Rationale:

The purpose of today’s lab was to analyze the RaptorX results generated for the phage holin and endolysin proteins and compare the different structures.

Tools:

• RaptorX
• PubChem
• Jmol

Procedure:

• Initially began with looking at the RaptorX PDB images generated, however they did not give much information in regards to the catalytic regions especially as we had no information regarding specific residues.
• Tried switching to PubChem, and though we were able to spin the protein, there was still no information regarding the actual amino acids.
• Eventually, downloaded JMOL, which offered the information we were looking for, and we were able to find the Histidine, Leucine, Histidine region of the catalytic Domain.

Results:

Histidine, Leucine, Histidine Catalytic Region

Elesar Endolysin

NapoleonB Endolysin

Conclusions:

The supposed catalytic regions were found, however there is much about this program that is unknown and there is definitely a learning curve to it. The tyrosine and acidic residue locations are still unknown in the protein.

Next Steps:

Figuring out how to utilize JMOL effectively is number one priority as it has the ability to give incredible amounts of information regarding the protein structures above. The missing tyrosine and acidic residues still need to be identified in the protein.