Cargando…
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...
Autores principales: | , , , , , , , |
---|---|
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 |
_version_ | 1783416486361038848 |
---|---|
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. |
format | Online Article Text |
id | pubmed-6503917 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT takabakiyofumi subatomicresolutionxraystructuresofgreenfluorescentprotein AT taiyang subatomicresolutionxraystructuresofgreenfluorescentprotein AT ekiharuhiko subatomicresolutionxraystructuresofgreenfluorescentprotein AT daohoanganh subatomicresolutionxraystructuresofgreenfluorescentprotein AT hanazonoyuya subatomicresolutionxraystructuresofgreenfluorescentprotein AT hasegawakazuya subatomicresolutionxraystructuresofgreenfluorescentprotein AT mikikunio subatomicresolutionxraystructuresofgreenfluorescentprotein AT takedakazuki subatomicresolutionxraystructuresofgreenfluorescentprotein |