Coding

Part:BBa_K305003:Design

Designed by: Maarten van den Nieuwenhof, Ramon Sieber, Arend Jan Suk   Group: iGEM10_Groningen   (2010-09-27)
Revision as of 00:38, 27 October 2010 by AJ (Talk | contribs) (→‎Design Notes)

Hydrophobic protein chaplin E (chpE)


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

The RBS sequence used for this part can be found in several B. subtilis genes and is known to efficiently initiate translation. The spacer sequence between the RBS and start codon originates form the B. subtilis wapA gene. The CDS was optimized for B. subtilis by the GenScript OptimumGeneTM software (see images).

Frequency of optimal codons before optimization. The x-axis 100 value is set for the codon with the highest usage frequency for a given amino acid in B. subtilis.
Frequency of optimal codons after optimization


Structural Prediction

Structural prediction of the protein without the signaling sequence by [http://zhanglab.ccmb.med.umich.edu/I-TASSER/ I-TASSER] yielded the following results. No tertiary structure has been identified by x-ray crystallography or NMR.

[http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S49452/ structural prediction] without signaling sequence

Source

Streptomyces coelicolor genomically encoded protein, codon optimized for B. subtilis and sythesized by Mr. Gene.

References

Claessen, D; Rink, R; de Jong, W et al. 2003. A novel class of secreted hydrophobic proteins is involved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils. Genes Dev 17 1714-1726