Interactions and Mechanisms Controlling Assembly and Function of Multiprotein Systems in Membranes

1. Interactions and MechanismsControlling Assembly and Functionof Multiprotein Systems in Membranes Michal Ben-nun Ana Damjanovic Thorsten Ritz Jerome Baudry Emad Tajkhorshid Klaus Schulten Beckman Institute, University of Illinois http://www.ks.uiuc.edu

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

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

4. lipids bR monomer 2-D crystalline organization of the purple membrane ~ 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. Asp96 Arg82 Crystallographic water molecules Crystallographic water molecules in initial structure After 1 ns MD: Crystallographic water molecules diffuse outside PM, except molecules located within the Arg82 Asp96 channel (in white)

11. Asp96 retinal Arg82 Structure of the hexagonal unit cell-3 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 AXP21264-500Mhz 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 torsionalangle 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, 447-462 (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”