Group: Jessee Svoboda, Paula Carrodeguas, Iman Karibzhanova, Peter Hanna
From homework 4: Group Brainstorm on Bacteriophage Engineering What do we know:
E. coli DnaJ binds to denatured proteins to prevent/disassemble aggregates (native function in heat-shock). DnaJ binds to the hydrophilic tail of MS2-L protein. point mutation of highly conserved proline in DnaJ results in no lysis (so maybe no more binding of MS2-L tail?) removal of MS2-L tail recovers lysis function (meaning DnaJ is only necessary when tail exists) suggests hydrophilic tail aggregates in some way that prevents lysis except in presence of DnaJ to stop aggregation so stability should be improved if we can figure out how the tail is interacting with the tail of other MS2-L molecules, and then mutating that away so there is no aggregation and dependence on DnaJ graph TB; A[sequence and structure of MS2-L] –>|if geometry and chemical interactions are known| B[view interactions between MS2-L copies] A –>|if geometry and interactions are not known| C[model interactions with AlphaFold or something that can do protein interactions] B –>|visual analysis and mutation modeling| D[Identify important residues in MS2-L tail interactions] C –>|visual analysis and mutation modeling| D[Identify important residues in MS2-L tail interactions] D –>|use knowledge of hydrophobicity/charge/etc. OR use ESM2 mutational scan and select ones that it finds unlikely| E[Select dissimilar AAs to substitute in interacting residues] E –>|AlphaFold or similar| F[model protein folding in new AA sequence with selected mutations] F –>|something that can model protein interactions| G[model interactions between mutant MS2-L copies] G –>|select mutations that have similar hydrophilicity as original tail but less interaction with each other and maybe also with DnaJ| H[test mutations in lab] Potential problems: