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Takaba K, Tai Y, Eki H, Dao HA, Hanazono Y, Hasegawa K, Miki K, Takeda K. Subatomic resolution X-ray structures of green fluorescent protein. IUCRJ 2019; 6:387-400. [PMID: 31098020 PMCID: PMC6503917 DOI: 10.1107/s205225251900246x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/17/2019] [Indexed: 05/06/2023]
Abstract
Green fluorescent protein (GFP) is a light-emitting protein that does not require a prosthetic group for its fluorescent activity. As such, GFP has become indispensable as a molecular tool in molecular biology. Nonetheless, there has been no subatomic elucidation of the GFP structure owing to the structural polymorphism around the chromophore. Here, subatomic resolution X-ray structures of GFP without the structural polymorphism are reported. The positions of H atoms, hydrogen-bonding network patterns and accurate geometric parameters were determined for the two protonated forms. Compared with previously determined crystal structures and theoretically optimized structures, the anionic chromophores of the structures represent the authentic resonance state of GFP. In addition, charge-density analysis based on atoms-in-molecules theory and noncovalent interaction analysis highlight weak but substantial interactions between the chromophore and the protein environment. Considered with the derived chemical indicators, the lone pair-π interactions between the chromophore and Thr62 should play a sufficient role in maintaining the electronic state of the chromophore. These results not only reveal the fine structural features that are critical to understanding the properties of GFP, but also highlight the limitations of current quantum-chemical calculations.
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Affiliation(s)
- Kiyofumi Takaba
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yang Tai
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruhiko Eki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hoang-Anh Dao
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Shi S, Kumar P, Lee KF. Generation of photonic entanglement in green fluorescent proteins. Nat Commun 2017; 8:1934. [PMID: 29203839 PMCID: PMC5715022 DOI: 10.1038/s41467-017-02027-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 11/02/2017] [Indexed: 11/20/2022] Open
Abstract
Recent development of spectroscopic techniques based on quantum states of light can precipitate many breakthroughs in observing and controlling light-matter interactions in biological materials on a fundamental quantum level. For this reason, the generation of entangled light in biologically produced fluorescent proteins would be promising because of their biocompatibility. Here we demonstrate the generation of polarization-entangled two-photon state through spontaneous four-wave mixing in enhanced green fluorescent proteins. The reconstructed density matrix indicates that the entangled state is subject to decoherence originating from two-photon absorption. However, the prepared state is less sensitive to environmental decoherence because of the protective β-barrel structure that encapsulates the fluorophore in the protein. We further explore the quantumness, including classical and quantum correlations, of the state in the decoherence environment. Our method for photonic entanglement generation may have potential for developing quantum spectroscopic techniques and quantum-enhanced measurements in biological materials. Quantum-enhanced applications such as quantum spectroscopy of biological samples could take advantage from in situ generation of quantum states of light. Here, the authors characterize polarization-entangled photon states generated through spontaneous four-wave mixing in enhanced green fluorescent proteins.
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Affiliation(s)
- Siyuan Shi
- Department of Physics and Astronomy, Center for Photonic Communication and Computing, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3112, USA.
| | - Prem Kumar
- Department of Physics and Astronomy, Center for Photonic Communication and Computing, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3112, USA. .,Department of Electrical Engineering and Computer Science, Center for Photonic Communication and Computing, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3118, USA.
| | - Kim Fook Lee
- Department of Electrical Engineering and Computer Science, Center for Photonic Communication and Computing, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208-3118, USA.
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