Uncovering the role of dimerization on dynamics and inhibitor stability in human versus Xenopus LTA4H

We investigate the conformational stability and binding of the inhibitor bestatin to Xenopus laevis leukotriene A4 hydrolase (xlLTA4H) in both monomeric and dimeric states using all-atom molecular dynamics (MD) simulations. Despite the crystallographic observation of a homodimer, our simulations suggest that dimerization does not significantly enhance conformational stability compared to the monomeric form. Bestatin binding induces modest stabilization at the active site, with notable suppression of C-terminal domain dynamics in monomers. In contrast, dimerization preserves the native-like crystal conformation, particularly in the absence of inhibitor, and introduces interchain coupling that dampens the inhibitor-induced dynamic restraint of the C-terminal domain. In dimeric xlLTA4H, bestatin exhibits dynamic behavior within the active site, and its interactions are less stable, particularly with residues in the hydrophobic pocket, compared to the human homolog. R-value analysis, defined as the normalized stability of residue-ligand interactions across the simulation trajectory, confirms weaker interactions in the xlLTA4H dimer, with increased transient contacts and reduced stability at key active-site residues. Dynamic cross-correlation and coupled motion analyses reveal a strong dynamic coupling between the active site and the C-terminal domain in monomers, which is attenuated in the xlLTA4H dimer due to interchain interactions. These results indicate that dimerization in xlLTA4H may reduce ligand-binding stability, despite the ligand maintaining a consistent binding pose in the crystal structure. Our findings highlight the complex interplay between protein oligomerization, dynamic networks, and inhibitor binding, underscoring the importance of considering physiological conditions and dynamic behavior beyond static structural data in drug design for LTA4H.