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Majekodunmi T, Britton D, Montclare JK. Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation. Chem Rev 2024; 124:9113-9135. [PMID: 39008623 PMCID: PMC11327963 DOI: 10.1021/acs.chemrev.3c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.
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Affiliation(s)
- Temiloluwa Majekodunmi
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Biomedical Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States
- Department of Radiology, New York University Langone Health, New York, New York 10016, United States
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2
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Heinrich G, Kondratiuk M, Gooßen LJ, Wiesenfeldt MP. Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy. Nat Protoc 2024; 19:1529-1556. [PMID: 38409535 DOI: 10.1038/s41596-023-00951-3] [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] [Received: 03/01/2023] [Accepted: 11/16/2023] [Indexed: 02/28/2024]
Abstract
The instrumental analysis of reaction mixtures is usually the rate-determining step in the optimization of chemical processes. Traditionally, reactions are analyzed by gas chromatography, HPLC or quantitative NMR spectroscopy on high-field spectrometers. However, chromatographic methods require elaborate work-up and calibration protocols, and high-field NMR spectrometers are expensive to purchase and operate. This protocol describes an inexpensive and highly effective analysis method based on low-field benchtop NMR spectroscopy. Its key feature is the use of fluorine-labeled model substrates that, because of the wide chemical shift range and high sensitivity of 19F, enable separate, quantitative detection of product and by-product signals even on low-field, permanent magnet spectrometers. An external lock/shim device obviates the need for deuterated solvents, permitting the direct, noninvasive measurement of crude reaction mixtures with minimal workup. The low field-strength facilitates a homogeneous excitation over a wide chemical shift range, minimizing systematic integration errors. The addition of the optimal amount of the nonshifting relaxation agent tris(acetylacetonato) iron(III) minimizes relaxation delays at full resolution, reducing the analysis time to 32 s per sample. The correct choice of processing parameters is also crucial. A step-by-step guideline is provided, the influence of all parameters, including adjustments needed when using high-field spectrometers, is discussed and potential pitfalls are highlighted. The wide applicability of the analytical protocol for reaction optimization is illustrated by three examples: a Buchwald-Hartwig amination, a Suzuki coupling and a C-H arylation reaction.
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Affiliation(s)
- G Heinrich
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - M Kondratiuk
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - L J Gooßen
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany
| | - M P Wiesenfeldt
- Faculty for Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
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3
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Poškaitė G, Wheatley DE, Wells N, Linclau B, Sinnaeve D. Obtaining Pure 1H NMR Spectra of Individual Pyranose and Furanose Anomers of Reducing Deoxyfluorinated Sugars. J Org Chem 2023; 88:13908-13925. [PMID: 37754916 PMCID: PMC10563139 DOI: 10.1021/acs.joc.3c01503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Indexed: 09/28/2023]
Abstract
Due to tautomeric equilibria, NMR spectra of reducing sugars can be complex with many overlapping resonances. This hampers coupling constant determination, which is required for conformational analysis and configurational assignment of substituents. Given that mixtures of interconverting species are physically inseparable, easy-to-use techniques that enable facile full 1H NMR characterization of sugars are of interest. Here, we show that individual spectra of both pyranoside and furanoside forms of reducing fluorosugars can be obtained using 1D FESTA. We discuss the unique opportunities offered by FESTA over standard sel-TOCSY and show how it allows a more complete characterization. We illustrate the power of FESTA by presenting the first full NMR characterization of many fluorosugars, including of the important fluorosugar 2-deoxy-2-fluoroglucose. We discuss in detail all practical considerations for setting up FESTA experiments for fluorosugars, which can be extended to any mixture of fluorine-containing species interconverting slowly on the NMR frequency-time scale.
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Affiliation(s)
- Gabija Poškaitė
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - David E. Wheatley
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Neil Wells
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Bruno Linclau
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Department
of Organic and Macromolecular Chemistry, Ghent University, Campus
Sterre, Krijgslaan 281-S4, Ghent 9000, Belgium
| | - Davy Sinnaeve
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
- CNRS, EMR9002 Integrative Structural Biology, F-59000 Lille, France
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Silva Terra AI, Rossetto M, Dickson CL, Peat G, Uhrín D, Halse ME. Enhancing 19F Benchtop NMR Spectroscopy by Combining para-Hydrogen Hyperpolarization and Multiplet Refocusing. ACS MEASUREMENT SCIENCE AU 2023; 3:73-81. [PMID: 36817010 PMCID: PMC9936801 DOI: 10.1021/acsmeasuresciau.2c00055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 06/18/2023]
Abstract
Benchtop NMR spectrometers provide a promising alternative to high-field NMR for applications that are limited by instrument size and/or cost. 19F benchtop NMR is attractive due to the larger chemical shift range of 19F relative to 1H and the lack of background signal in most applications. However, practical applications of benchtop 19F NMR are limited by its low sensitivity due to the relatively weak field strengths of benchtop NMR spectrometers. Here we present a sensitivity-enhancement strategy that combines SABRE (Signal Amplification By Reversible Exchange) hyperpolarization with the multiplet refocusing method SHARPER (Sensitive, Homogeneous, And Resolved PEaks in Real time). When applied to a range of fluoropyridines, SABRE-SHARPER achieves overall signal enhancements of up to 5700-fold through the combined effects of hyperpolarization and line-narrowing. This approach can be generalized to the analysis of mixtures through the use of a selective variant of the SHARPER sequence, selSHARPER. The ability of SABRE-selSHARPER to simultaneously boost sensitivity and discriminate between two components of a mixture is demonstrated, where selectivity is achieved through a combination of selective excitation and the choice of polarization transfer field during the SABRE step.
