Rationale:

The purpose of today’s lab was to further our knowledge and ability of JMOL to better understand our protein structures.

Tools:

• JMOL
• JMOL Instruction Guide

Procedure:

• Began by familiarizing ourselves with the commands used in JMOL to produce effective results.
• Once completed, all Histidine, Tyrosines, and Aspartic acids were labeled in the protein with the colors red, blue, and yellow respectively.
• Following this, wireframe was turned on to allow us to see in which direction these residues faced, allowing us to visualize which residues interacted with each other best.
• Next, the group hypothesized which residues would best fit our catalytic region based off motility, orientation, and distance from the 4 histidines that are essentially bound in place.

Results:

These are the proposed catalytic regions found in 3 different phages from 3 different clusters (AM, FE, and FF)

NapoleonB Endolysin

Corgi Endolysin

Elesar Endolysin

Conclusions:

It can be concluded that these catalytic domains are conserved well throughout the M23 Peptidase family and Arthrobacter phages. The aspartic acid as well seems to be structurally conserved as every endolysin examined contained an acidic residue of aspartic acid on the neighboring beta sheet, which suggest it plays a role in the reaction.

Next Steps:

The next steps for this project are to use the knowledge of these endolysin proteins to help call function to NKF genes in different Arthrobacter phages.