Multisite λ-Dynamics for Protein–DNA Binding Affinity Prediction

作者：Carmen Al Masri, Jonah Z. Vilseck, Jin Yu, Ryan L. Hayes · 发表于：Journal of Chemical Theory and Computation · 年份：2025 · DOI：10.1021/acs.jctc.4c01408 · 被引用次数：3 · 研究领域：RNA and protein synthesis mechanisms、Protein Structure and Dynamics、Bacterial Genetics and Biotechnology

High Resolution Image Download MS PowerPoint Slide 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 (ΔΔ G b ) of the WRKY transcription factor upon mutating its W-box binding site (G G T C AA) to a nonspecific sequence (G A T A AA). Among the schemes tested, the single λ per base pair protocol demonstrated the fastest convergence and highest precision. Extending this protocol to additional mutants (GGTC C G and GG A CAA) yielded ΔΔ G b values that successfully ranked binding affinities, showcasing its strong potential for high-throughput screening of DNA binding sites.