An Intact PHD Finger and PHD-BRD Interdomain Linker Are Crucial for Binding of the Chromatin Remodeler Factor TIP5 to the Histone Octamer

The bromodomain adjacent to zinc finger (BAZ) family protein TIP5 (transcription termination factor I (TTF-I)/interacting protein 5) contains a plant homeodomain (PHD) zinc finger module that recognizes unmodified histone H3 lysine 4. This study demonstrates that the immobilized PHD domain recruits the histone octamer complex. Depletion of zinc cations from the finger or disruption via mutagenesis completely abolished this interaction. Interestingly, the binding ability of the depleted protein was partially recovered under high concentrations of KCl. Extending the PHD domain with a PHD-bromodomain (BRD) interdomain linker led to a substantial increase in binding affinity, with the magnitude progressively dependent on the linker length. To gain insight into these preferential binding interfaces, AlphaFold 3 structure predictions were performed. Within the histone octamer complex, histone H3 was identified as a primary, but not sole, binding partner for TIP5 partial proteins. An increase in predicted total van der Waals interactions correlated with the presence of the linker and its extension; however, an anomaly stemming from the calculated stickiness of the short linker version was encountered. Increased hydrogen-bonding in models with the short linker mirrored the observed affinity. Conversely, the long linker reduced predicted hydrogen (H)-bonds below that for the PHD alone. Finally, structural analysis of the disrupted zinc finger motif revealed the fewest hydrogen bonds.