Molecular Basis of Selectivity in Human Elastin-Binding Protein toward Elastin Peptides and Galactosugars

Elastin-derived peptides (EDPs) modulate key cellular processes through binding to the elastin-binding protein (EBP), yet the molecular basis underlying their differential activities remains unclear. In this study, we combined systematic molecular docking with duplicate 1 μs molecular dynamics (MD) simulations to characterize the binding modes and interaction networks of biologically active (LGTIPG, PGAIPG) and inactive (VVGPGA, VPVGGA, GGVPG) elastin-derived peptides (EDPs) within the V32 pocket of EBP. Our results reveal two partially overlapping functional regions within the V32 pocket: residues 98–114, preferentially engaged by biologically active peptides and galactosugars, and residues 83–104, primarily utilized by inactive peptides. This supports a model in which active peptides and galactosugars share a common region, while inactive peptides preferentially occupy an adjacent, partially overlapping subregion, challenging the notion of entirely separate EBP binding sites. Active peptides formed strong, persistent interactions, particularly through D98 and E99, whereas inactive peptides relied primarily on salt bridges with E137 and hydrogen bonds with S101. MM/PBSA binding free energies were in full agreement with experimental activity trends, indicating that binding affinity and pocket preference jointly determine biological activity. Notably, although type VIII β-turns are traditionally linked to EDP bioactivity, the peptides remained predominantly extended when bound to EBP, highlighting that binding-site selection and interaction networks, rather than β-turn formation, govern peptide activity. The surface residues P233 and I234 appeared as potential mediators of EBP’s interactions with Neu-1 and PPCA within the elastin receptor complex, supporting previous findings.