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Subatomic resolution X-ray structures of green fluorescent protein

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 st...

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Autores principales: Takaba, Kiyofumi, Tai, Yang, Eki, Haruhiko, Dao, Hoang-Anh, Hanazono, Yuya, Hasegawa, Kazuya, Miki, Kunio, Takeda, Kazuki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503917/
https://www.ncbi.nlm.nih.gov/pubmed/31098020
http://dx.doi.org/10.1107/S205225251900246X
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author Takaba, Kiyofumi
Tai, Yang
Eki, Haruhiko
Dao, Hoang-Anh
Hanazono, Yuya
Hasegawa, Kazuya
Miki, Kunio
Takeda, Kazuki
author_facet Takaba, Kiyofumi
Tai, Yang
Eki, Haruhiko
Dao, Hoang-Anh
Hanazono, Yuya
Hasegawa, Kazuya
Miki, Kunio
Takeda, Kazuki
author_sort Takaba, Kiyofumi
collection PubMed
description 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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spelling pubmed-65039172019-05-16 Subatomic resolution X-ray structures of green fluorescent protein Takaba, Kiyofumi Tai, Yang Eki, Haruhiko Dao, Hoang-Anh Hanazono, Yuya Hasegawa, Kazuya Miki, Kunio Takeda, Kazuki IUCrJ Research Papers 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. International Union of Crystallography 2019-04-03 /pmc/articles/PMC6503917/ /pubmed/31098020 http://dx.doi.org/10.1107/S205225251900246X Text en © Kiyofumi Takaba et al. 2019 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/
spellingShingle Research Papers
Takaba, Kiyofumi
Tai, Yang
Eki, Haruhiko
Dao, Hoang-Anh
Hanazono, Yuya
Hasegawa, Kazuya
Miki, Kunio
Takeda, Kazuki
Subatomic resolution X-ray structures of green fluorescent protein
title Subatomic resolution X-ray structures of green fluorescent protein
title_full Subatomic resolution X-ray structures of green fluorescent protein
title_fullStr Subatomic resolution X-ray structures of green fluorescent protein
title_full_unstemmed Subatomic resolution X-ray structures of green fluorescent protein
title_short Subatomic resolution X-ray structures of green fluorescent protein
title_sort subatomic resolution x-ray structures of green fluorescent protein
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6503917/
https://www.ncbi.nlm.nih.gov/pubmed/31098020
http://dx.doi.org/10.1107/S205225251900246X
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