1
|
Špačková J, Goldberga I, Yadav R, Cazals G, Lebrun A, Verdié P, Métro TX, Laurencin D. Fast and Cost-Efficient 17 O-Isotopic Labeling of Carboxylic Groups in Biomolecules: From Free Amino Acids to Peptide Chains. Chemistry 2023; 29:e202203014. [PMID: 36333272 DOI: 10.1002/chem.202203014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 11/08/2022]
Abstract
17 O NMR spectroscopy is a powerful technique, which can provide unique information regarding the structure and reactivity of biomolecules. However, the low natural abundance of 17 O (0.04 %) generally requires working with enriched samples, which are not easily accessible. Here, we present simple, fast and cost-efficient 17 O-enrichment strategies for amino acids and peptides by using mechanochemistry. First, five unprotected amino acids were enriched under ambient conditions, consuming only microliter amounts of costly labeled water, and producing pure molecules with enrichment levels up to ∼40 %, yields ∼60-85 %, and no loss of optical purity. Subsequently, 17 O-enriched Fmoc/tBu-protected amino acids were produced on a 1 g/day scale with high enrichment levels. Lastly, a site-selective 17 O-labeling of carboxylic functions in peptide side-chains was achieved for RGD and GRGDS peptides, with ∼28 % enrichment level. For all molecules, 17 O ssNMR spectra were recorded at 14.1 T in reasonable times, making this an important step forward for future NMR studies of biomolecules.
Collapse
Affiliation(s)
| | | | - Rishit Yadav
- ICGM, CNRS, UM, ENSCM, 34293, Montpellier, France
| | | | | | | | | | | |
Collapse
|
2
|
Liu M, He Y, Shan C, Wojtas L, Ghiviriga I, Fathalla O, Yan Y, Li X, Shi X. Anion mediated, tunable isoguanosine self-assemblies: decoding the conformation influence and solvent effects. Chem Sci 2021; 12:7569-7574. [PMID: 34163848 PMCID: PMC8171338 DOI: 10.1039/d1sc00988e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/12/2021] [Indexed: 12/18/2022] Open
Abstract
Systematic investigations were performed with various substituted groups at C8 purine and ribose. A series of isoG analogs, C8-phenyl substituted isoG were synthesized and applied for Cs+ coordination. The structural proximity between purine and ribose limited pentaplex formation for C8-phenyl substituted isoG derivatives. Based on this observation, deoxy isoG derivative with modification on ribose (tert-butyldimethylsilyl ether) was applied to assemble with the Cs+ cation. Critical solvent (CDCl3 and CD3CN) and anion (BPh4 -, BARF-, and PF6 -) effects were revealed, leading to the controllable formation of various stable isoG pentaplexes, including singly charged decamer, doubly charged decamer, and 15-mer, etc. Finally, the X-ray crystal structure of [isoG20Cs3]3+(BARF-)3 was successfully obtained, which is the first example of multiple-layer deoxy isoG binding with the Cs+ cation, providing solid evidence of this new isoG ionophore beyond two-layer sandwich self-assembly.
