Excited state dynamics of protein

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Excited state dynamics of protein
Special seminar on protein dynamics Harvard
University, February 2004

• H.G. Bohr, Quantum Protein (QuP) Center,
  Technical University of Denmark,
• Kgs. Lyngby, Denmark

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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 ...

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Structure of Photolyase from E. Coli Park et al.
Science 1995, 2681866, Carell et al. Curr. Op.
Chem. Biol. 2001, 5491
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FADH ? FADH- Aubert et al. Nature, 2000, 405586
Time-resolved absorption spectroscopy has
demonstrated
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Coenzyme energy transfer Epple Carell J. Am.
Chem. Soc., 1999, 1217318, Carell et al. Curr.
Op. Chem. Biol., 2001, 5491

• 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.

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Electron transfer from FADH- to the T-T
dimer Antony et al. J. Am. Chem. Soc. 2000,
1221057, Sanders Wiest J. Am. Chem. Soc. 1999,
1215127

• 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

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T-T dimer splitting Durbeej Eriksson, J. Am.
Chem. Soc. 2000, 12210126

• 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

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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

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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)

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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

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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

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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

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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

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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

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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