Vision and Ultrafast Chemistry
Light
Visual signaling
Rod
G-protein signaling pathway
Rhodopsin
Cone
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
GPCR, vision in all species
Bacteriorhodopsin
Photosynthesis, proton pump
Organization of the
Purple Membrane of Halobacteria
Baudry et al,
J. Phys. Chem.
(in press)
hn
assembly
V
Ben-Nun et al
Faraday Disc.
110: 447-462 (1998)
protein
Molnar et al
J. Mol. Struct.
(in press)
molecular electronics
H+
function
Constructing and Simulating the Purple Membrane
assembly
function
protein
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Vibrational Spectroscopy (Kyoto)
Organic Synthesis (Rehovot)
Quantum Chemistry (Heidelberg)
Photophysics (Siena)
Protein Simulation (Urbana)
Pharmacolgy (New York)
molecular electronics
Molecular Dynamics Program Used: NAMD2
256
192
128
64
0
0
64
128
192
# processors
256
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.
Thermodynamics of the Purple Membrane
PM thickness
NpT simulation:
constant temperature,
variable volume
Reduction of PM
thickness during
NpT simulation
In-plane dimensions
Distribution of external water after MD
Equilibration of PM: rearrangement of water molecules
Before MD
After MD
water
protein
“c” dimension perpendicular to the membrane
Top view of PM: Water
molecules penetrate the
PM, but not the protein,
stop at Arg82 & Asp96
Asp96
retinal
Arg82
Color in Vision
cone cells
Visual receptors of rhodopsin family are
classified based on their color sensitivity
Rhodopsin Family of Proteins
• Seven transmembrane helices
• Retinal chromophore bound
to a lysine via the Schiff base
Me
Me
Me
N
Me
Me
H
protonated Schiff base retinal (PSBR)
Color Regulation
Visual receptors detect light by electronic excitation of retinal
at different wavelengths.
400nm
500nm
600nm
Absorption spectra of retinal in different visual receptors
Question:
How does the protein tune the absorption
spectrum of retinal?
Spectral Tuning in Archaeal
Rhodopsins
Sensory Rhodopsin II (sRII)
Repellent response to blue-green light
Spectral features
• Absorption maximum
is strongly blue-shifted
(70 nm from bR).
• Prominent sub-band.
sRII
hR
bR
500nm
sRI
600nm
Sequences Structures of bR and sRII
X-ray Structures of bR and sRII
Landau et al.
Unique opportunity to
study spectral shift given
by the availability of
X-ray structures.
• Structures are homologous.
(e.g., all-trans retinals)
orange: sRII (Natronobacterium pharanois)
• Spectra are significantly
purple: bR (Halobacterium salinarum)
different.
Binding Sites of bR and sRII
bR
Similar structure
• Aromatic residues.
• Hydrogen-bond network.
(counter-ion asparatates,
internal water molecules)
sRII
Mutagenic substitutions
(Shimono et al.)
T204A/V108M/G130S of
sRII produces only 20 nm
(30%) spectral shift.
What is the main determinant(s) of
spectral 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).
Mechanism of Spectral Tuning
• Electrostatic interaction between
the retinal Schiff base and protein
S2
positive charge
Me
Me
S0
S1
S2
Me
+
+
N
Me
Me
H
O
S1
S1
S0
O
C
S2
Asp (Glu)
S0
isolated
in protein
• Electronic reorganization of retinal
due to polarization of retinal’s wave function
Results
sRII
bR
500nm
600nm
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.
Contributions from Residues
Structural Determinants of
Spectral Shift
G helix is displaced
in sRII.
Distance between the
Schiff base and the
counter-ion is shorter.
G helix
N16 – Cg (Asp201: sRII) : 4.5 A
N16 – Cg (Asp212: bR) : 5.2 A
QM/MM optimized structures
orange: sRII, purple: bR
Rhodopsin Photodynamics
Quantum (Wave Packets) Dynamic
in protein, 1-dimensional surface
Ben-Nun et al., Faraday Discussion, 110, 447 - 462 (1998)
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 Topography
on the Photoisomerization of Retinal
Michal Ben-nun
Emad Tajkhorshid
Shigehito Hayashi
Jerome Baudry
$$: Beckman Institute, NSF, HFSP, NIH-NCRR