Comparing LigandMPNN and Directed Evolution for Altering the Effector-Binding Site in the RamR Transcription Factor.

ABSTRACT: Recently, the number of ML-based tools for protein design has greatly expanded. Although there have been many successful uses of these tools for improved stability, solubility, and ligand binding, there have been fewer uses of these tools for designing proteins that have intrinsic allosteric mechanisms. In this regard, allosteric transcription factors (aTFs) are a class of regulatory proteins that includes repressors and activators that respond to environmental signals by allosteric communication to regulate their binding with DNA elements. The data exist for evaluating design algorithms for their ability to take allostery into account, as many aTFs have previously been engineered to respond to new ligands, enabling their use as biosensors. In particular, previous work from our lab used di

SUBMITTER: Clark-ElSayed A 

PROVIDER: S-EPMC12265539 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature