Team:Paris Bettencourt/Optimization

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@iGEM_Paris

Optimization

Based on the results of the Testing and Modeling groups, we arrived at the following simple model for how StarCores function.

Box 1: Why are StarCore Proteins Difficult to Express?
Based on the results of the Testing and Modeling groups, we arrived at the following simple model for how StarCores function. StarCores act by destabilizing the bacterial membrane, similar to conventional AMPs. StarCore activity is mediated by a nonspecific mechanism, probably charge. AMP-Core fusions are difficult to express, probably because the do not fold well.

With these considerations in mind, we set out to improve on the basic StarCore designs developed in the Design Section. Our method of choice was targeted saturation mutagenesis. We developed a 12 000 variant library of StarCores varying mainly in the number and location of their positive charges. We systematically screened this library for activity, then explored the key determinants of activity with a custom-made machine learning software.

We were expecting that the free AMPs behaved differently when they are fused to a protein scaffold. The previously available literature that describe free AMPs does not seem to apply for our constructs. Consequently, we choose to devise a new model for studying the optimization of fused AMPs. Therefore, we design a library of 12k variant that we attached to mCherry through a linker in order to optimize the already characterized effectiveness of core-AMPs.

Results

Design of the AMP Twist Library

At the core of the StarCore library are three AMPs: Ovispirin, X, Y. We chose to fuse each AMP to the fluorescent protein mCherry. This allowed us to easily quantify the protein expression level. It also served as a “simulated core” that allowed us to test AMP activity in the context of a large fusion protein. As we learned in the production section, protein expression and folding are critical to obtaining an effective StarCore.

We chose to focus library diversity on positively charged residues. Charge density is known to critically affect both protein folding and AMP function. Therefore, we systematically generated mutations to move, concentrate and amplify positive charges. These mutations are described in figure 1.

Screening 12 000 AMP clones for specific activity

We cloned the DNA sequence library into a T7-based expression vector and transformed it into a strain of self-lysing E. coli. Cells were grown to mid-log phase then induced for StarCore expression and self-lysis. The resulting lysates were added to fresh cultures of E. coli. Peptide expression was measured by mCherry fluorescence and effects on growth were quantified by OD.