The binding structure and affinity of photodamaged duplex DNA with members of the photolyase/cryptochrome family: A computational study
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- Sato Ryuma
- Center for Computational Sciences, University of Tsukuba
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- Harada Ryuhei
- Center for Computational Sciences, University of Tsukuba
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- Shigeta Yasuteru
- Center for Computational Sciences, University of Tsukuba
抄録
<p>Photolyases (PHRs) and cryptochromes (CRYs) belong to the same family known as blue-light photoreceptors. Although their amino acid sequences and corresponding structures are similar to each other, they exert different functions. PHRs function as an enzyme to repair UV-induced deoxyribonucleic acid (DNA) lesions such as a cyclobutane pyrimidine dimer (CPD) and a (6-4) photoproduct ((6-4)pp), whereas CRYs are a circadian photoreceptor in plants and animals and at the same time they control the photoperiodic induction of flowering in plants. When a new type cryptochrome was identified, it was assumed that another type of CRYs, cryptochrome-DASH (CRY-DASH), which is categorized as a subfamily of photolyase/cryptochrome family, would possess the DNA photolyase activity. However, CRY-DASH had a weak DNA photolyase activity, but the reason for this is still unclear. To clarify the reason, we performed molecular dynamics (MD) simulations for a complex of CPD-PHR or CRY-DASH with damaged double-stranded DNA (dsDNA) and estimated the binding free energy, ΔGbind, between the protein and the damaged dsDNA by using a molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) method. ΔGbind for both proteins were –35 and 57 kcal mol–1, respectively, indicating that the structural stability of CRY-DASH was lower than that of CPD-PHR upon the damaged dsDNA binding. In particular, the number of amino acid residues relevant to the damaged dsDNA binding on the CRY-DASH surface was smaller than that on CPD-PHR. Therefore, the present result suggests that CRY-DASH has a weak DNA photolyase activity because it has a lower binding affinity than CPD-PHR.</p>
収録刊行物
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- Biophysics and Physicobiology
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Biophysics and Physicobiology 15 (0), 18-27, 2018
一般社団法人 日本生物物理学会
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詳細情報 詳細情報について
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- CRID
- 1390001205764901888
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- NII論文ID
- 130006316166
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- ISSN
- 21894779
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- 本文言語コード
- en
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- データソース種別
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- JaLC
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- CiNii Articles
- KAKEN
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- 使用不可