Collapse
Affiliation(s)
- Mengjia Liu
- Department of Chemistry, University of South Florida 4202 E. Fowler Avenue Tampa Florida 33620 USA
| | - Ying He
- Department of Chemistry, University of South Florida 4202 E. Fowler Avenue Tampa Florida 33620 USA
| | - Chuan Shan
- Department of Chemistry, University of South Florida 4202 E. Fowler Avenue Tampa Florida 33620 USA
| | - Lukasz Wojtas
- Department of Chemistry, University of South Florida 4202 E. Fowler Avenue Tampa Florida 33620 USA
| | - Ion Ghiviriga
- Department of Chemistry, University of Florida 125 Buckman Drive Gainesville Florida 32611 USA
| | - Omar Fathalla
- Department of Chemistry, University of South Florida 4202 E. Fowler Avenue Tampa Florida 33620 USA
| | - Yu Yan
- Department of Chemistry, University of South Florida 4202 E. Fowler Avenue Tampa Florida 33620 USA
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida 4202 E. Fowler Avenue Tampa Florida 33620 USA
- College of Chemistry and Environmental Engineering, Shenzhen University Shenzhen 518055 People's Republic of China
| | - Xiaodong Shi
- Department of Chemistry, University of South Florida 4202 E. Fowler Avenue Tampa Florida 33620 USA
| |
Collapse
|
3
|
Lin B, Hung I, Gan Z, Chien PH, Spencer HL, Smith SP, Wu G. 17 O NMR Studies of Yeast Ubiquitin in Aqueous Solution and in the Solid State. Chembiochem 2020; 22:826-829. [PMID: 33058374 DOI: 10.1002/cbic.202000659] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/14/2020] [Indexed: 12/18/2022]
Abstract
We report a general method for amino acid-type specific 17 O-labeling of recombinant proteins in Escherichia coli. In particular, we have prepared several [1-13 C,17 O]-labeled yeast ubiquitin (Ub) samples including Ub-[1-13 C,17 O]Gly, Ub-[1-13 C,17 O]Tyr, and Ub-[1-13 C,17 O]Phe using the auxotrophic E. coli strain DL39 GlyA λDE3 (aspC- tyrB- ilvE- glyA- λDE3). We have also produced Ub-[η-17 O]Tyr, in which the phenolic group of Tyr59 is 17 O-labeled. We show for the first time that 17 O NMR signals from protein terminal residues and side chains can be readily detected in aqueous solution. We also reported solid-state 17 O NMR spectra for Ub-[1-13 C,17 O]Tyr and Ub-[1-13 C,17 O]Phe obtained at an ultrahigh magnetic field, 35.2 T (1.5 GHz for 1 H). This work represents a significant advance in the field of 17 O NMR studies of proteins.
Collapse
Affiliation(s)
- Binyang Lin
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ivan Hung
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Zhehong Gan
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Po-Hsiu Chien
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA
| | - Holly L Spencer
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| |
Collapse
|
4
|
Czernek J, Brus J. Polymorphic Forms of Valinomycin Investigated by NMR Crystallography. Int J Mol Sci 2020; 21:E4907. [PMID: 32664570 PMCID: PMC7404035 DOI: 10.3390/ijms21144907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/22/2022] Open
Abstract
A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously available solid-state NMR (SSNMR) data are combined with the plane-wave DFT computations in the NMR crystallography framework. Structural/spectroscopical predictions (the PBE functional/GIPAW method) are obtained to characterize four polymorphs of VLM. Interactions which confer a conformational stability to VLM molecules in these crystalline forms are described in detail. The way how various structural factors affect the values of SSNMR parameters is thoroughly analyzed, and several SSNMR markers of the respective VLM polymorphs are identified. The markers are connected to hydrogen bonding effects upon the corresponding (13C/15N/1H) isotropic chemical shifts of (CO, Namid, Hamid, Hα) VLM backbone nuclei. These results are expected to be crucial for polymorph control of VLM and in probing its interactions in dosage forms.
Collapse
Affiliation(s)
- Jiří Czernek
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovsky Square #2, 16206 Prague, Czech Republic;
| | | |
Collapse
|
5
|
Xu Y, Szell PM, Kumar V, Bryce DL. Solid-state NMR spectroscopy for the analysis of element-based non-covalent interactions. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213237] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
6
|
Tabacchi G, Fabbiani M, Mino L, Martra G, Fois E. The Case of Formic Acid on Anatase TiO 2 (101): Where is the Acid Proton? Angew Chem Int Ed Engl 2019; 58:12431-12434. [PMID: 31310450 DOI: 10.1002/anie.201906709] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Indexed: 01/20/2023]
Abstract
Carboxylic-acid adsorption on anatase TiO2 is a relevant process in many technological applications. Yet, despite several decades of investigations, the acid-proton localization-either on the molecule or on the surface-is still an open issue. By modeling the adsorption of formic acid on top of anatase(101) surfaces, we highlight the formation of a short strong hydrogen bond. In the 0 K limit, the acid-proton behavior is ruled by quantum delocalization effects in a single potential well, while at ambient conditions, the proton undergoes a rapid classical shuttling in a shallow two-well free-energy profile. This picture, supported by agreement with available experiments, shows that the anatase surface acts like a protecting group for the carboxylic acid functionality. Such a new conceptual insight might help rationalize chemical processes involving carboxylic acids on oxide surfaces.
