Coding

Part:BBa_K1462480:Design

Designed by: zhanru Chen   Group: iGEM14_SCUT   (2014-10-10)

PDZ Ligand


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

This is the PDZ ligand of the PDZ protein. The PDZ ligand, with the fusion of the PDZ domain , we can use it as a binding unit to built up the scaffold protein that contains the funtion we want. We hope that we can use it to combine the CA and funtion as the part of the carbon capture.

Source

At the date of 7th, July, we did the overlap PCR to get this gene with the help of our designed primer.
Upstream primer: GTTTCTTCGAATTCGCGGCCGCTTCTAGAGGTGTCAAGGAGTCTTTGGTC
Downstream primer：GTTTCTTCCTGCAGCGGCCGCTACTAGTGACCAAAGACTCCTTGACACC

We added the RFC 23 beside the PDZ ligand. After doing the PCR, it could be added after the targeted enzyme.

References

[1] John E Dueber, Gabriel C Wu, G Reza Malmirchegini, et al.Synthetic protein scaffolds provide modular control over metabolic flux.Nat Biotechnol. 2009 Aug;27(8):753-9.
[2] Schultz, J. et al. Specific interactions between the syntrophin PDZ domain and voltage-gated sodium channels. Nat Struct Biol 5, 19-24 (1998).
[3] Kim, A.S., Kakalis, L.T., Abdul-Manan, N., Liu, G.A. & Rosen, M.K. Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein. Nature 404, 151-158 (2000).
[4] Wu, X. et al. Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. Structure 3, 215-226 (1995).
[5] Harris, B.Z., Hillier, B.J. & Lim, W.A. Energetic determinants of internal motif recognition by PDZ domains. Biochemistry 40, 5921-5930 (2001).
[6] Dueber, J.E., Yeh, B.J., Chak, K. & Lim, W.A. Reprogramming control of an allosteric signaling switch through modular recombination. Science 301, 1904-1908 (2003).
[7] Nguyen, J.T., Turck, C.W., Cohen, F.E., Zuckermann, R.N. & Lim, W.A. Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science 282, 2088-2092 (1998).