Multisite λ-Dynamics for Protein-DNA Binding Affinity Prediction.

Transcription factors (TFs) regulate gene expression by binding to specific DNA sequences, playing critical roles in cellular processes and disease pathways. Computational methods, particularly λ-Dynamics, offer a promising approach for predicting TF relative binding affinities. This study evaluates the effectiveness of different λ-Dynamics perturbation schemes in determining binding free energy changes (ΔΔG_b) of the WRKY transcription factor upon mutating its W-box binding site (GGTCAA) to a nonspecific sequence (GATAAA). Among the schemes tested, the single λ per base pair protocol demonstrated the fastest convergence and highest precision. Extending this protocol to additional mutants (GGTCCG and GGACAA) yielded ΔΔG_b values that successfully ranked binding affinities, showcasing its strong potential for high-throughput screening of DNA binding sites.