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NSF Summer School UIUC 2003Molecular Machines of the Living Cell : Photosynthetic Unit from Light Absorption to ATP SynthesisMelih Sener
ThorstenRitz
IoanKosztin
Ana Damjanovic Theoretical Biophysics Group
Beckman Institute
(also Sanghyun Park, Deyu Lu, and Ulrich Kleinekathoefer)
BPTI3K atoms
Estrogen Receptor36K atoms (1996)
ATP Synthase327K atoms
(2001)
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.
Molecular Machines of the
Living Cell
mitochondrion
nucleus
endoplasmic reticulum
gene storage, regulation, and expression; protein synthesis and degradation; energy conversion and storage; cell motion; cell signaling; metabolic pathways; …
Study of integral cell functions:
Animal cellPlant cell
Habitats of Photosynthetic Life Forms
Photosynthetic Apparatus of Purple Bacteria
LH-II LH-I
cytochrome c2
ATPase
cytoplasm
periplasm
ADP ATP
hbc1
H+
H+
e-
Q/QH2/Q
RC
RC - Photosynthetic Reaction Center
LH – Light Harvesting Complex
LH-II LH-I
bc1
RC
Structure of RC+LH-I+Cyt System
LH-I
RCFocussing on the Structure of RC + LH-I
cytochrome c2
QuickTime™ and aYUV420 codec decompressorare needed to see this picture.
Focussing on the Structure of RC+LH-I+Cyt
System of Water - Lipids - Protein
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Lipids only
Focussing on the Structure of RC+LH-I+Cyt
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Lipids and Proteins
Focussing on the Structure of RC+LH-I+Cyt
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Proteins only
Focussing on the Structure of RC+LH-I+Cyt
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Proteins and Chromophores
Focussing on the Structure of RC+LH-I+Cyt
QuickTime™ and aYUV420 codec decompressorare needed to see this picture.
Chromophores only
Focussing on the Structure of RC+LH-I+Cyt
QuickTime™ and aYUV420 codec decompressorare needed to see this picture.
Chromophores only
Focussing on the Structure of RC+LH-I+Cyt
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Electron Transfer Chain in RC + Cyt c Complex
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Role of the Protein Matrix on Electron Transfer
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 thesurrounding protein.
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
Protein matrix is a bath of oscillators linearlycoupled to the electron transfer according to
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.
Electron Transfer Process Coupled to the Protein Matrix
Rate for an ensemble of oscillators (spin boson model, Legett et al)
But we didn’t know all the coupling constants cj ? All we needed to know was J
Relaxation rate
Electron Transfer Process Coupled to the Protein Matrix
Relaxation rate
energy gap correlation function
energy gap
rms deviation of energy gap
from MD1989
1994
E
Temperature Dependence of Electron Transfer Rate
special pair pheophytin
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.
Electron TransferCoupling protein motion to electron transfer via MD
• 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.
Electron TransferThe energy gap function
)()()( tEtEt RP −=ε• R: reactant state (reduced)
• P: product state (oxidized)
• obtain an MD trajectory• evaluate at each frame of the first trajectory through a second NAMD run
Tutorial:
)(tε
You will do two consecutive NAMD runs.
Electron TransferMD simulation of the electron transfer process
• ~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)
kcal/mol
time(fs)
)(tε
QuickTime™ and aYUV420 codec decompressorare needed to see this picture.
Electron TransferThe energy gap function
kcal/mol
time(fs)
Result from the first 500fs
Electron TransferThe energy gap function
kcal/mol
kcal/mol
time(fs)
time(fs)
You will be given a longer trajectory…
Electron TransferThe energy gap function
kcal/mol
kcal/mol
time(fs)
time(fs)
kcal/mol
Genomic Organization of the Light Harvesting Complexes