Proton pumping in bacteriorhodopsin with QM/MM SCC-DFTB

1. Proton pumping in bacteriorhodopsin with QM/MM SCC-DFTB Nicoleta Bondar,1 Marcus Elstner,2 Stefan Fischer,3 Sándor Suhai,4 and Jeremy C. Smith1 1Computational Molecular Biophysics, IWR, University of Heidelberg, Germany 2University of Braunschweig, Germany 3Computational Biochemistry, IWR, University of Heidelberg 4Molecular Biophysics Department, German Cancer Research Center, Germany

2. Acknowledgements IWR, University of Heidelberg Prof. Jeremy C. Smith Dr. Stefan Fischer German Cancer Research Center Prof. Sándor Suhai University of Braunschweig Prof. Marcus Elstner University of Bremen Prof. Thomas Frauenheim €: The German Cancer Research Center (DKFZ) Heidelberg The German Research Foundation (DFG)

3. Bacteriorhodopsin proton pumping Involves proton transfers between the retinal chromophore and aspartic residues Long-distance proton transfer (~11 Å) from aspartate on the cytoplasmic side to the retinal: Short-distance proton transfer (3-4 Å) from retinal to aspartate on the extracellular side: Extracellular side Extracellular side

4. Retinal Lys216 Thr89 Asp212 w402 Asp85 Computing reaction pathways for bacteriorhodopsin proton pumping Quantum Mechanical / Molecular Mechanical QM: SCC-DFTB, B3LYP/6-31G** MM: CHARMM 10ms range 10s range ns range

5. Accuracy of SCC-DFTB in describing bacteriorhodopsin proton transfer

6. Accuracy of SCC-DFTB in describing bacteriorhodopsin proton transfer AM1, PM3, and the standard SCC-DFTB overestimate the acetate-retinal proton affinity.

7. Accuracy of SCC-DFTB in describing bacteriorhodopsin proton transfer Regardless of the basis set used, B3LYP overestimates the Schiff base proton affinity.

8. Accuracy of SCC-DFTB in describing bacteriorhodopsin proton transfer Effective error cancellation.

9. Accuracy of SCC-DFTB in describing bacteriorhodopsin proton transfer SCC-DFTB (SRP) agrees reasonably well with B3LYP/6-31G** and MP2/6-311+G** in describing the retinal-acetate relative deprotonation energy.

10. QM/MM proton transfer activation energies B3LYP/6-31G** and SCC-DFTB values agree to within 2.1 kcal/mol (rms value). Accuracy of SCC-DFTB in describing bacteriorhodopsin proton transfer QM/MM-optimized structures SCC-DFTB/MM-optimized B3LYP 6-31G**/MM-optimized

11. Retinal Lys216 Thr89 Asp212 w402 Asp85 Computing reaction pathways for bacteriorhodopsin proton pumping Reaction path calculations 1ms range 10s range ns range

12. Energy discontinuities are present in the coordinate-driving reaction path. Energy discontinuities correspond to large RMSD differences. The jumps in the structure hide high energy peaks. Normalized (protein) RMSD Computing pathways for proton transfer The difficulties of choosing the reaction coordinate d = d1 – d2

13. R P Computing pathways for proton transfer Conjugate Peak Refinement • All degrees of freedom in the protein, no driving constraints • Optimizes an initial guess of the path S1 S2 Fischer & Karplus, Chem Phys Lett 1992

14. R P Computing pathways for proton transfer Conjugate Peak Refinement • All degrees of freedom in the protein, no driving constraints • Optimizes an initial guess of the path S1 • Explore by varying the initial path S2 Fischer & Karplus, Chem Phys Lett 1992

15. Normalized reaction coordinate Computing pathways for proton transfer Conjugate Peak Refinement Coordinate driving Retinal Thr89 R Lys216 P Asp212 Asp85 w402 … many paths must be computed with different starting coordinates

16. Energetics of bacteriorhodopsin proton pumping Proton-donor group points in the direction opposite to the net transfer Proton-donor group points in the direction of the net transfer

17. Energetics of bacteriorhodopsin proton pumping Bondar, Smith, Fischer, Photochem. Photobiol. Sci. 2006 deprotonated protonated

18. Energetics of bacteriorhodopsin proton pumping Bondar, Smith, Fischer, Photochem. Photobiol. Sci. 2006 retinal reprotonation deprotonated protonated deprotonated

19. Energetics of bacteriorhodopsin proton pumping X Formation of the proton-transfer reactant state Bondar, Smith, Fischer, Photochem. Photobiol. Sci. 2006 retinal reprotonation K protonated deprotonated protonated deprotonated

20. Mechanism of the first proton transfer step Bondar,Elstner,Suhai, Smith, Fischer. Structure 2004 CP Experimental enthalpy barrier: ~13 kcal/mol (Ludman et al, Biophys J. 1998) EC Direct: E# = 12.4 kcal/mol CP CP EC EC Asp212,w402 path: E# = 11.5 kcal/mol Thr89 path: E# = 13.6 kcal/mol

21. 5 Twisted K state Twisted bR state 19 12 Directionality in the early photocycle steps cytoplasm QM/MM K-state model Energy storage 7 kcal/mol in retinal twist + 7kcal/mol in perturbation of h-bonding interactions Twisting of the retinal chain is tuned such that - Enough energy is stored to drive the photocycle - Thermal cis-trans isomerization is energetically unfavourable Bondar, Fischer, Suhai, Smith, JPCB 2005