1. FPMOD: A 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

2. 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.

3. 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

4. Simulation Process Fusion protein construction using script-lines
Sample conformational space by rigid-body rotation

5. Conformational Space

6. Conformational Space

7. Conformational Space

8. Conformational Space

9. Conformational Space

10. 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

11. Prediction vs. Experiment
Donor emission peak
Acceptor emission peak
No Ca2+
with Ca2+
No Ca2+
With Ca2+
Change E%
17.0%
12.3%
-4.7%

12. Prediction vs. Experiment
No Ca2+
with Ca2+
No Ca2+
With Ca2+
Change E%
1.7%
3.1%
1.4%

13. 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.

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

15. QUESTIONS?