Our Final Group project for HTGAA 2025:

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Group Final Project: Improving the infectivity of the MS2 Bacteriophage

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Objective

The main goal of this project is to design and computationally validate point mutations in the MS2 bacteriophage L-protein that potentially affect:

  1. Interaction with host chaperone DnaJ
  2. Lytic pore assembly in bacterial membranes

These mutations will then be tested experimentally to confirm their predicted effects.

Full L-protein sequence :

METRFPQQSQQTPASTNRRRPFKHEDYPCRRQQRSSTLYVLIFLAIFLSKFTNQLLLSLLEAVIRTVTTLQQLLT

L-Protein fragments

1 metrfpqqsq qtpastnrr (1-19)
2 r pfkhedypcr rqqrsst (20-38)
3 lyv liflaiflsk ftnql (39-56)
**4 lsll eavirtvttl qqllt (57-75)**

DnaJ Protein:

MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDSQKRAAYDQYGHAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAARGADLRYNMELTLEEAVRGVTKEIRIPTLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQQTCPHCQGRGTLIKDPCNKCHGHGRVERSKTLSVKIPAGVDTGDRIRLAGEGEAGEHGAPAGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEIEVPTLDGRVKLKVPGETQTGKLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQELQESFGGPTGEHNSPRSKSFFDGVKKFFDDLTR

There were 4 fragments so we decided to divide these in 4 group members, I had selected the 4th part of the sequence to analyze i.e 4 lsll eavirtvttl qqllt (57-75).

top_protein_mutations.csv

top_20_protein_mutations_scores.csv

top_10_protein_mutations_scores.csv