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NSF Summer School UIUC 2003 Molecular Machines of the Living Cell : Photosynthetic Unit from Light Absorption to ATP S

NSF Summer School UIUC 2003 Molecular Machines of the Living Cell : Photosynthetic Unit from Light Absorption to ATP Synthesis. Ioan. Melih . Thorsten. Kosztin. Sener. Beckman Institute. Ritz. Theoretical Biophysics Group. Ana . Damjanovic.

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NSF Summer School UIUC 2003 Molecular Machines of the Living Cell : Photosynthetic Unit from Light Absorption to ATP S

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  1. NSF Summer School UIUC 2003 Molecular Machines of the Living Cell : Photosynthetic Unit from Light Absorption to ATP Synthesis Ioan Melih Thorsten Kosztin Sener Beckman Institute Ritz Theoretical Biophysics Group Ana Damjanovic (also Sanghyun Park, Deyu Lu, and Ulrich Kleinekathoefer)

  2. Research Opportunities in the Teraflop Era Towards Larger Molecules • Studying protein-protein and protein-nucleic acid recognition and assembly. • Investigating integral functional units (membrane proteins, signal transduction, motors, bioenergetic apparatus). • Bridging the gap between computationally feasible and functionally relevant time scales. • Combining classical molecular dynamics simulations with quantum chemical forces. • Describing integral cell functions. BPTI 3K atoms Estrogen Receptor 36K atoms (1996) ATP Synthase 327K atoms (2001)

  3. Molecular Machines of the Living Cell nucleus Animal cell Plant cell endoplasmic reticulum mitochondrion Study of integral cell functions: gene storage, regulation, and expression;protein synthesis and degradation;energy conversion and storage;cell motion;cell signaling;metabolic pathways; …

  4. Habitats of Photosynthetic Life Forms

  5. Photosynthetic Apparatus of Purple Bacteria H+ ADP ATP cytoplasm Q/QH2/Q hn ATPase bc1 RC LH-II LH-I periplasm e- H+ cytochrome c2 RC - Photosynthetic Reaction Center LH – Light Harvesting Complex

  6. Structure of RC+LH-I+Cyt System bc1 RC LH-II LH-I cytochrome c2 RC Focussing on the Structure of RC + LH-I LH-I

  7. Focussing on the Structure of RC+LH-I+Cyt System of Water - Lipids - Protein

  8. Focussing on the Structure of RC+LH-I+Cyt Lipids only

  9. Focussing on the Structure of RC+LH-I+Cyt Lipids and Proteins

  10. Focussing on the Structure of RC+LH-I+Cyt Proteins only

  11. Focussing on the Structure of RC+LH-I+Cyt Proteins and Chromophores

  12. Focussing on the Structure of RC+LH-I+Cyt Chromophores only

  13. Focussing on the Structure of RC+LH-I+Cyt Chromophores only

  14. Electron Transfer Chain in RC + Cyt c Complex

  15. Role of the Protein Matrix on Electron Transfer

  16. Role of Thermal Disorder on Electron Transfer in the Photosynthetic Reaction Center We wanted to describe how electron transfer is coupled to the thermal motion of the surrounding protein.

  17. Electron Transfer Process Coupled to the Protein Matrix We assumed that the electron transfer QA- QB -> QA QB- is coupled to an ensemble of oscillators representing the protein matrix Hamiltonian Dong Xu and Klaus Schulten. Chemical Physics, 182: 91--117, 1994. Klaus Schulten. In D. Bicout and M. J. Field, editors, Proc. Ecole de Physique des Les Houches, pp 85--118, Les Editions de Physique, Springer, Paris, 1995. Klaus Schulten. Science, 290:61--62, 2000. Protein matrix is a bath of oscillators linearly coupled to the electron transfer according to

  18. Electron Transfer Process Coupled to the Protein Matrix Rate for an ensemble of oscillators (spin boson model, Legett et al) Relaxation rate But we didn’t know all the coupling constants cj ? All we needed to know was J

  19. Electron Transfer Process Coupled to the Protein Matrix Relaxation rate 1994 E energy gap from MD 1989 energy gap correlation function rms deviation of energy gap

  20. Temperature Dependence of Electron Transfer Rate special pairpheophytin Dong Xu and Klaus Schulten. Chemical Physics, 182: 91--117, 1994. Klaus Schulten. In D. Bicout and M. J. Field, editors, Proc. Ecole de Physique des Les Houches, pp 85--118, Les Editions de Physique, Springer, Paris, 1995. Klaus Schulten. Science, 290:61--62, 2000.

  21. Coupling protein motion to electron transfer via MD Electron Transfer • Cytochrome c2 from purple bacterium Rhodobacter sphaeroides. • Serves as electron carrier between bc1-complex and reaction center When the gene encoding cytochrome c2 is deleted from Rb. sphaeroides, the bacterium is unable to grow photosynthetically.

  22. The energy gap function Electron Transfer • R: reactant state (reduced) • P: product state (oxidized) Tutorial: You will do two consecutive NAMD runs. • obtain an MD trajectory • evaluate at each frame of the first trajectory through a second NAMD run

  23. Electron Transfer MD simulation of the electron transfer process kcal/mol time(fs) • ~12000 atoms solvated system • Already minimized and equilibrated • You will continue from a restart file • (so, you do not need to worry about velocity relaxation)

  24. Electron Transfer The energy gap function kcal/mol Result from the first 500fs time(fs)

  25. Electron Transfer The energy gap function kcal/mol You will be given a longer trajectory… time(fs) kcal/mol time(fs)

  26. Electron Transfer The energy gap function kcal/mol kcal/mol time(fs) kcal/mol time(fs)

  27. Genomic Organization of the Light Harvesting Complexes

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