NSF Summer School UIUC 2003

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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)
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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)
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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
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Habitats of Photosynthetic Life Forms
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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
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Structure of RCLH-ICyt System
bc1
RC
LH-II
LH-I
cytochrome c2
RC
Focussing on the Structure of RC LH-I
LH-I
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Focussing on the Structure of RCLH-ICyt
System of Water - Lipids - Protein
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Focussing on the Structure of RCLH-ICyt
Lipids only
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Focussing on the Structure of RCLH-ICyt
Lipids and Proteins
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Focussing on the Structure of RCLH-ICyt
Proteins only
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Focussing on the Structure of RCLH-ICyt
Proteins and Chromophores
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Focussing on the Structure of RCLH-ICyt
Chromophores only
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Focussing on the Structure of RCLH-ICyt
Chromophores only
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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 the surrounding
protein.
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Electron Transfer Process Coupled to the Protein
Matrix
We assumed that the electron transfer QA- QB -gt
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, 29061--62, 2000.
Protein matrix is a bath of oscillators
linearly coupled to the electron transfer
according to
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Electron Transfer Process Coupled to the Protein
Matrix
Rate for an ensemble of oscillators (spin boson
model, Legett et al)
Relaxation rate
But we didnt know all the coupling constants cj
? All we needed to know was J
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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
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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, 29061--62, 2000.
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Electron Transfer
Coupling 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 Transfer
The energy gap function

• 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

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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)

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Electron Transfer
The energy gap function
kcal/mol
Result from the first 500fs
time(fs)
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Electron Transfer
The energy gap function
kcal/mol
You will be given a longer trajectory
time(fs)
kcal/mol
time(fs)
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Electron Transfer
The energy gap function
kcal/mol
kcal/mol
time(fs)
kcal/mol
time(fs)
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Genomic Organization of the Light Harvesting
Complexes
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