Coding

Part:BBa_K2141001

Designed by: Altug Uludag, Nedim Haciosmanoglu, Galip Can Guclu, Yagmur Guneri, Melis Akgun   Group: iGEM16_Istanbul_Tech   (2016-10-04)

Clover-aSN(1-60)-mRuby2

This part is designed for detection of methamphetamine by using meth-binding, truncated alpha-synuclein (aSN) protein, which changes conformation when methamphetamine is bound. Two fluorescent proteins, CloverGFP and mRuby2, present in our design to obtain FRET signal. CloverGFP and mRuby2 were reported as one of the most effective FRET couples.


Clover - alpha synuclein (1-60) - mRuby2 complex


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 1726
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 1030

Characterization

Molecular Dynamic Simulations

We used CHARMM force field and NAMD software to simulate our model. Representation of our model can be seen in the figures below, obtained by NAMD.

ASN NAMD.png

After 100 ns simulation time, with friction force at the terminals of the alpha-synuclein to represent the fluorescent proteins, we obtained the result that alpha-synuclein is suitable for FRET system. We plot the distance graph performed with VMD software, result is shown below.

ASN FRET graph.png

References

Tavossoly et al., 2012 / Imamura et al., 2009

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