Coding

Part:BBa_K1462470:Design

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

SH3 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 SH3 ligand of the SH3 protein. The SH3 ligand, with the fusion of the SH3 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 RuBiSco and funtion as the part of the carbon capture.


Source

PCR from our designed primer. The sequence is from the paper.At the date of 7th, July, we did the overlap PCR to get this gene with the help of our designed primer.
Upstream primer: GTTTCTTCGAATTCGCGGCCGCTTCTAGACCACCACCAGCTTTGCCACCAAAGAGAAG
Downstream primer：GTTTCTTCCTGCAGCGGCCGCTACTAGTTCTTCTTCTCTTTGGTGGCAAAGCTGGTG

We added the RFC 23 beside the SH3 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).