Atomistic mapping of the Sclerostin-LRP6 binding interface using molecular dynamics simulation and essential dynamics.

This study investigates the molecular mechanism by which Sclerostin (SOST), a secreted cystine-knot protein with a structured core and functionally relevant highly flexible or intrinsically disordered regions (IDRs), inhibits the LRP6 co-receptor, a central component of canonical Wnt beta-catenin signaling that regulates bone homeostasis and represents a key therapeutic target in osteoporosis. Although previous structural and biochemical studies have suggested a multivalent mode of SOST engagement involving the LRP6 E1E2 region, the molecular determinants of high-affinity inhibition remain incompletely defined due to the construction of truncations and unresolved disordered segments. In this Investigation, we applied atomistic molecular dynamics (MD) simulations of the human SOST-LRP6 E1E2 ectodomain complex to examine its stability and residue-level interaction behavior in solution. The simulations indicate that SOST engages LRP6 through two coordinated regions. Specifically, the loop 2 region of SOST, particularly the conserved NAI motif, maintains stable interactions with the E1 domain, while the C-terminal region of SOST, including the previously described HNQS motif as well as additional downstream residues, interacts with the E2 domain. These extended interactions provide a mechanistic explanation for the higher binding affinity observed for full-length SOST compared with truncated variants. In contrast to prior structural studies, this work reveals an anchor-stabilized, chemically diverse interaction network in which persistent loop 2/E1 and C-terminal/E2 contacts maintain receptor engagement while surrounding contacts dynamically remodel, providing deeper insight into bone-related signaling mechanisms.