Difference between revisions of "Part:BBa K5396004"
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<partinfo>BBa_K5396004 short</partinfo> | <partinfo>BBa_K5396004 short</partinfo> | ||
| − | This | + | This Barbie1 protein is modified with an additional amino acid (cysteine). |
| − | + | =Usage and Biology= | |
| − | == | + | |
| + | To design Barbie1 we utilized the BaCBM2 structural model generated by AlphaFold2 to conduct docking assays on six types of plastic: polypropylene (PP), polyethylene (PE), polyethylene terephthalate (PET), nylon (NY), polyvinyl chloride (PVC), and polystyrene (PS). Using Gnina software, we assessed plastic affinity with relaxed parameters, followed by the elimination of overlaps through ChimeraX for visualization and sequence manipulation. A reverse folding process was applied to the docking outputs using LigandMPNN, filtering the original protein set to retain unique positions based on their scores. This approach generated a total of 36,000 sequences (6,000 per plastic type), leading to the identification of an optimized protein sequence named '''Barbie1''', which has the increased ability to bind to plastics when compared to BaCBM2. | ||
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| + | https://static.igem.wiki/teams/5396/registry/barbie1-3d.png | ||
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| + | '''Figure 1.''' 3D simulation of Barbie1-Cys protein. | ||
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| + | The cysteine modification in the sequence allows a strong interaction between the protein and our sensor surface, due to the affinity between the SH group and the Au(111) surface. This increase in interaction with the sensor is essential for amplifying the signal of microplastics in electrochemical measurements. | ||
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| + | =Part Generation= | ||
| + | |||
| + | The Barbie1-Cys fragment was generated from a PCR reaction using primers that specifically amplify the linker-Barbie1-linker region of <partinfo>BBa_K5396001</partinfo> | ||
| + | |||
| + | The reverse primer used in this reaction adds a codon that encodes the amino acid cysteine at the end of the sequence. | ||
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Latest revision as of 20:31, 1 October 2024
Barbie1-Cys
This Barbie1 protein is modified with an additional amino acid (cysteine).
Usage and Biology
To design Barbie1 we utilized the BaCBM2 structural model generated by AlphaFold2 to conduct docking assays on six types of plastic: polypropylene (PP), polyethylene (PE), polyethylene terephthalate (PET), nylon (NY), polyvinyl chloride (PVC), and polystyrene (PS). Using Gnina software, we assessed plastic affinity with relaxed parameters, followed by the elimination of overlaps through ChimeraX for visualization and sequence manipulation. A reverse folding process was applied to the docking outputs using LigandMPNN, filtering the original protein set to retain unique positions based on their scores. This approach generated a total of 36,000 sequences (6,000 per plastic type), leading to the identification of an optimized protein sequence named Barbie1, which has the increased ability to bind to plastics when compared to BaCBM2.
Figure 1. 3D simulation of Barbie1-Cys protein.
The cysteine modification in the sequence allows a strong interaction between the protein and our sensor surface, due to the affinity between the SH group and the Au(111) surface. This increase in interaction with the sensor is essential for amplifying the signal of microplastics in electrochemical measurements.
Part Generation
The Barbie1-Cys fragment was generated from a PCR reaction using primers that specifically amplify the linker-Barbie1-linker region of BBa_K5396001
The reverse primer used in this reaction adds a codon that encodes the amino acid cysteine at the end of the sequence.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 91
- 1000COMPATIBLE WITH RFC[1000]