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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [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: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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2
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Ghosh P, Nandy T, Singh PC, Ghosh D. Substitution enables significant new decay channels for a non-canonical amino acid. Phys Chem Chem Phys 2022; 24:17695-17702. [PMID: 35838114 DOI: 10.1039/d2cp00465h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV-Vis absorption spectra and emission peaks of indole and 7-fluoroindole are measured and it is observed that 7-fluoroindole quenches the fluorescence signals significantly compared to indole. This observation is elucidated via reconstruction of the potential energy surfaces, determination of the conical intersections, and dynamical studies. It is observed that a single fluorine substitution on indole leads to the appearance of several accessible low-energy conical intersections that cause fast nonradiative decay. In this paper, we have investigated the nonradiative processes of Ind and 7F-Ind theoretically using high-level methods, such as EOM-EE-CCSD, SA-CASSCF, MS-CASPT2/6-311++G(d,p) levels of theory, to study these pathways and their feasibility.
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Affiliation(s)
- Paulami Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Tonima Nandy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Prashant C Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
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3
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Lu M, Toptygin D, Xiang Y, Shi Y, Schwieters CD, Lipinski EC, Ahn J, Byeon IJL, Gronenborn AM. The Magic of Linking Rings: Discovery of a Unique Photoinduced Fluorescent Protein Crosslink. J Am Chem Soc 2022; 144:10809-10816. [PMID: 35574633 PMCID: PMC9233106 DOI: 10.1021/jacs.2c02054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Fluorosubstituted tryptophans serve
as valuable probes for fluorescence
and nuclear magnetic resonance (NMR) studies of proteins. Here, we
describe an unusual photoreactivity introduced by replacing the single
tryptophan in cyclophilin A with 7-fluoro-tryptophan. UV exposure
at 282 nm defluorinates 7-fluoro-tryptophan and crosslinks it to a
nearby phenylalanine, generating a bright fluorophore. The crosslink-containing
fluorescent protein possesses a large quantum yield of ∼0.40
with a fluorescence lifetime of 2.38 ns. The chemical nature of the
crosslink and the three-dimensional protein structure were determined
by mass spectrometry and NMR spectroscopy. To the best of our knowledge,
this is the first report of a Phe–Trp crosslink in a protein.
Our finding may break new ground for developing novel fluorescence
probes and for devising new strategies to exploit aromatic crosslinks
in proteins.
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Affiliation(s)
- Manman Lu
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - Dmitri Toptygin
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Charles D. Schwieters
- Computational Biomolecular Magnetic Resonance Core, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Emma C. Lipinski
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - In-Ja L. Byeon
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - Angela M. Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
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4
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Mouli MSSV, Agrawal HG, Kumar M, Mishra AK. Luminescent and morphological behavior of the aromatic dipeptide pair having singular structural variability. LUMINESCENCE 2022. [PMID: 35560861 DOI: 10.1002/bio.4275] [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: 03/01/2022] [Revised: 04/15/2022] [Accepted: 05/07/2022] [Indexed: 11/07/2022]
Abstract
In the present manuscript, the luminescence and the self-assembly behavior of the two aromatic dipeptides having singular structure variable are investigated. The terminally protected dipeptides tryptophan-tyrosine (WYp ) and tryptophan-phenylalanine (WFp ) were synthesized using standard solution phase procedure. Significant solvatochromic effect was observed for both the dipeptidyl entities; while the influence was more pronounced in case of the WYp entity when compared to WFp . Interesting morphological variation was observed for WFp and WYp , wherein discrete and interconnected nanospheres were observed for the respective dipeptides. The results obtained signifies the influence of the singular structural variation on modulating the overall functional behavior of the short peptides motifs.
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Affiliation(s)
- M S S Vinod Mouli
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Harsha Gopal Agrawal
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Mohit Kumar
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
| | - Ashutosh Kumar Mishra
- Department of chemistry, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India
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Qianzhu H, Abdelkader EH, Herath ID, Otting G, Huber T. Site-Specific Incorporation of 7-Fluoro-L-tryptophan into Proteins by Genetic Encoding to Monitor Ligand Binding by 19F NMR Spectroscopy. ACS Sens 2022; 7:44-49. [PMID: 35005899 DOI: 10.1021/acssensors.1c02467] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A mutant aminoacyl-tRNA synthetase identified by a library selection system affords site-specific incorporation of 7-fluoro-L-tryptophan in response to an amber stop codon. The enzyme allows the production of proteins with a single hydrogen atom replaced by a fluorine atom as a sensitive nuclear magnetic resonance (NMR) probe. The substitution of a single hydrogen atom by another element that is as closely similar in size and hydrophobicity as possible minimizes possible perturbations in the structure, stability, and solubility of the protein. The fluorine atom enables site-selective monitoring of the protein response to ligand binding by 19F NMR spectroscopy, as demonstrated with the Zika virus NS2B-NS3 protease.
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Affiliation(s)
- Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H. Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - 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
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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Nandy T, Singh PC. Photophysical Properties of Noncanonical Amino Acid 7-Fluorotryptophan Sharply Different from Those of Canonical Derivative Tryptophan: Spectroscopic and Quantum Chemical Calculations. J Phys Chem B 2021; 125:6214-6221. [PMID: 34081478 DOI: 10.1021/acs.jpcb.1c03319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to the limited number of naturally existing canonical amino acids, several noncanonical amino acids have been designed to understand the diverse complex biological functions. Fluorinated amino acids are one of the important noncanonical amino acids that have been used to understand the different complex processes of proteins. In this study, the photophysical properties of the noncanonical amino acid 7-fluorotryptophan (7F-Trp) in different solvents have been investigated using extensive spectroscopic as well as quantum chemical calculation methods and compared with those of tryptophan (Trp). The spectroscopic and quantum chemical calculation data suggest that unlike Trp, 7F-Trp can be used to detect the excited-state proton transfer from solvents depending on its acidity, which makes 7F-Trp a potential candidate for sensing the excited-state proton transfer from the solvent molecules.
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Affiliation(s)
- Tonima Nandy
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Sciences, Kolkata 700032, India
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