title: Energetics of radical transfer in DNA photolyase.
abstract: Charge separation and radical transfer in DNA photolyase from Escherichia coli is investigated by computing electrostatic free energies from a solution of the Poisson-Boltzmann equation. For the initial charge separation 450 meV are available. According to recent experiments [Aubert et al. Nature 2000, 405, 586-590] the flavin receives an electron from the proximal tryptophan W382, which consequently forms a cationic radical WH(*)(+)382. The radical state is subsequently transferred along the triad W382-W359-W306 of conserved tryptophans. The radical transfer to the intermediate tryptophan W359 is nearly isoenergetic (58 meV uphill); the radical transfer from the intermediate W359 to the distal W306 is 200 meV downhill in energy, funneling and stabilizing the radical state at W306. The resulting cationic radical WH(*)(+)306 is further stabilized by deprotonation, yielding the neutral radical W(*)306, which is 214 meV below WH(*)(+)306. The time scale of the charge recombination process yielding back the resting enzyme with FADH(*) is governed by reprotonation of W306, with a calculated lifetime of 1.2 ms that correlates well with the measured lifetime of 17 ms. In photolyase from Anacystis nidulans the radical state is partially transferred to a tyrosine [Aubert et al. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 5423-5427]. In photolyase from Escherichia coli, there is a tyrosine (Y464) close to the distal tryptophan W306 that could play this role. We show that this tyrosine cannot be involved in radical transfer, because the electron transfer from tyrosine to W306 is much too endergonic (750 meV) and a direct hydrogen transfer is likely too slow. Coupling of specific charge states of the tryptophan triad with protonation patterns of titratable residues of photolyase is small.
authors.affiliation: Department of Biology, Chemistry, and Pharmacy, Institute of Chemistry, Free University of Berlin, Takustrasse 6, D-14195 Berlin, Germany.
authors.forename: Dragan M
authors.initials: DM
authors.lastname: Popović
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Zmirić
authors.forename: Snezana D
authors.initials: SD
authors.lastname: Zarić
authors.forename: Ernst-Walter
authors.initials: EW
authors.lastname: Knapp
mesh_terms: D004255:Deoxyribodipyrimidine Photo-Lyase / Q000737:chemistry*; D004789:Enzyme Activation; D004926:Escherichia coli / Q000201:enzymology; D005182:Flavin-Adenine Dinucleotide / Q000737:chemistry; D005415:Flavins / Q000737:chemistry; D005609:Free Radicals / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D010084:Oxidation-Reduction; D010777:Photochemistry; D011487:Protein Conformation; D055672:Static Electricity; D013816:Thermodynamics; D014364:Tryptophan / Q000737:chemistry
chemical_list: D005415:Flavins; D005609:Free Radicals; D005182:Flavin-Adenine Dinucleotide; D014364:Tryptophan; D004255:Deoxyribodipyrimidine Photo-Lyase