Loop Plasticity Drives Paralog-Specific Recognition in BET ET Domains

Area of Science:

• Molecular biology
• Structural biology
• Biophysics

Background:

• The bromodomain and extraterminal domain (BET) protein family recognizes diverse peptide motifs via conserved ET domains.
• Understanding the structural basis for paralog-specific binding preferences within the BET family remains a challenge.

Purpose of the Study:

• To elucidate the structural origins of paralog selectivity in the ET domains of BET proteins, specifically BRD3-ET and BRD4-ET.
• To investigate how sequence variations influence the dynamics and peptide-binding modes of BET paralogs.

Main Methods:

• Extensive molecular dynamics (MD) simulations of BRD3-ET and BRD4-ET.
• Integration of experimental data for unbound and peptide-bound states.

Main Results:

• Paralog selectivity is driven by subtle differences in the dynamics of the α2-α3 loop, not large structural changes.
• Two divergent residues (positions 35 and 36) in the α2-α3 loop modulate flanking helices (η1 and η2).
• These modulations control the peptide-binding cavity opening, influencing binding modes and accommodating distinct peptide motifs.

Conclusions:

• Sequence-encoded dynamical differences in the α2-α3 loop dictate the number, stability, and geometry of accessible binding modes.
• Provides a structural rationale for the paralog-specific targeting of BET proteins, crucial for therapeutic development.