Sato Ryuma, Harada Ryuhei, Shigeta Yasuteru
Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577 Japan.
Biophys Physicobiol. 2018 Jan 20;15:18-27. doi: 10.2142/biophysico.15.0_18. eCollection 2018.
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, Δ, between the protein and the damaged dsDNA by using a molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. Δ for both proteins were -35 and 57 kcal mol, 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.
光解酶（PHRs）和隐花色素（CRYs）属于被称为蓝光光感受器的同一家族。尽管它们的氨基酸序列和相应结构彼此相似，但它们发挥着不同的功能。PHRs作为一种酶来修复紫外线诱导的脱氧核糖核酸（DNA）损伤，如环丁烷嘧啶二聚体（CPD）和（6-4）光产物（（6-4）pp），而CRYs是植物和动物中的一种昼夜节律光感受器，同时它们控制植物开花的光周期诱导。当一种新型隐花色素被鉴定出来时，人们推测另一种类型的CRYs，即隐花色素-DASH（CRY-DASH），它被归类为光解酶/隐花色素家族的一个亚家族，会具有DNA光解酶活性。然而，CRY-DASH具有较弱的DNA光解酶活性，但其原因仍不清楚。为了阐明原因，我们对CPD-PHR或CRY-DASH与受损双链DNA（dsDNA）的复合物进行了分子动力学（MD）模拟，并使用分子力学/泊松-玻尔兹曼表面积（MM/PBSA）方法估计了蛋白质与受损dsDNA之间的结合自由能Δ。两种蛋白质的Δ分别为-35和57千卡/摩尔，这表明在与受损dsDNA结合时，CRY-DASH的结构稳定性低于CPD-PHR。特别是，CRY-DASH表面上与受损dsDNA结合相关的氨基酸残基数量比CPD-PHR上的少。因此，目前的结果表明，CRY-DASH具有较弱的DNA光解酶活性是因为它的结合亲和力比CPD-PHR低。
