Structure-Function Relationship of Retinal Proteins

1
Structure-Function Relationship of Retinal
Proteins
2
Structure of Retinal Proteins
C
F
B
A
D
E
G
GPCRs
Retinal proteins or rhodopsins belong to the
superfamily of seven-transmembrane helical (7TM)
proteins. Seven helices, with N-terminus on the
extracellular side and C-terminus on the
cytoplasmic side of the membrane (not necessarily
G-protein coupled)
3
Retinal Proteins -- Rhodopsins

• Covalently linked to a lysine
• Usually protonated Schiff base
• all-trans and 11-cis isomers

Chromophore
4
Bacteriorhodopsin -- bR

• The simplest ion pump in biology

• The simplest photosynthetic center

• The best characterized membrane protein

• Technological applications in molecular
  electronics

• The first membrane protein with a known
  atomic-detail 3D structures

5
bR role in Bioenergetics
ATP
ADP
ATP Synthase
6
Schematic proton path in bacteriorhodopsin
Cytoplasmic side
Transmambrane helices
Transmambrane helices
Extracellular side
7
Active Channels Need a Switch Mechanism
H
H
H
hn
H
H
H
H
H
H
H
H
H
H
H
What is the switch in bR? How does it work?
8
Photocycle of bR
Photo-induced
5 ms
3 ps
1 ms
5 ms
40 ms
5 ms
All intermediates are trapped in low temperature
and have been characterized by vibrational and
absorption spectroscopy.
9
No membrane protein has been studied as
extensively as bR
Photo-induced
5 ms
3 ps
1 ms
5 ms
40 ms
5 ms
All intermediates have also been characterized by
X-ray crystallography!
10
Schematic proton path in bacteriorhodopsin
Cytoplasmic side
Transmambrane helices
Transmambrane helices
Extracellular side
11
BRs Photocycle
HOOC-D96
bR568

K216
N
H
D85-COO
cytoplasmic
5ms
HOOC-E204
3ps
K603
O645
H
HOOC-D96
HOOC-D96

H
K216
N
N

H
K216
D85-COO
D85-COOH
HOOC-E204
OOC-E204
1ms
5ms
OOC-D96
HOOC-D96
H

K216
N
N

K216
H
D85-COOH
D85-COO
OOC-E204
HOOC-E204
L543
N550
40ms
5ms
HOOC-D96
extracellular
N
light driven proton pump
K216
D85-COOH
M410
OOC-E204
12
BRs Photocycle
HOOC-D96
bR568

K216
N
H
D85-COO
5ms
HOOC-E204
3ps
K603
O645
HOOC-D96
HOOC-D96

H
K216
N
N

H
K216
D85-COO
D85-COOH
HOOC-E204
OOC-E204
1ms
5ms
OOC-D96
HOOC-D96
H

K216
N
N

K216
H
D85-COOH
D85-COO
OOC-E204
HOOC-E204
L543
N550
40ms
5ms
HOOC-D96
N
Conformational Change of Helices
K216
D85-COOH
M410
Kuhlbarandt, Nature, 406,569 (2000)
OOC-E204
13
Study of bR at three levels

• ?Chromophore
• Analysis of the structure
• Calculation of excited state dynamics

• ?Protein
• Chromophore-protein interaction
• QM-MM calculations
• MD simulation of the photocycle

?bR in the purple membrane Modeling of the
protein in lipid bilayers
14
Retinoids
Retinal Schiff base Membrane, covalently bound,
chromophore
Retinoic Acid Nucleus, receptor site, ligand (no
photoactivity)
15
Unconventioanl chemistry
The necessity of quantum mechanical treatment of
the chromophore Conjugated p-electronic system,
delocalization The effect of protein matrix on
the ligand
QM is expensive Most of the time, one needs to
use models
16
Effect of Conjugation on pKa (Gas Phase Proton
Affinity)
Proton Affinity PA EAH-(EAEH)
17
Effect of the methyl groups on pKa
Proton Affinity PA EAH-(EAEH)
No more room for additional methyl groups on the
backbone
18
What is the effect of isomerization?
19
Isomerization State and Proton Affinity
Proton Affinity PA EAH-(EAEH)
cc B2,B3-di-cis isomer ct B2-s-cis, B3-trans
isomer tc B2-strans, B3-cis isomer tt all-trans
isomer.
Isomerization does not have a strong impact on PA!
20
What is the effect of isomerization?
21
Retinal binding pocket in bR
Counterion Asp85 Asp212
WATER
22
Effect of the environment on PA
Proton Affinity PA EAH-(EAEH)
23
In situ isomerization and pKa
24
Coupling of electronic excitation and
conformational change in bR
13
7
9
11
15
25
Ground and Excited State Potential Energy
Surfaces of Retinal
trans
cis
26
Ab Initio QM/MM Excited State MD Simulation
QM
Quantum mechanical (QM) treatment of the
chromophore, and force field (MM) treatment of
the embedding protein
27
Isomerization Barriers in retinal
Proton Affinity PA EAH-(EAEH)
Ground state isomerization
Low barriers against double bond isomerization
28
A twisted chromophore in bR?

• A twisted chromophore is also experimentally
  reported.
• X-ray structures of bR report the twisted form of
  chromophore
• The twist is found around the terminal double
  bonds
• It may influence pKa of the chromophore