Difference between revisions of "Part:BBa K5396001"

Revision as of 19:31, 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.

Computational Modeling

Proteins with carbohydrate-binding modules (CBM) can not only be found as single units but also in more units or as part of larger multi-domain proteins. In light of the importance of understanding the thermodynamics basis for structural composition, the newest version of Alpha Fold 3 (AF3) was used [doi.org/10.1038/s41586-024-07487-w]. The model was used to optimize protein-protein interaction and test high-order oligomers. To effectively model the water filter system closer to reality, the first step was to predict the state of the proteins.

The proposed proteins to be evaluated in Alpha Pulldown are the B1-CBM (pink), BaCBM2 (blue), and 1A3N (green), which is a reference protein that forms the deoxy human hemoglobin.

Figure X. Protein comparative of the tested proteins. In (a), it is shown the BARBIE1 structure, in (b) the BaCBM2, and in (c) the 1A3N protein.

With 4 subunits as shown in Figure X+1, the 1A3N multicomplex protein forms a pocket in the middle region to store oxygen molecules. Since this reference protein was resolved with more subunits, it can serve as a baseline for the prediction of the other proteins.

Figure X+1. 1A3N protein representation with four repeating units.

About the predicted template modeling (pTM) values:

Concerning the interface predicted template modeling (iPTM) values:

Figure X+2. pTM and iPTM values calculated by AlphaFold3 for BARBIE1, BaCBM2, and 1A3N with different repeating units.

As it can be seen in Figure X+2, both BARBIE1, BaCBM2, and 1A3N achieved high scores as monomers. On the other hand, only the 1A3N as a multimer achieved higher values, such as its two and three subunits iPTM, as expected. Therefore, it is possible to affirm that it is very unlikely for both B1-CBM and BaCBM2 to form a multimer, which can be assured by the deoxy human hemoglobin results. This result allows the modeling of B1-CBM as a monomer, which simplifies the system.

Sequence and Features