1. Vision and Ultrafast Chemistry

2. Cone Rod Light Rhodopsin Visual signaling G-protein signaling pathway

3. Visual Receptor Protein Rhodopsin Humphrey et. al., J. Molec. Graphics, 14:33-38, 1996 Freely available, with source code from http://www.ks.uiuc.edu/Research/vmd/

4. RhodopsinBacteriorhodopsin GPCR, vision in all speciesPhotosynthesis, proton pump

5. V H+H+ h assembly protein function molecular electronics Organization of the Purple Membrane of Halobacteria Baudry et al, J. Phys. Chem. (in press) Ben-Nun et al Faraday Disc. 110: 447-462 (1998) Molnar et al J. Mol. Struct. (in press)

6.  Vibrational Spectroscopy (Kyoto)  Organic Synthesis (Rehovot)  Quantum Chemistry (Heidelberg)  Photophysics (Siena)  Protein Simulation (Urbana)  Pharmacolgy (New York) assembly protein function Constructing and Simulating the Purple Membrane molecular electronics

7. Molecular Dynamics Program Used: NAMD2 # processors hexagonal unit cell 23700 atoms per unit cell Periodic boundary conditions in 3D (multilayers); NpT (constant pressure) simulations; Particle Mesh Ewald (no electrostatic cutoff); ~2 weeks/ns on 4 Alpha AXP21264-500Mhz procs.

8. NpT simulation: constant temperature, variable volume Reduction of PM thickness during NpT simulation PM thickness In-plane dimensions Thermodynamics of the Purple Membrane

9. “c” dimension perpendicular to the membrane Nb of atoms Before MD After MD water protein Distribution of external water after MD Top view of PM: Water molecules penetrate the PM, but not the protein, stop at Arg82 & Asp96 Equilibration of PM: rearrangement of water molecules Asp96 Arg82 retinal

10. Color in Vision Visual receptors of rhodopsin family are classified based on their color sensitivity cone cells

11. Rhodopsin Family of Proteins protonated Schiff base retinal (PSBR) Seven transmembrane helices Retinal chromophore bound to a lysine via the Schiff base

12. Color Regulation 500nm600nm400nm Absorption spectra of retinal in different visual receptors Visual receptors detect light by electronic excitation of retinal at different wavelengths. Question: How does the protein tune the absorption spectrum of retinal?

13. Repellent response to blue-green light Spectral Tuning in Archaeal Rhodopsins sRII bR hR sRI 500nm600nm Spectral features Absorption maximum is strongly blue-shifted (70 nm from bR). Prominent sub-band. Sensory Rhodopsin II (sRII)

14. Sequences Structures of bR and sRII

15. X-ray Structures of bR and sRII Landau et al. orange: sRII (Natronobacterium pharanois) purple: bR (Halobacterium salinarum) Unique opportunity to study spectral shift given by the availability of X-ray structures. Structures are homologous. (e.g., all-trans retinals) Spectra are significantly different.

16. Binding Sites of bR and sRII bR sRII Similar structure Aromatic residues. Hydrogen-bond network. (counter-ion asparatates, internal water molecules) T204A/V108M/G130S of sRII produces only 20 nm (30%) spectral shift. Mutagenic substitutions (Shimono et al.) What is the main determinant(s) of spectral tuning?

17. Calculation of Absorption Spectra of bR and sRII Combined quantum mechanical/molecular mechanical (QM/MM) calculations. Retinal is described by ab initio MO (HF/CASSCF). Protein environment by molecular mechanics force field (AMBER94).

18. S2S2 S0S0 S1S1 S0S0 S1S1 S2S2 isolatedin protein Mechanism of Spectral Tuning Electrostatic interaction between the retinal Schiff base and protein Electronic reorganization of retinal due to polarization of retinal’s wave function S0S0 S1S1 S2S2 + + positive charge O C O Asp (Glu)

19. Results S 1 -S 0 : 6.1 (exp. 7.2) kcal/mol. (shift of main absorption band) The shift is mainly due to electronic reorganization. S 2 -S 1 : 1.7 (exp. 4.0) kcal/mol. (appearance of side band in sRII) Optically forbidden in bR, but a peak (side-band) appears in sRII due to intensity borrowing from the S 1 state, which is optically allowed. 500nm bR sRII 600nm

20. Contributions from Residues

21. Structural Determinants of Spectral Shift N 16 – C  (Asp201: sRII) : 4.5 A N 16 – C  (Asp212: bR) : 5.2 A QM/MM optimized structures orange: sRII, purple: bR G helix G helix is displaced in sRII. Distance between the Schiff base and the counter-ion is shorter.

22. Quantum (Wave Packets) Dynamic in protein, 1-dimensional surface Ben-Nun et al., Faraday Discussion, 110, 447 - 462 (1998) Rhodopsin Photodynamics

23. Calculation of transition amplitude

28. Control of Branching Ratios by Intersection Topography

29. On-the-fly ab initio QM/MM MD Simulation An analogue of retinal (three double bonds) in bR (20 QM atoms, 96 basis functions) CASSCF (6,6) / AMBER

30. The Role of Conical Intersection Topography on the Photoisomerization of Retinal Emad Tajkhorshid Jerome Baudry Michal Ben-nun $$: Beckman Institute, NSF, HFSP, NIH-NCRR Shigehito Hayashi