Bacteriophage Engineering Group Project Inputs_William & Mary Node Group 1 2 Group Project_Protein Design 1 Selected Goal: Increased stability (easiest)
Brainstorm Session Questions:
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.”) We’ll attempt to run multi-environment/conditional modeling and simulation to down-select lysis stability approaches that show the greatest resilience across environments/conditions. The team has selected a project focused on enhancing the stability of the Lysis Protein, a decision influenced by the group’s current experience level. The primary objective is to improve thermodynamic stability while concurrently preserving the native protein fold and maintaining functional integrity. The proposed methodology involves utilizing BLAST for identifying homologous sequences, followed by Clustal Omega to ascertain conserved residues susceptible to mutation intolerance. Subsequently, ESM2 will be employed to score candidate substitutions based on evolutionary plausibility. This will be succeeded by the application of ESM-Fold to predict and refine the integrity of the protein fold, as well as to optimize existing backbones. The results may then be further subjected to EvolvePro for accelerated directed evolution. Tools like Boltz-1 and ProteinMPNN offer a capability for redesigning solvent-exposed residues and optimizing the core packing of the protein. We can cross their performance for comparison. All selected variant candidates are slated for computational stress-testing under a range of environmental conditions that could potentially induce destabilization. Selected variant candidates that pass the stress test are prioritized for downstream experimental validation. Why do you think those tools might help solve your chosen sub-problem? The previous bullet point addresses tool functionality in our workflow, explaining why and how various tools will assist us in accomplishing our goal Name one or two potential pitfalls (e.g., “We lack enough training data on phage–bacteria interactions.”). One potential pitfall is that we may have insufficient in vitro quality and quantity of data to test the environmental constraints of interest. Thus wet-lab work would be needed to back-up the findings, in addition to follow-up There are open questions regarding the validity of the stated research approach (i.e., if the approach makes sense relative to the larger goal of increased stability) Include a schematic of your pipeline See workflow schematic below Group Project_Protein Design 2 3 See results below