Collapse
Affiliation(s)
- Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100, Como, Italy
| | - Marco Fabbiani
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Lorenzo Mino
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Gianmario Martra
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centre, University of Torino, via P. Giuria 7, I-10125, Torino, Italy
| | - Ettore Fois
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100, Como, Italy
| |
Collapse
|
7
|
Tabacchi G, Fabbiani M, Mino L, Martra G, Fois E. The Case of Formic Acid on Anatase TiO
2
(101): Where is the Acid Proton? Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gloria Tabacchi
- Department of Science and High TechnologyUniversity of Insubria and INSTM via Valleggio 9 I-22100 Como Italy
| | - Marco Fabbiani
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Lorenzo Mino
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Gianmario Martra
- Department of Chemistry and Nanostructured Interfaces and Surfaces NIS interdepartmental centreUniversity of Torino via P. Giuria 7 I-10125 Torino Italy
| | - Ettore Fois
- Department of Science and High TechnologyUniversity of Insubria and INSTM via Valleggio 9 I-22100 Como Italy
| |
Collapse
|
8
|
Métro TX, Gervais C, Martinez A, Bonhomme C, Laurencin D. Unleashing the Potential of 17 O NMR Spectroscopy Using Mechanochemistry. Angew Chem Int Ed Engl 2017; 56:6803-6807. [PMID: 28455940 DOI: 10.1002/anie.201702251] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Indexed: 12/31/2022]
Abstract
17 O NMR spectroscopy has been the subject of vivid interest in recent years, because there is increasing evidence that it can provide unique insight into the structure and reactivity of many molecules and materials. However, due to the very poor natural abundance of oxygen-17, 17 O labeling is generally a prerequisite. This is a real obstacle for most research groups, because of the high costs and/or strong experimental constraints of the most frequently used 17 O-labeling schemes. Here, we show for the first time that mechanosynthesis offers unique opportunities for enriching in 17 O a variety of organic and inorganic precursors of synthetic interest. The protocols are fast, user-friendly, and low-cost, which makes them highly attractive for a broad research community, and their suitability for 17 O solid-state NMR applications is demonstrated.
Collapse
Affiliation(s)
- Thomas-Xavier Métro
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM, Campus Triolet, Place E. Bataillon, CC 1703, 34095, Montpellier cedex 05, France
| | - Christel Gervais
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR 7574, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris, France
| | - Anthony Martinez
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253, CNRS, UM, ENSCM, Campus Triolet, Place E. Bataillon, CC1701, 34095, Montpellier cedex 05, France
| | - Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), UMR 7574, Sorbonne Universités, UPMC Univ Paris 06, 4 Place Jussieu, 75005, Paris, France
| | - Danielle Laurencin
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253, CNRS, UM, ENSCM, Campus Triolet, Place E. Bataillon, CC1701, 34095, Montpellier cedex 05, France
| |
Collapse
|
9
|
Métro TX, Gervais C, Martinez A, Bonhomme C, Laurencin D. Unleashing the Potential of17O NMR Spectroscopy Using Mechanochemistry. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas-Xavier Métro
- Institut des Biomolécules Max Mousseron (IBMM); UMR 5247, CNRS; Université de Montpellier, ENSCM, Campus Triolet; Place E. Bataillon, CC 1703 34095 Montpellier cedex 05 France
| | - Christel Gervais
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP); UMR 7574; Sorbonne Universités, UPMC Univ Paris 06; 4 Place Jussieu 75005 Paris France
| | - Anthony Martinez
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253, CNRS, UM, ENSCM; Campus Triolet; Place E. Bataillon, CC1701 34095 Montpellier cedex 05 France
| | - Christian Bonhomme
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP); UMR 7574; Sorbonne Universités, UPMC Univ Paris 06; 4 Place Jussieu 75005 Paris France
| | - Danielle Laurencin
- Institut Charles Gerhardt de Montpellier (ICGM), UMR 5253, CNRS, UM, ENSCM; Campus Triolet; Place E. Bataillon, CC1701 34095 Montpellier cedex 05 France
| |
Collapse
|