To probe interaction of the H3 mimicking peptides with TRIM24, TRIM33α and TRIM33β, we conducted molecular dynamics (MD) simulations. Using the X-ray crystal structure of the TRIM33α PHD-BRD bound to H3 1-20 K9Me 3 K14AcK18Ac (PDB code 3U5O), 37 models of each TRIM reader domain bound to H3 1-20 K9Me 3 K18Ac were generated through alignment and used to perform MD simulations (see SI for details). The simulations were analyzed using Protein-Ligand Interaction Profiler 59 to identify hydrophilic and hydrophobic contacts between the TRIM PHD-BRDs and the H31-20K9Me3K18Ac peptide (Figure ). H3K18Ac was found to make the most contacts with each BRD, but the nature of the interaction differed between systems. A similar number of hydrophilic and hydrophobic contacts were identified between the peptide and the TRIM24 or TRIM33β BRDs. Conversely, hydrophobic contacts formed the majority of interactions between H3K18Ac and the TRIM33α BRD, which might compensate for the lack of hydrogen bonding between H3K18Ac and N1039 in TRIM33α. We next undertook a more detailed analysis of hydrophilic interactions between the BRDs and H3K18Ac and its flanking residues, H3R17 and H3Q19 (Figure ). For TRIM24 and TRIM33β, H3K18Ac directly interacts with N980/N1039 via the KAc carbonyl group (Figure -Interaction 4), as has been observed for other canonical BRDs. This observation is consistent with the N980F/N1039F mutants substantially disrupting binding of the H31-27K18Ac peptide binding to these PHD-BRDs (Table ). Y935 also interacts intermittently with this carbonyl (Figure -Interaction 5). Selective binding of both TRIM33 isoforms to H3K18Ac over other KAc residues is guided by an electrostatic interaction between E981 and H3R17 (Figure -Interaction 1). While the E981-H3R17 interaction is indeed observed in the X-ray crystal structure of TRIM33α bound to H3 1-20 K9Me 3 K14AcK18Ac (PDB code 3U5O), 37 a less common, polar interaction between H3R17 and E1061/E1044 (TRIM33α/β) on the BC loop is observed (Figure -Interaction 2).