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

Abstract

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. SignificanceIn this paper, we validated all-atom simulations of free and collagen-bound MMP1 and gained insights into MMP1 function. We have found that collagen changes dynamics, allostery, and ligand binding in MMP1. Collagen strain, known to be age-dependent, also changes MMP1 dynamics and ligand binding. Interdomain allosteric paths do not go through the linker connecting the MMP1 domains. Instead, paths from the collagen-specific allosteric residue to the active site have non-bonded interactions. Screening of small molecules against collagen-specific MMP1 residue suggests that collagen alters ligand binding to MMP1. These results will significantly impact understanding MMPs and small molecule screening against proteins. Substrate-specific allosteric residues may enable controlling one function of MMPs without altering their other functions, leading to fewer side effects.