Group Final Project
Group Brainstorm on Bacteriophage Engineering
Find a group of ~3–4 students
Read through the Phage Reading material listed under “Reading & Resources” below.
Review the Bacteriophage Final Project Goals for engineering the L Protein:
- Increased stability (easiest)
- Higher titers (medium)
- Higher toxicity of lysis protein (hard)
Brainstorm Session
Choose one or two main goals from the list that you think you can address computationally (e.g., “We’ll try to stabilize the lysis protein,” or “We’ll attempt to disrupt its interaction with E. coli DnaJ.”).
Write a 1-page proposal (bullet points or short paragraphs) describing:
- Which tools/approaches from recitation you propose using (e.g., “Use Protein Language Models to do in silico mutagenesis, then AlphaFold-Multimer to check complexes.”).
- Why do you think those tools might help solve your chosen sub-problem?
- Name one or two potential pitfalls (e.g., “We lack enough training data on phage–bacteria interactions.”).
- Include a schematic of your pipeline.
Names: Danna Betancourt, Rodrigo Arredondo, Valeria Q. Ortega, Jessica Wu
As discussed in “Phage Therapy: Past, Present and Future”, phage therapy represents an interesting alternative to antibiotic treatments, especially as recent developments allow researchers to engineer bacteriophages and their proteins. Our final group project for HTGAA Spring 2026 focuses on improving the bacteriophage MS2’s ability to kill its host bacteria E. coli by engineering its lysis protein MS2-L.
As an interdisciplinary team with different levels of experience in biotechnology, we propose increasing the stability of MS2-L. The lysis protein relies on the chaperone DnaJ for proper protein folding, a process E. coli can disrupt. However, it has been previously demonstrated that mutations deleting the N-terminal half of the MS2-L remove its dependence on DnaJ while also accelerating bacterial lysis. We believe this direction is promising for discovering variants that have structural stability within its host.
Our proposed approach begins with ProteinMPNN to look for alternative amino acid sequences that will improve the stability of MS2-L, then the sequences can be evaluated using AlphaFold and AlphaFold-Multimer to verify compatibility with their biological function and their interaction with DnaJ, with Alphafold specialized to model oligomeric complexes like MS2 and AlphaFold-Multimer tailored to predict protein-protein interactions like the one between MS2 and DnaJ.
Lastly, we must identify promising sequences for experimentation. We can do this by comparing variants quantitatively, e.g. using a deep mutational scan to see how each variant holds up when introduced to point mutations. This will narrow our candidate list to the most promising candidates for synthesis and experimental validation, reducing costs and promoting data-informed decision-making.
Any pitfalls are tied to the reliability of our tools; computational predictions of stability may not fully reflect protein behavior. For example, AlphaFold-Multimer has a systematic bias toward interactions between ordered protein regions, with a reduced accuracy for disordered regions and transient interactions such as those of a chaperone and its complex.
We are also held back by a narrow scope. Phage therapy depends on several biological variables beyond a single protein, and there is currently a lack of pharmacokinetic and pharmacodynamic studies on phage therapy. This means that we can make MS2-L more stable, but other factors could limit the effectiveness of the bacteriophage.
