* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Molecular Dynamics Simulations of the Purple Membrane
Theories of general anaesthetic action wikipedia , lookup
History of molecular evolution wikipedia , lookup
SNARE (protein) wikipedia , lookup
Lipid bilayer wikipedia , lookup
G protein–coupled receptor wikipedia , lookup
Multi-state modeling of biomolecules wikipedia , lookup
Protein adsorption wikipedia , lookup
Circular dichroism wikipedia , lookup
Implicit solvation wikipedia , lookup
Protein–protein interaction wikipedia , lookup
Size-exclusion chromatography wikipedia , lookup
Biochemistry wikipedia , lookup
Nuclear magnetic resonance spectroscopy of proteins wikipedia , lookup
Signal transduction wikipedia , lookup
Photosynthetic reaction centre wikipedia , lookup
Western blot wikipedia , lookup
Cell-penetrating peptide wikipedia , lookup
Endomembrane system wikipedia , lookup
Cell membrane wikipedia , lookup
Interactions and Mechanisms Controlling Assembly and Function of Multiprotein Systems in Membranes Michal Ben-nun Jerome Baudry Ana Damjanovic Emad Tajkhorshid Klaus Schulten Beckman Institute, University of Illinois http://www.ks.uiuc.edu Thorsten Ritz Organization of the Photosynthetic Unit of Purple Bacteria assembly hn proteins function molecular electronics H+ V Organization of the Purple Membrane of Halobacteria hn V assembly protein molecular electronics H+ function 2-D crystalline organization of the purple membrane lipids ~ 75 Å bR monomer Top and side views of the purple membrane 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 Asymmetry of the Purple Membrane Extracellular Blue : basic residues Red : acidic residues Green : polar residues White : apolar residues Grey : lipids intracellular 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 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 Crystallographic water molecules 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) Structure of the hexagonal unit cell-3 Asp96 retinal Arg82 External hydration (larger orange spheres) penetrates into bR up to the Arg82 & Asp96 levels Bacteriorhodopsin Monomer retinal •Simplest ion pump in biology •Best characterized membrane protein (GPCRs) •Simplest photosynthetic center •Several molecular electronics applications 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 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. 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) Does water rearrangement lead to a proton switch in bR? Asp96 13-cis retinal after photo-isomerization N Asp85 Asp212 Arg82 N two scenarios N Asp85 H+ Arg82 Water coming from cytoplasmic channel, Arg82 “down” Asp85 Arg82 Water coming from extracellular channel, Arg82 “up”