Molecular dynamics simulation and free energy decomposition of the NHR2 tetramer. (A) MM-GB/SA calculations combined with free energy decomposition were used to determine the contribution of each amino acid within NHR2 to tetramer stabilization. Residues are numbered according to the RUNX1/ETO amino acid sequence. (B) Helical wheel representation of the NHR2 domain showing the positions of the m5 and cm5 residues. (C) NHR2 dimer showing the hot spot generated by residues W498, W502, D533, E536, and W540. The dotted line represents the border between the 2 antiparallel α-helices C1 and C2. The blue dots mark the location of the largest indentation found in the binding epitope. (D) Intermolecular contacts involving W540, D533, and E536. (E) Intermolecular contacts involving W502 and W498.