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Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH

Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD i...

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Autores principales: Sato, Ryuma, Mori, Yoshiharu, Matsui, Risa, Okimoto, Noriaki, Yamamoto, Junpei, Taiji, Makoto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Biophysical Society of Japan 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610064/
https://www.ncbi.nlm.nih.gov/pubmed/33194514
http://dx.doi.org/10.2142/biophysico.BSJ-2020010
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author Sato, Ryuma
Mori, Yoshiharu
Matsui, Risa
Okimoto, Noriaki
Yamamoto, Junpei
Taiji, Makoto
author_facet Sato, Ryuma
Mori, Yoshiharu
Matsui, Risa
Okimoto, Noriaki
Yamamoto, Junpei
Taiji, Makoto
author_sort Sato, Ryuma
collection PubMed
description Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD.
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spelling pubmed-76100642020-11-13 Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH Sato, Ryuma Mori, Yoshiharu Matsui, Risa Okimoto, Noriaki Yamamoto, Junpei Taiji, Makoto Biophys Physicobiol Regular Article Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD. The Biophysical Society of Japan 2020-09-04 /pmc/articles/PMC7610064/ /pubmed/33194514 http://dx.doi.org/10.2142/biophysico.BSJ-2020010 Text en 2020 THE BIOPHYSICAL SOCIETY OF JAPAN https://creativecommons.org/licenses/by-nc-sa/4.0/This article is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 Inter­national License. To view a copy of this license, visit 
https://creativecommons.org/licenses/by-nc-sa/4.0/.
spellingShingle Regular Article
Sato, Ryuma
Mori, Yoshiharu
Matsui, Risa
Okimoto, Noriaki
Yamamoto, Junpei
Taiji, Makoto
Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH
title Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH
title_full Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH
title_fullStr Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH
title_full_unstemmed Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH
title_short Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH
title_sort theoretical insights into the dna repair function of arabidopsis thaliana cryptochrome-dash
topic Regular Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610064/
https://www.ncbi.nlm.nih.gov/pubmed/33194514
http://dx.doi.org/10.2142/biophysico.BSJ-2020010
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