Excited state dynamics of protein

1. Special seminar on protein dynamics Harvard University, February 2004 Excited state dynamics of protein H.G. Bohr, Quantum Protein (QuP) Center, Technical University of Denmark, Kgs. Lyngby, Denmark

2. Photolyase • Photolyase structure & function • Structure • Function • FADH• ―› FADH- • Coenzyme energy transfer • Electron transfer from FADH- to the T-T dimer • T-T dimer splitting • Projects ...

3. Structure of Photolyase from E. Coli Park et al. Science 1995, 268:1866, Carell et al. Curr. Op. Chem. Biol. 2001, 5:491

5. FADH• ―› FADH- • Aubert et al. Nature, 2000, 405:586 Time-resolved absorption spectroscopy has demonstrated:

6. Coenzyme energy transfer Epple & Carell J. Am. Chem. Soc., 1999, 121:7318, Carell et al. Curr. Op. Chem. Biol., 2001, 5:491 • FADH – MTHF distance ~ 20 Å • Radioationless energy transfer in ~ 200 ps (Förster • theory) • Experimental model studies: Long coenzyme- • coenzyme distance favors T-T dimer splitting, even • though it disfavors energy transfer – possibly due to • electron transfer to MTHF instead of to the T-T dimer.

7. Electron transfer from FADH- to the T-T dimer Antony et al. J. Am. Chem. Soc. 2000, 122:1057, Sanders & Wiest J. Am. Chem. Soc. 1999, 121:5127 • Binding of the T-T dimer to photolyase: Docking and MD studies: 3-10 Å between FADH- • and T-T-dimer • Electron transfer rate in agreement with experimental data (Extended Hückel theory) • U-bend FADH- essential, because electron transfer occurs via the adenine moiety

8. T-T dimer splitting Durbeej & Eriksson, J. Am. Chem. Soc. 2000, 122:10126 • Thermodynamics of energy transfer and reaction, TDDFT study • Earlier work at HF, MP2 or semiempirical level with modest basis sets is deemed unreliable • Only 2.3 kcal/mol barrier for the T-T dimer bond breaking

9. New Work done at QuP • T-T dimer binding • Coenzyme energy transfer • Reaction mechanism • (dimer splitting) including the enzyme • pathway • Reaction path in excited state • Neutral dimer splitting more exothermic by ~ 20 kcal/mol than anion radical dimer splitting (DFT calculation). Larger barrier ? • Orbital symmetry rules: The neutral dimer splitting may occur via excited state

10. DFT calculations at QuP/DKFZ • B3LYP calculation for two thymine monomer interaction • B3LYP calculation for thymine duplex • B3LYP calculation for DNA (dithymine) • B3LYP calculation of DNA (photo denatured dithymine)

11. B3LYP calculation for two thymine monomer interaction • B3LYP/6-31G* energy -897.216847 Hartrees • 31.7 kcal/mole more stable then lowest energy thymine duplex

12. B3LYP calculation for two thymine monomer interaction • B3LYP/6-31G* energy -897.216846 Hartrees • 31.7 kcal/mole more stable then lowest energy thymine duplex • Degenerate with previous structure

13. thymine duplex • B3LYP/6-31G* energy -987.127896 Hartrees • B3LYP/6-31G* energy -987.166315 Hartrees • The second structure is 24.1 kcal/mole more stable, but 31.7 kcal less stable than thymine dimer

14. B3LYP calculation for DNA (dithymine dimer) • Without the other base pairs and correct treatment of dispersion, the thymine monomers appear to repell each other • A larger model system appears to be necessary

15. B3LYP calculation for DNA (dithymine duplex) • One of the possible structures for damaged DNA due to radiation damage • A larger model system does not appear to be necessary here

16. Acknowledgment of collaborators and funding • Holger B. Nielsen, NBI, Cophenhagen, DK • F. Bari Malik, SIU, Carbondale, IL USA • K.J. Jalkanen, QuP, Kgs. Lyngby, DK • S. Suhai, DKFZ, Heidelberg, DE • Danish National Research Foundation • DKFZ, Heidelberg, DE for access to HP and IBM computational resources