Sequencing Alignments, Folding Proteins, and Discovering NapoleonB’s Endolysin’s Catalytic Site (4/8/19)
Rationale:
Start analyzing endolysins and holins in the AM cluster.
Procedure:
- Performed Multiple Sequence Alignment with AM cluster endolysins along with FF cluster phage Elesar’s and FE cluster phage Corgi’s endolysins.
- Performed Multiple Sequence Alignment with AM cluster holins along with BI cluster phages Madamoto’s and Bing’s holins.
- Folded protein structures with RaptorX.
- Explored and discovered NapoleonB’s endolysin’s catalytic site with Jmol.
Results:
The following image is the results from Multiple Sequence Alignment with AM cluster endolysins along with FF cluster phage Elesar’s and FE cluster phage Corgi’s endolysins from Clustal Omega.
The following image is a phylogenetic tree from endolysin Multiple Sequence Alignment.
The following image is the results from Multiple Sequence Alignment with AM cluster holins along with BI cluster phages Madamoto’s and Bing’s holins from Clustal Omega.
The following image is a phylogenetic tree from holin Multiple Sequence Alignment.
The following image shows NapoleonB’s endolysin’s catalytic site.
Conclusion:
The Multiple Sequence Alignment and phylogenetic tree show high similarly between phages. NapoleonB’s endolysin’s catalytic site, which has the responsibility to cleave the bacterial host’s peptidoglycan membrane, appears to be located in beta-sheets.
Future Work:
Predicted endolysin and holin structures will be analyze more.