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Affiliation(s)
| | | | - Claire L. Dickson
- EaStCHEM
School of Chemistry, University of Edinburgh, EdinburghEH9 3FJ, U.K.
| | - George Peat
- EaStCHEM
School of Chemistry, University of Edinburgh, EdinburghEH9 3FJ, U.K.
| | - Dušan Uhrín
- EaStCHEM
School of Chemistry, University of Edinburgh, EdinburghEH9 3FJ, U.K.
| | - Meghan E. Halse
- Department
of Chemistry, University of York, YorkYO10 5DD, U.K.
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5
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Synthesis of Trifluoromethylated Monoterpene Amino Alcohols. Molecules 2022; 27:molecules27207068. [PMID: 36296661 PMCID: PMC9607099 DOI: 10.3390/molecules27207068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
For the first time, monoterpene trifluoromethylated β-hydroxy-benzyl-O-oximes were synthesized in 81–95% yields by nucleophilic addition of the Ruppert–Prakash reagent (TMSCF3) to the corresponding β-keto-benzyl-O-oximes based on (+)-nopinone, (−)-verbanone and (+)-camphoroquinone. Trifluoromethylation has been determined to entirely proceed chemo- and stereoselective at the C=O rather than C=N bond. Trifluoromethylated benzyl-O-oximes were reduced to the corresponding α-trifluoromethyl-β-amino alcohols in 82–88% yields. The structure and configuration of the compounds obtained have been established.
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Ben-Tal Y, Boaler PJ, Dale HJA, Dooley RE, Fohn NA, Gao Y, García-Domínguez A, Grant KM, Hall AMR, Hayes HLD, Kucharski MM, Wei R, Lloyd-Jones GC. Mechanistic analysis by NMR spectroscopy: A users guide. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 129:28-106. [PMID: 35292133 DOI: 10.1016/j.pnmrs.2022.01.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
A 'principles and practice' tutorial-style review of the application of solution-phase NMR in the analysis of the mechanisms of homogeneous organic and organometallic reactions and processes. This review of 345 references summarises why solution-phase NMR spectroscopy is uniquely effective in such studies, allowing non-destructive, quantitative analysis of a wide range of nuclei common to organic and organometallic reactions, providing exquisite structural detail, and using instrumentation that is routinely available in most chemistry research facilities. The review is in two parts. The first comprises an introduction to general techniques and equipment, and guidelines for their selection and application. Topics include practical aspects of the reaction itself, reaction monitoring techniques, NMR data acquisition and processing, analysis of temporal concentration data, NMR titrations, DOSY, and the use of isotopes. The second part comprises a series of 15 Case Studies, each selected to illustrate specific techniques and approaches discussed in the first part, including in situ NMR (1/2H, 10/11B, 13C, 15N, 19F, 29Si, 31P), kinetic and equilibrium isotope effects, isotope entrainment, isotope shifts, isotopes at natural abundance, scalar coupling, kinetic analysis (VTNA, RPKA, simulation, steady-state), stopped-flow NMR, flow NMR, rapid injection NMR, pure shift NMR, dynamic nuclear polarisation, 1H/19F DOSY NMR, and in situ illumination NMR.
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Affiliation(s)
- Yael Ben-Tal
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Patrick J Boaler
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Harvey J A Dale
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Ruth E Dooley
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom; Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Nicole A Fohn
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Yuan Gao
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Andrés García-Domínguez
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Katie M Grant
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Andrew M R Hall
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Hannah L D Hayes
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Maciej M Kucharski
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Ran Wei
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Guy C Lloyd-Jones
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom.
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7
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Coote P, Bermel W, Arthanari H. Optimization of phase dispersion enables broadband excitation without homonuclear coupling artifacts. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 325:106928. [PMID: 33652210 PMCID: PMC8012116 DOI: 10.1016/j.jmr.2021.106928] [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: 10/08/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
In NMR spectroscopy, many specialized shaped pulses are available for broadband excitation, beyond the bandwidth of conventional high-powered hard pulses. These shaped pulses typically have long duration. However, long-duration pulses are unsuitable for spectra containing significant homonuclear couplings, such as polyfluorinated compounds in 19F NMR. J-coupling evolution during the excitation pulse leads to spectral artifacts and incorrect peak integrals. Here, we report an approach to optimal control pulse design which significantly reduces the pulse length required to excite large bandwidths of chemical shift frequencies. The target state phase is not chosen beforehand but is instead only constrained to be linearly dependent on offset frequency. The first-order phase of the target state is then treated as a free-variable, to be optimized at the same time as the RF waveform itself. The resulting spectra are easily phased using standard NMR processing software. We observe that the required pulse length is significantly shorter than for currently available in-phase excitation schemes. Spectral artifacts from homonuclear couplings are avoided. We also demonstrate that pure in-phase excitation can be obtained over the same bandwidth by appending two inversion pulses, at the expense of increased overall duration.
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Affiliation(s)
- Paul Coote
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Dana Farber Cancer Institute, Boston, MA, USA
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Dana Farber Cancer Institute, Boston, MA, USA.
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