FPMOD: A Modeling Tool for Sampling the Conformational Space of Fusion Proteins

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FPMODA Modeling Tool for Sampling the
Conformational Space of Fusion Proteins

• Jason Chiang
• Department of Electrical and Computer Engineering
• Institute of Biomaterials and Biomedical
  Engineering
• June 9, 2006

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MOTIVATION

• The existing modeling tools that can either
  create fusion proteins or sample conformational
  space, but none of them can do both tasks in a
  single platform.
• Once the conformational space is known, the
  average conformation for one fusion protein can
  then be predicted and so do their behaviors.
• Therefore, we developed a software called FPMOD
  (Fusion Protein MODeler).
• As a demonstration, FPMOD was used to predict the
  FRET efficiency changes of different FRET Ca2
  protein biosensors, which is one of the main
  interest of our lab.
• We verify the functionality of FPMOD by comparing
  the predicted simulation results to the in vitro
  experimental data.

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Fluorescence Resonance Energy Transfer

• transfer of energy between donor and acceptor
  fluorescent proteins with partial spectral
  overlap
• Efficiency of FRET is distance- and
  orientation-dependent

http//probes.invitrogen.com/handbook/boxes/0422.h
tml
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Simulation Process

• Fusion protein construction using script-lines
• Sample conformational space by rigid-body rotation

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Conformational Space
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Conformational Space
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Conformational Space
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Conformational Space
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Conformational Space
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RESULTS AND DISCUSSION

• So, we designed two FRET Ca2 biosensor models,
  simulated their E changes due to Ca2-induction
  using FPMOD, and compared the simulation results
  to in vitro experimental data

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Prediction vs. Experiment
Acceptor emission peak
Donor emission peak
No Ca2
with Ca2
No Ca2 With Ca2 Change
E 17.0 12.3 -4.7
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Prediction vs. Experiment
No Ca2
with Ca2
No Ca2 With Ca2 Change
E 1.7 3.1 1.4
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CONCLUSIONS

• We developed a modeling tool called FPMOD to
  sample the possible conformations of fusion
  proteins using rigid-body domain rotation
  algorithms.
• FPMOD was then used to predict the E changes of
  FRET Ca2 biosensors and the results were
  qualitatively consistent with in vitro
  experimental data
• In the future, each fusion protein conformation
  will be quantitatively evaluated based on free
  energy, where lower energy is favored. Therefore,
  the sampled conformational space would account
  for protein forces such as van der Waals and
  electrostatic forces, as well.

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ACKNOWLEDGEMENTS

• Supervisor Dr. Kevin Truong
• Lab members Isaac Li Elizabeth Pham
• National Science and Engineering Research Council
  (NSERC)
• Canadian Foundation of Innovation (CFI)

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QUESTIONS?