Vision and Ultrafast Chemistry

ConeRod

Light

Rhodopsin

Visual signaling

G-protein signaling pathway

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/

Rhodopsin Bacteriorhodopsin

GPCR, vision in all species Photosynthesis, proton pump

V

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 alFaraday Disc.110: 447-462 (1998)

Molnar et alJ. Mol. Struct.(in press)

Vibrational Spectroscopy (Kyoto)Vibrational Spectroscopy (Kyoto) Organic Synthesis (Rehovot)Organic Synthesis (Rehovot) Quantum Chemistry (Heidelberg)Quantum Chemistry (Heidelberg) Photophysics (Siena)Photophysics (Siena) Protein Simulation (Urbana)Protein Simulation (Urbana) Pharmacolgy (New York)Pharmacolgy (New York)

assembly

proteinfunction

Constructing and Simulating the Purple Membrane

molecular electronics

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.

0

64

128

192

256

0 64 128 192 256

NpT simulation: constant temperature, variable volume

Reduction of PM thickness duringNpT simulation

PM thickness

In-plane dimensions

Thermodynamics of the Purple Membrane

“c” dimension perpendicular to the membrane

Nb

of a

t om

s

Before MDAfter 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

Arg82retinal

Color in Vision

Visual receptors of rhodopsin family are classified based on their color sensitivity

cone cells

Rhodopsin Family of Proteins

protonated Schiff base retinal (PSBR)

• Seven transmembrane helices• Retinal chromophore bound to a lysine via the Schiff base

NMeMeMeMeMeH

Color Regulation

500nm 600nm400nm

Absorption spectra of retinal in different visual receptors

Visual receptors detect light by electronic excitation of retinalat different wavelengths.

Question:How does the protein tune the absorption

spectrum of retinal?

Repellent response to blue-green light

Spectral Tuning in Archaeal Rhodopsins

sRIIbR

hRsRI

500nm 600nm

Spectral features• Absorption maximum is strongly blue-shifted (70 nm from bR).• Prominent sub-band.

Sensory Rhodopsin II (sRII)

Sequences Structures of bR and sRII

X-ray Structures of bR and sRII

Landau et al.

orange: sRII (Natronobacterium pharanois)

purple: bR (Halobacterium salinarum)

Unique opportunity to study spectral shift givenby the availability of X-ray structures.

• Structures are homologous. (e.g., all-trans retinals)• Spectra are significantly different.

Binding Sites of bR and sRIIbR

sRII

Similar structure• Aromatic residues.• Hydrogen-bond network. (counter-ion asparatates, internal water molecules)

T204A/V108M/G130S ofsRII produces only 20 nm (30%) spectral shift.

Mutagenic substitutions(Shimono et al.)

What is the main determinant(s) ofspectral tuning?

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).

S2

S0

S1

S0

S1

S2

isolated in 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

S0

S1

S2+ +

positive charge

OC

O

Asp (Glu)

NMeMeMeMeMeH

Results

S1-S0 : 6.1 (exp. 7.2) kcal/mol. (shift of main absorption band) The shift is mainly due to electronic reorganization. S2-S1 : 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 S1 state, which is optically allowed.

500nm

bRsRII

600nm

Contributions from Residues

Structural Determinants of Spectral Shift

N16 – C(Asp201: sRII) : 4.5 A

N16 – C(Asp212: bR) : 5.2 A QM/MM optimized structuresorange: sRII, purple: bR

G helix

G helix is displaced in sRII.

Distance between the Schiff base and the counter-ion is shorter.

Quantum (Wave Packets) Dynamicin protein, 1-dimensional surface

Ben-Nun et al., Faraday Discussion, 110, 447 - 462 (1998)

Rhodopsin Photodynamics

Calculation of transition amplitude

Control of Branching Ratios by Intersection Topography

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

The Role of Conical Intersection Topographyon the Photoisomerization of Retinal

Emad Tajkhorshid

Jerome Baudry

Michal Ben-nun

$$: Beckman Institute, NSF, HFSP, NIH-NCRR

Shigehito Hayashi