Part:BBa_K3461001
Mutated Phage P2 That Binds to S. pyogenes
This part is the mutated version of phage P2, one of the 418 different "mutated" versions. We sequenced this part in order to to identify specific properties of mutated Phage P2 that are able to bind to S. pyogenes.
To do this, we utilized three different softwares: The Scripps Research Insitute’s Autodock Vina, BIOVIA Discovery Studio, and MODELLER. Autodock Vina is the main tool we used to predict the binding affinity between the phage and the bacteria. Therefore, the first step was to validate the software as well as having the binding affinity for the control group. The Scripps Research Insitute’s Autodock Vina was validated as we docked Phage P2 with the receptor of its natural host, Lactococcus lactis. This also serves as our control group. However, the 3D model of the macromolecule on L. lactis in which Phage P2 binds onto wasn’t available. Therefore, utilizing previous research and 2D structures of the macromolecule from A dual-chain assembly pathway generates the high structural diversity of cell-wall polysaccharides in Lactococcus lactis, we were able to model the receptor by utilizing BIOVIA Discovery Studio to predict possible bond angles. Hence, we were able to computationally model a three-dimensional structure of the L. lactis receptor. The Scripps Research Insitute’s Autodock Vina was validated as we docked Phage P2 with the receptor of its natural host, Lactococcus lactis. This also serves as our control group. However, the 3D model of the macromolecule on L. lactis in which Phage P2 binds onto wasn’t available. Therefore, utilizing previous research and 2D structures of the macromolecule from A dual-chain assembly pathway generates the high structural diversity of cell-wall polysaccharides in Lactococcus lactis, we were able to model the receptor by utilizing BIOVIA Discovery Studio to predict possible bond angles. Hence, we were able to computationally model a three-dimensional structure of the L. lactis receptor. <p>This mutated version of phage P2 is one of the 418 different "mutated" versions. Initially, we docked Phage P2 with S. Pyogenes and found the binding affinity to be -4.5 kcal/mol. This is relatively low compared to the docking of Phage P2 with its natural host Lactococcus lactis, which was -11.38 kcal/mol. Since the original Phage P2 and S. Pyogenes has a low binding affinity, we mutated it into 418 versions and docked all of them to find the one with this highest binding affinity. After 418 trials, we found the average binding affinity to be -4.9 kcal/mol, the maximum to be -3.5 kcal/mol, and the minimum to be -6.6 kcal/mol. The minimum occurred at Phage P2 #327, which we included here, indicating that though it may not bind to S. Pyogenes as well as it would to L. Lactis, it has significantly improved its binding affinity from the natural form of Phage P2. Hence, Phage P2 #327 was ready to be compared with the phage from the wet lab.
<img src="P2_on_Peptidoglycan.png"> Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal PstI site found at 520
Illegal PstI site found at 526 - 12INCOMPATIBLE WITH RFC[12]Illegal PstI site found at 520
Illegal PstI site found at 526
Illegal NotI site found at 188 - 21COMPATIBLE WITH RFC[21]
- 23INCOMPATIBLE WITH RFC[23]Illegal PstI site found at 520
Illegal PstI site found at 526 - 25INCOMPATIBLE WITH RFC[25]Illegal PstI site found at 520
Illegal PstI site found at 526 - 1000COMPATIBLE WITH RFC[1000]
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