Rationale: write abstract and continue comparing protein structures

Process:

1. wrote abstract
2. selected phages and entered amino acid sequences for their TMPs into raptorX

Results:

Abstract:

Tape measure proteins (TMPs) help determine bacteriophage tail length and facilitate DNA transit into the bacterial cell during infection [2]. Tail length is a key characteristic for classifying a bacteriophage into a tail morphology family (Myoviridae, Siphoviridae, or Podoviridae), and therefore TMPs play a role in determining tail morphology [2]. Arthrobacter phage TMPs are highly conserved in each phage cluster, and it has been noted that arthrobacter Myoviridae phage seem to have an abnormal number of similarities to phages in the Siphoviridae family [1].  This experiment was conducted to determine if Arthrobacter phage TMPs contain any conserved structural or genetic domains within each tail family tested (Myoviridae or Siphoviridae), and to determine if there is any consistent conservation found throughout all Arthrobacter phage TMPs. This was determined bioinformatically by scanning the amino acid sequences of 43 randomly selected Arthrobacter phage TMPs for motifs or other similarities in addition to comparing hypothetically folded TMPs. The distances between the atom backbone of the proteins were used to calculate the root-mean-square distance (RMSD) in order to compare two different structures. In effort to further characterize NapoleonB, each TMP was aligned against NapoleonB’s TMP.*** Preliminary results suggest at least one conserved motif between all TMPs. The protein structures also seem to suggest at least visual similarities between Myoviridae TMPs with more data to be collected. Based on the avaliable data, it appears that TMPs vary widely with a few key areas of similarity that can be further researched.  

***Results are unfinished  

Next Steps:

TM-align all folded proteins with NapoleonB’s structure