Ternary complexes in protein–DNA interactions: Kinetics and mechanisms

Transcription factors (TFs) play a central role in gene regulation by binding specific DNA sequences. Although extensive research has uncovered various mechanisms governing binary TF·DNA complexes, relatively few structural and mechanistic studies exist for ternary complexes or larger assemblies. This study employs coarse-grained molecular dynamics simulations to investigate how DNA conformation, TF properties, and protein-protein interactions influence ternary complex formation. We focus on 2 TF·TF·DNA systems: Sox2·octamer transcription factor 1 (Oct1)·DNA and SRF·SAP1·DNA, each involving 2 TFs, one of which binds to a bent DNA segment and the other to a more linear DNA region. Our findings reveal that, in both systems, the kinetics of ternary complex formation is primarily governed by nonspecific TF-DNA interactions. Additionally, we find that the DNA conformational change does not always dominate the kinetics, suggesting that a complex interplay of biophysical factors influence ternary complex formation. When the TFs exhibit divergent nonspecific affinities, as in the Sox2·Oct1·DNA system, the binding order is dictated largely by diffusion along nonspecific DNA and stabilized through protein-protein interactions. In contrast, when both TFs display comparable nonspecific affinities, as observed in the SRF·SAP1·DNA system, the binding order becomes more dependent on site-specific recognition and, consequently, on the underlying DNA conformation. This distinction enables the emergence of different mechanisms depending on the structural state of the DNA. This study highlights how the interplay between TF molecular properties, DNA sequence and deformability, and protein-protein interactions together shape the kinetics and molecular mechanisms underlying ternary TF·TF·DNA complex formation.