Rationale: Create outline for project and compare different protein structures

Process:

1. Lucy and I planned out what we thought we needed to do to complete project
2. began comparing structures using TM-align and chose different phages fold the TMP of
3. began testing to see what the fastest and easiest way to fold lots of proteins is

Results:

Outline:

Title Comparison of Tape Measure Proteins in Siphoviridae and Myoviridae Tail Families Using Arthrobacter Phage

Guiding Question: What distinguishes tape measure proteins across Siphoviridae and Myoviridae tail families in Arthrobacter Phage and are there conserved domains?

Abstract:

• TMPs play a major role in determining phage tail families and how phage infect their hosts
• Amino acid sequences for arthrobacter phage TMPs were compared to find regions of similarity or difference to examine whether or not there is conservation between Myoviridae and Siphoviridae TMPs
• Hypothetical proteins structures were generated to compare the structural differences in TMPs to see if structural components were conserved even if amino acid sequences were not
• ***We don’t have fully fleshed out conclusion or results but we will alter our abstract as needed

List of tools used:

• I-tasser
• Clustal Omega
• MEME Motif
• TM align

Introduction (Background Information):

• Tape Measure Proteins (TMPs) help control tail length/type and how a phage infects its bacterial host
• Arthrobacter phage cluster appear to exist in all three tail types (Podoviridae, Myoviridae, and Siphoviridae) but Podoviridae do not call TMPs
• Previous research suggests that in arthrobacter phage myoviridae and siphoviridae TMPs are more similar than in phage that infect other hosts
• Previous research suggests that structure is conserved more than the specific amino acid sequence
• Protein structures can be compared statistically by finding the root-mean-square deviation (RMSD) or the measure of the average distance between the backbone atoms of superimposed proteins

Types of Data Collected:

• Computer generated folded proteins
• MEME motifs showing conserved motif domains
• Clustal Omega amino acid sequence comparisons
• TM alignments that give numerical comparisons of protein structures

Results (to date):

• Amino acid sequences for TMPs in each cluster appear to be highly conserved (identical or only 2-3 amino acid differences) – found using clustal omega comparisons
• Amino acid sequences for TMPs in each tail family do not appear to be highly conserved but the type of amino acid (as determined by clustal omega color coding) appear to be more conserved – found using clustal omega comparisons
• Have started to model predicted protein structures and myoviridae proteins are visually more similar to each other than to siphoviridae proteins
  • However: NapoleonB (sipovirade) and Chubster (myoviridae) are more mathematically similar than Chubster and Sonny (myoviridae)
• Structures are scoring relatively low in similarity and tend to fall in “random structural similarity” category
• Using MEME motif software several cross cluster but within tail family motifs have been identified in addition to two motifs that seem to appear in both Myovirade and Sipovirade phage

Conclusions (if any have been drawn):

1. TMPs are highly conserved
2. Preliminary data seems to suggest that structure is more conserved than amino acid sequences
3. There are motifs that contain regions of highly conserved amino acids or amino acid types suggesting that these maybe the conserved domains (or as close as TMPs get)

Decided to go with raptorX because while it may not be as accurate, it produces foldings at a much higher rate so using it allows us to have actual data to work with.

Next Steps:

Continue folding all 43 proteins and compare them all to NapoleonB and then create a scatter plot of RMSD scores