Difference between revisions of "Part:BBa K3461001"
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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.
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<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.</p>
  
 
<img src="P2_on_Peptidoglycan.png">
 
<img src="P2_on_Peptidoglycan.png">

Revision as of 05:08, 13 October 2020


Mutated Phage P2 That Binds to S. pyogenes

This part is the mutated version of phage P2, one of the 418 different "mutated" versions. The purpose of this part is to identify specific properties of mutated Phage P2 that are able to bind to S. pyogenes.


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


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 520
    Illegal PstI site found at 526
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 520
    Illegal PstI site found at 526
    Illegal NotI site found at 188
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 520
    Illegal PstI site found at 526
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 520
    Illegal PstI site found at 526
  • 1000
    COMPATIBLE WITH RFC[1000]