To ground the proposed CAS-based framework in a concrete biological challenge, we present a focused case study: the evolution of synthetic PETase variants for enhanced plastic degradation. Polyethylene terephthalate (PET) is a ubiquitous and persistent plastic polymer, and natural PET-degrading enzymes (notably from Ideonella sakaiensis) have shown limited activity and stability under industrial conditions. Here, we simulate the adaptive molecular evolution of synthetic PETase analogs using our multi-parametric scoring function and complex adaptive system (CAS)-driven engine.
1. Purpose of the Simulation
This dummy dataset and mutational simulation are not meant to replicate actual laboratory evolution but rather to:
Demonstrate the proof-of-concept of the theoretical framework
Illustrate how topological, thermodynamic, and probabilistic models interact during in silico evolution
Show the system's ability to generate diverse and emergent mutational pathways, potentially exceeding baseline enzyme activity
2. Initial Template and Variant Encoding
Starting sequence: Wild-type PETase (PDB ID: 5XH3), containing ~290 amino acids.
Encoded features per variant: Residue interaction graph (RIG) matrix. Predicted G_folding (kcal/mol). Docking affinity to PET dimer (G_binding). Dynamical entropy of folding pathway (S_dyn). Mutation vector (binary/ternary substitution encoding).Â
Each variant is represented as:
{ "id": "V137",
