Folding kinetics of recognition loop peptides from a photolyase and cryptochrome-DASH.
Cryptochromes (CRY) and photolyases (PL) use a common flavin adenine dinucleotide cofactor and homologous protein scaffold to accomplish numerous, seemingly dissimilar functions. PL repairs UV-damaged DNA in a mechanism requiring light and DNA base flipping. CRY cannot repair DNA, and instead function in core biological processes including plant photomorphogenesis, circadian rhythm, and magnetoreception. One subclass, CRY-DASH, does catalyze repair of single-stranded DNA; compromised base flipping may deactivate its tight binding to duplex DNA substrates. We recently demonstrated that the a "recognition loop" involved in DNA binding by both PL and CRY-DASH is among the most flexible regions in the two proteins, and exhibits especially heightened dynamics in CRY-DASH. Here, we establish that these distinct dynamics are encoded by the loop sequences: we quantify the flexibility of the isolated loop peptides through the kinetics and activation parameters for their folding. Mirroring the dynamics within the proteins, the CRY-DASH recognition loop peptide folds 2.5-fold faster than its counterpart in PL, predominantly due to a lower enthalpy of activation. We propose that these distinct dynamics are functionally significant in DNA recognition. Binding duplex DNA in the catalytically-active base-flipped conformation imposes significant order on the recognition loop, and a corresponding entropic penalty. This may be surmounted by the more preorganized PL recognition loop, but may impose too large a barrier for the more dynamic loop in CRY-DASH. These results suggest that evolution of protein dynamics, through local sequence tuning in the recognition loop, may be an important mechanism for functional diversification in PL and CRY.
Brolich
Matthew A
MA
Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada.
Wang
Lisa
L
O'Neill
Melanie A
MA
D000595:Amino Acid Sequence; D000818:Animals; D002384:Catalysis; D056931:Cryptochromes / Q000737:chemistry*; D018360:Crystallography, X-Ray; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000737:chemistry*; D004789:Enzyme Activation; D006801:Humans; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding
D056931:Cryptochromes; D010455:Peptides; D004255:Deoxyribodipyrimidine Photo-Lyase