Difference between revisions of "Part:BBa K5396001"

Revision as of 17:51, 9 September 2024

Barbie1_RFP_3xMad10

BARBIE1 is a synthetic protein derived from BaCBM2 (BBa_K5396000) through a process of reverse engineering. It has the increased ability to bind to plastics when compared to BaCBM2.

The BARBIE1 protein is fused with the red fluorescent protein (RFP)[ ], which exhibits an excitation maximum at 558 nm and an emission maximum at 583 nm. This fusion enhances the visualization of BARBIE1 by fluorescence-based methods.

Protein Design

Starting from the BaCBM2 structure model generated by the AlphaFold2 software, we performed docking assays with six types of plastic: polypropylene (PP), polyethylene (PE), polyethylene terephthalate (PET), nylon (NY), polyvinyl chloride (PVC) and polystirene (PS). We made the docking using Gnina software with relaxed parameters to screen many proteins and features for plastic affinity, which was calculated as shown below, where P stands for Protein and L for Ligand

PL \xrightarrow{} P + L \quad \xrightarrow{} \quad K_D = \frac{[P][L]}{[PL]}

Thereafter, the produced overlaps were removed by the docking assays using the ChimeraX software, as well as used for visualization and sequence manipulation. A reverse folding was then performed with the protein output from the docking using the LigandMPNN tool. The original protein set generated from the docking was filtered to maintain just unique positions, considering the associated score , without overlap between them.

By doing that, 6.000 sequences were generated for each ligand, totalizing 6 plastics x 6.000 sequences = 36.000 sequences, as illustrated in Figure 1. The consensus sequence from the 36000 sequence originated our most optimized protein sequence sensitive for several plastics types named as BARBIE1!

Figure 1. Protein-ligand docking representation of the BARBIE1 protein docked with PP, PE, PET, NY, PVC.

The BARBIE1 protein was redocked with the same plastics as before, once more using Gnina software. The result comparing its affinity with BaCBM2 in silico assays performed are described in the barplot of Figure 5. Comparing the predicted affinity between the original and the modified protein, it is notable a substantial increase for all plastics, in particular for PE, PP, and PS, highlighting the effectiveness of the processing pipeline.

Besides the monomers tests, we also wanted to test the affinity using different sizes of plastic in order to guarantee that this could be a valuable parameter to future analysis and experiments. Therefore, the tested ligands were PE and PET plastics with 50 and 25 repeating units, respectively. As a result, the previous behavior at maintaining a higher KD for BARBIE1 when compared to BaCBM2 was preserved.

Sequence and Features