MODELING AWARD CONTENT
Placement of the Downstream box for amilCP
In this project we want to produce a bacterium expressing amilCP only at low temperature. The majority of the 5’ regulatory sequence, the cspA 5’UTR, is upstream of the start codon. However, a small but important sequence motif, called the DS box, is present after the start codon, and is translated as part of the target protein. Therefore, it is important to consider the structure and function of the target protein, particularly the N-terminal region, in order to correctly place the DS box insertion so that it does not alter the structure or function. However, there is no experimental structure for amilCP. Therefore, we use a computational approach, homology modeling, to create a model of amilCP and identify a safe insertion site in the sequence that would not alter the structure.