledge of this important class is far behind soluble proteins. Despite several recent technical developments, the most challenging feature still is the generation of high-quality samples in environments suitable for the selected application. Reconstitution of membrane proteins into lipid bilayers will generate the most native-like environment and is therefore commonly desired. However, it poses tremendous problems to solution-state NMR analysis due to the dramatic increase in particle size resulting in high rotational correlation times. Nevertheless, a few promising strategies for the solution NMR analysis of membrane inserted proteins are emerging and will be discussed in this chapter. We focus on the generation of membrane protein samples in nanodisc membranes by cell-free systems and will describe the characteristic advantages of that platform in providing tailored protein expression and folding environments. We indicate frequent problems that have to be overcome in cell-free synthesis, nanodisc preparation, and customization for samples dedicated for solution-state NMR. Detailed instructions for sample preparation are given, and solution NMR approaches suitable for membrane proteins in bilayers are compiled. We further discuss the current strategies applied for signal detection from such difficult samples and describe the type of information that can be extracted from the various experiments. In summary, a comprehensive guideline for the analysis of membrane proteins in native-like membrane environments by solution-state NMR techniques will be provided.
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Affiliation(s)
- Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Julija Mezhyrova
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Aisha Laguerre
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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Higman VA. Solid-state MAS NMR resonance assignment methods for proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 106-107:37-65. [PMID: 31047601 DOI: 10.1016/j.pnmrs.2018.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 06/09/2023]
Abstract
The prerequisite to structural or functional studies of proteins by NMR is generally the assignment of resonances. Since the first assignment of proteins by solid-state MAS NMR was conducted almost two decades ago, a wide variety of different pulse sequences and methods have been proposed and continue to be developed. Traditionally, a variety of 2D and 3D 13C-detected experiments have been used for the assignment of backbone and side-chain 13C and 15N resonances. These methods have found widespread use across the field. But as the hardware has changed and higher spinning frequencies and magnetic fields are becoming available, the ability to use direct proton detection is opening up a new set of assignment methods based on triple-resonance experiments. This review describes solid-state MAS NMR assignment methods using carbon detection and proton detection at different deuteration levels. The use of different isotopic labelling schemes as an aid to assignment in difficult cases is discussed as well as the increasing number of software packages that support manual and automated resonance assignment.
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Affiliation(s)
- Victoria A Higman
- Department of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TU, UK.
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