Fig. 5: MD simulations of Meis1-HD in complex with WT or variant meisDNAs.

a Superimposition of Meis1-HD in complex with (left) WT and (right) T1C meisDNAs. b Intermolecular H-bonding interaction of the L1 loop region in the (left) Meis1-HD–WT and (right) Meis1-HD–T1C complexes. c Intermolecular H-bonding interaction of residues W322, R328, and R329 in the (left) Meis1-HD–WT and (right) Meis1-HD–G2A complexes. d Hydrophobic core created between the α1 and α3 helices in the (left) Meis1-HD–WT and (right) Meis1-HD–G2A complexes. e Distances of (upper) X2-N7↔R329-Nη1 and (lower) F292-CO↔M334-CO, where X2 is G2 or A2, in the (left) Meis1-HD–WT and (right) Meis1-HD–G2A complexes as a function of the simulation time. The distances are indicated as green solid lines in (d). f Intermolecular H-bonding interaction of the α3 helix in the (left) Meis1-HD–WT and (right) Meis1-HD–C4T complexes. g Distances of X4’-N7 ↔ R328-Nη1, where X4’ is G4’ or A4’, in the (left) Meis1-HD–WT and (right) Meis1-HD–C4T complexes as a function of the simulation time. These distances are indicated as green solid lines in (f). The representative structures are the centroids of the largest clusters among 10 conformational clusters obtained with the k-means clustering method. The largest clusters of WT, T1C, G2A, and C4T meisDNAs occupy 26.6%, 37.4%, 38.1%, and 25.9% of the trajectory, respectively.