Group Formed Proposal:
https://docs.google.com/document/d/1ENvPHhRbBgtl0ERrfqmomJKxPg68nfvCugrPQrDdM7o/edit?tab=t.0 Documentation:
https://pages.htgaa.org/2026a/ritika-saha/homework/week-05-hw-protein-design-part-ii/index.html By: 2026a-nourelden-rihan, 2026a-ritika-saha, 2026a-rahul-yaji, 2026a-keerthana-gunaretnam
We decided to focus on the main area of increasing the stability of the MS2 phage lysis protein L, with a possible secondary goal of reducing the dependency on host DnaJ, while still maintaining the lysis action. The tools AlphaFold, Clustal Omega, BLAST, ESM, and ESMFold were discussed. BLAST can pull out homologous lysis proteins from the databases. Clustal Omega can create MSAs to identify essential L48-S49 residues, and the pore-forming regions that must not be mutated. ESM can create mutation heatmaps, which can guide the use of ESMFold to obtain highest score foldings in mutatable regions. AlphaFold Multimer predicts whether the subunits of our protein can successfully create a pore in the host membrane, and also to check whether N-terminus can break the interaction with DnaJ. We also identified a few pitfalls, with majors ones dealing with limited training datasets, that may not be properly aligned towards creating a transmembrane lysis protein. Some other pitfalls include the lack of proper annotations for amurins; the possibility of an over-stable protein to form non-functional aggregates; and the vulnerability of modified protein to host proteases.