Energetic and structural dynamic drivers of transcription factor MycMax, Omomyc homodimer, and MaxMax recognition on DNA.

Basic helix-loop-helix leucine zipper (bHLHLZ) transcription factors (TFs), such as MycMax, MaxMax, and the engineered mutant Omomyc dimers, regulate gene expression by binding to the E-box (5'-CACGTG-3') motif in DNA. Here, we used microsecond molecular dynamics (MD) simulations along with MMGBSA energetic and hydrogen bonding (HB) analyses to investigate how MycMax, Omomyc, and MaxMax dimers interact with both canonical E-box and homogeneous polyA reference sequences. Our MD results indicate that protein-DNA van der Waals (VDW) interactions and surface complementarity dominate the binding affinity measurements. Per-residue decomposition underscores the central role of conserved arginine residues at the protein-DNA binding interface, while HB information readout (or KL divergence) analyses reveal a biased DNA strand association that reinforces protein sequence recognition for specificity. Although MaxMax binds to the canonical E-box energetically stably, it loses the stability on polyA DNA more than the other two TFs, suggesting an essential reliance of MaxMax on the E-box motif for TF-DNA interaction coordination. MycMax exhibits moderate stability energetically and shows more variable dynamical responses to local DNA sequences. In contrast, the Omomyc dimer retains slightly higher binding affinity or energetic stability than MycMax on both E-box and polyA DNA, suggesting an enhanced ability to sequester MycMax in oncogenic settings. These findings provide new physical insights into dimeric bHLHLZ-TFs on DNA recognition and reveal potential strategies for targeting Myc-driven transcription or overexpression in cancer.