Difference between revisions of "Part:BBa J58105:Design"
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===Design Notes===
 
===Design Notes===
 
[[Image:vanbp2.png|thumb|300px|Open and closed conformation of synthetic vanilline binding protein designed using an automatic computational design procedure.]]
 
[[Image:vanbp2.png|thumb|300px|Open and closed conformation of synthetic vanilline binding protein designed using an automatic computational design procedure.]]
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We have used a structure for the closed rbsB (D-ribose binding protein, periplasmic) which has an x-ray structure with pdb 2DRI (271 residues).
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We have used a structure for the closed rbsB (D-ribose binding protein, periplasmic) which has an x-ray structure with pdb 2DRI (271 residues). The vanilline molecule has a small structure and is not so different from the TNT and other ligands used by the designs of Hellinga.[[Image:vanilline.png|thumb|100px|Vanilline molecule.]]
  
  

Revision as of 23:20, 29 October 2006

Synthetic periplasmic binding protein that docks a vanillin molecule


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

Open and closed conformation of synthetic vanilline binding protein designed using an automatic computational design procedure.
We have used a structure for the closed rbsB (D-ribose binding protein, periplasmic) which has an x-ray structure with pdb 2DRI (271 residues). The vanilline molecule has a small structure and is not so different from the TNT and other ligands used by the designs of Hellinga.
Vanilline molecule.


Source

We have followed the work of Prof. Hellinga [1] but using the methodology of [2].

References

[1] L.L. Looger, M.A. Dwyer, J. Smith, H.W. Hellinga. Computational design of receptor and sensor proteins with novel functions. Nature, 423, 185-190 (2003).

[2] A. Jaramillo, L. Wernisch, S. Hery and S.J. Wodak. Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc. Natl. Acad. Sci. 99 (2002), 13554-13559.