The substrate changes matrix metalloprotease-1 dynamics, allostery, and ligand binding affinity

Using single-molecule experiments, ensemble assays, and Molecular Dynamics (MD) simulations, we showed that collagen actively influences MMP1 interdomain dynamics. This paper extends the previous experimental work to validate MD simulations and gain more insights into MMP1-collagen interactions. We include virtual screening with free energy calculations to uncover key insights regarding substrate-dependent dynamics, allostery, and ligand binding. Our findings reveal that MMP1 interdomain dynamics are influenced by the strain in collagen, and collagen-specific allosteric residues exhibit strong correlations with the active site. Additionally, allosteric paths connecting these residues to the active site bypass the linker region. Collagen also induces changes in the configurations of the catalytic motif. Furthermore, MD simulation and virtual screening identify molecules that bind to allosteric residues, alter MMP1 dynamics, and potentially change activity. Free energy calculations highlight the essential role of the substrate in small molecule screening against a protein. We have developed a comprehensive framework for identifying substrate-specific allosteric residues in MMP1 and screening small molecules incorporating protein dynamics in the presence of substrates. These results significantly impact our understanding of MMP1 interactions with collagen fibrils and pave the way for selectively modulating specific MMP1 functions without altering its other functions in future applications.