Allosteric communications between protein domains via linker and substrate modulate the function

Degradation of collagen by matrix metalloprotease 1 (MMP1) is a model system to study allostery because the catalytic domain alone cannot degrade collagen. Both the catalytic and hemopexin domains are necessary, suggesting the essential role of allostery in function. We attached fluorescent dyes at two specific sites on the two domains of MMP1 to measure inter-domain dynamics. We calculated the distance between the two locations from the single molecule Forster Resonance Energy Transfer (smFRET) between the two dyes, measured using a Total Internal Reflection Fluorescence (TIRF) microscope. Low FRET conformations, where the two MMP1 domains are well-separated, are functionally relevant. These conformations are present in active MMP1 but significantly absent in inactive MMP1. Tetracycline, an MMP1 inhibitor, inhibits low FRET conformations. MMP9, an MMP1 enhancer, leads to more low FRET. Molecular dynamics (MD) simulations reproduce experimental features. More low FRET conformations are accompanied by more openings of the catalytic pocket, enabling the substrate to get closer to the catalytic site of MMP1. MD simulations further revealed that allosteric communications between the two MMP1 domains could be functionally influenced by collagen even when the linker is absent.