Interactions and MechanismsControlling Assembly and Function

of Multiprotein Systems in Membranes

Klaus SchultenBeckman Institute, University of Illinois

http://www.ks.uiuc.edu

Ana Damjanovic Thorsten Ritz

Emad TajkhorshidJerome Baudry

Michal Ben-nun

V

H+h

molecular electronics

proteins function

assembly

Organization of the Photosynthetic Unit of Purple Bacteria

V

H+h

assembly

protein function

molecular electronics

Organization of the Purple Membrane of Halobacteria

2-D crystalline organization of the purple membrane

bR monomer

lipids

~ 75 Å

Top and side views of the purple membrane

Structure of the hexagonal unit cell-1

•greengreen,,blueblue,,redred : bR monomers (Essen et al., P.N.A.S., 1998)•greygrey : PGP extra-trimer lipids. (Pebay-Peyroula et al., Structure, 1999)•purplepurple : squalene (Luecke et al., J. Mol. Biol., 1999)•orangeorange : intra-trimer glycolipids (Essen et al., P.N.A.S., 1998)•yellowyellow : intra-trimer Phosphatidyl Glycerol Phosphate lipid

top view lateral view

Asymmetry of the Purple Membrane

Extracellular

BlueBlue : basic residuesRedRed : acidic residues

GreenGreen : polar residuesWhiteWhite : apolar residues

GreyGrey : lipids

intracellular

Structure of the hexagonal unit cell-2Hydration of the unit cell

•Internal hydration (Luecke et al., J. Mol. Biol., 1999)•External hydration : molecular dynamics

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

Crystallographic water molecules in initial

structure

Asp96

Arg82

Crystallographic water molecules

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

Structure of the hexagonal unit cell-3

External hydration (larger orange spheres) penetrates into bR up to the Arg82 & Asp96 levels

Asp96

Arg82

retinal

•Simplest ion pump in biology•Best characterized membrane protein (GPCRs)•Simplest photosynthetic center•Several molecular electronics applications

Bacteriorhodopsin Monomer

retinal

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 AXP21264-500Mhz procs.

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

Structures at the minima of S0 and S1 surfacesand 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.

Quantum Dynamics on Multiple Electronic States

Description of photoprocess of retinal in protein

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, 447-462 (1998)

Full Multiple Spawning (Todd Martinez)

Asp96

Arg82

Asp212Asp85

N

Asp85

Asp85Arg82 Arg82

NN

H+

Does water rearrangement lead to a proton switch in bR?

13-cis retinal after photo-isomerization

Water coming from cytoplasmic channel, Arg82 “down”

Water coming from extracellular channel, Arg82 “up”

two scenarios