Loop Plasticity Drives Paralog-Specific Recognition in BET ET Domains

The bromodomain and extraterminal domain (BET) family uses its conserved ET domains to recognize diverse peptide motifs, yet exhibits paralog-specific binding preferences whose structural origins remain poorly understood. Using extensive molecular dynamics (MD) simulations of BRD3-ET and BRD4-ET and experimental data for the unbound and peptide-bound states, we show that paralog selectivity arises not from large structural rearrangements but from subtle differences in the dynamics of the α2-α3 loop. Two divergent residues at positions 35 and 36 in this loop modulate the formation of flanking helices (η1 and η2), which in turn control the opening of the peptide-binding cavity and determine how each paralog accommodates distinct binding modes. These sequence-encoded dynamical differences shape the number, stability, and geometry of accessible binding modes and provide a structural rationale for paralog-specific targeting of BET proteins.