Dataset Information


The binding structure and affinity of photodamaged duplex DNA with members of the photolyase/cryptochrome family: A computational study.

ABSTRACT: 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, ?Gbind, between the protein and the damaged dsDNA by using a molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. ?Gbind 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.


PROVIDER: S-EPMC5812317 | BioStudies | 2018-01-01

REPOSITORIES: biostudies

Similar Datasets

2012-01-01 | S-EPMC3430658 | BioStudies
2015-01-01 | S-EPMC4564169 | BioStudies
2006-01-01 | S-EPMC1635974 | BioStudies
1000-01-01 | S-EPMC4679004 | BioStudies
2009-01-01 | S-EPMC2678464 | BioStudies
2007-01-01 | S-EPMC1820510 | BioStudies
2008-01-01 | S-EPMC2634942 | BioStudies
2020-01-01 | S-EPMC7667820 | BioStudies
2010-01-01 | S-EPMC4329311 | BioStudies
2017-01-01 | S-EPMC5397253 | BioStudies