1. Beckman Institute, University of Illinois
Interactions and Mechanisms Controlling Assembly and Function of Multiprotein Systems in Membranes
Michal Ben-nun
Ana Damjanovic
Thorsten Ritz
Jerome Baudry
Emad Tajkhorshid
Klaus Schulten
Beckman Institute, University of Illinois

2. Organization of the Photosynthetic Unit of Purple Bacteria
assembly V H+ hn
proteins
function
molecular electronics

3. Organization of the Purple Membrane of HalobacteriaV H+ hn
assembly
function
protein
molecular electronics

4. 2-D crystalline organization of the purple membrane
bR monomer
lipids
~ 75 Å
Top and side views of the purple membrane

5. Structure of the hexagonal unit cell-1
top view
lateral view
green,blue,red : bR monomers (Essen et al., P.N.A.S., 1998)
grey : PGP extra-trimer lipids. (Pebay-Peyroula et al., Structure, 1999)
purple : squalene (Luecke et al., J. Mol. Biol., 1999)
orange : intra-trimer glycolipids (Essen et al., P.N.A.S., 1998)
yellow : intra-trimer Phosphatidyl Glycerol Phosphate lipid

6. Asymmetry of the Purple Membrane
Extracellular
intracellular
Blue : basic residues
Red : acidic residues
Green : polar residues
White : apolar residues
Grey : lipids

7. Structure of the hexagonal unit cell-2
Hydration of the unit cell
Internal hydration (Luecke et al., J. Mol. Biol., 1999)
External hydration : molecular dynamics

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

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

10. Crystallographic water molecules in initial structure
Asp96
Arg82
After 1 ns MD:
Crystallographic water molecules diffuse outside PM,
except molecules located within the Arg82 Asp96 channel (in white)

11. Structure of the hexagonal unit cell-3
Asp96
Arg82
retinal
External hydration (larger orange spheres) penetrates into bR up to the Arg82 & Asp96 levels

12. Bacteriorhodopsin Monomer
retinal
Simplest ion pump in biology
Best characterized membrane protein (GPCRs)
Simplest photosynthetic center
Several molecular electronics applications

13. Molecular Dynamics Simulations of the Purple Membrane
Molecular dynamics simulations with NAMD2
~23700 atoms per unit cell
Hexagonal unit cell
Periodic boundary conditions in 3D (multilayers)
NpT (constant pressure) simulations
Particle Mesh Ewald (no electrostatic cutoff)
~2 weeks/ns on 4 Alpha AXP Mhz procs.

14. Reaction coordinates for the conical intersection:
Torsion around C13=C14 and h- vector
Torsion and
h- vector
Conical intersection
S0 and S1 surfaces as a function of torsional angle and h- vector

15. Structures at the minima of S0 and S1 surfaces
and structure of the conical intersection
minima of S0
minima of S1
Search for conical intersection started from both optimized geometries and converged to same structure
Bond in Å, angles in degrees, (in brackets: values at the conical intersection).
Minima at S1 nearly coincides with lowest point of conical intersection
SA-CASSCF(10,10) geometry optimized on ground and excited states.

16. Quantum Dynamics on Multiple Electronic States
Description of photoprocess of retinal in protein
Full Multiple Spawning (Todd Martinez)
Final structure of a single
quantum dynamics trajectory
Other important quantum effects:
zero point energy
Specific heat
Energy relaxation
Ben-Nun et al., Faraday Discussion, 110, (1998)

17. Does water rearrangement lead to a proton switch in bR?
Asp96
13-cis retinal
after photo-isomerization N
Asp85
Asp212
Arg82
two scenarios N N
Asp85 H+
Asp85
Arg82
Arg82
Water coming from cytoplasmic channel, Arg82 “down”
Water coming from extracellular channel, Arg82 “up”