Protocol to use protein language models predicting and following experimental validation of function-enhancing variants of thymine-N-glycosylase

This protocol describes steps for optimizing thymine-DNA-glycosylase (TDG) using protein language models, including zero-shot enzyme optimization, construction of plasmids, double plasmid transfection, and high-throughput sequencing and data analysis. It holds promise for streamlining the engineering of gene editing tools while minimizing experimental workload. For complete details, see He et al., Molecular Cell 2024.