Lead: Roth (UIUC) Abdelzaher (UIUC) Huang (UIUC) Lei (IBM) Presented by: Tarek Abdelzaher.
NSF Summer School UIUC 2003 Molecular Machines of the Living Cell : Photosynthetic Unit from Light...
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![Page 1: NSF Summer School UIUC 2003 Molecular Machines of the Living Cell : Photosynthetic Unit from Light Absorption to ATP Synthesis Melih Sener Thorsten Ritz.](https://reader036.fdocuments.us/reader036/viewer/2022062718/56649eb45503460f94bbd0a4/html5/thumbnails/1.jpg)
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)
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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.
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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
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Habitats of Photosynthetic Life Forms
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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
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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
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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
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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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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
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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.
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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.
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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
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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
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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.
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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.
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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.
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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.
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Electron TransferThe energy gap function
kcal/mol
time(fs)
Result from the first 500fs
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Electron TransferThe energy gap function
kcal/mol
kcal/mol
time(fs)
time(fs)
You will be given a longer trajectory…
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Electron TransferThe energy gap function
kcal/mol
kcal/mol
time(fs)
time(fs)
kcal/mol
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Genomic Organization of the Light Harvesting Complexes
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