Inter-domain dynamics and fibrinolytic activity of matrix metalloprotease-1

Abstract

<jats:title>Abstract</jats:title><jats:p>The roles of protein conformational dynamics and allostery in function are well-known. However, the roles that inter-domain dynamics have in function are not entirely understood. We used matrix metalloprotease-1 (MMP1) as a model system to study the relationship between inter-domain dynamics and activity because MMP1 has diverse substrates. Here we focus on fibrin, the primary component of a blood clot. Water-soluble fibrinogen, following cleavage by thrombin, self-polymerize to form water-insoluble fibrin. We studied the inter-domain dynamics of MMP1 on fibrin without crosslinks using single-molecule Forster Resonance Energy Transfer (smFRET). We observed that the distance between the catalytic and hemopexin domains of MMP1 increases or decreases as the MMP1 activity increases or decreases, respectively. We modulated the activity using 1) an active site mutant (E219Q) of MMP1, 2) MMP9, another member of the MMP family that increases the activity of MMP1, and 3) tetracycline, an inhibitor of MMP1. We fitted the histograms of smFRET values to a sum of two Gaussians and the autocorrelations to an exponential and power law. We modeled the dynamics as a two-state Poisson process and calculated the kinetic rates from the histograms and autocorrelations. Activity-dependent inter-domain dynamics may enable allosteric control of the MMP1 function.</jats:p>

Quantification of allosteric communications in matrix metalloprotease-1 on alpha-synuclein aggregates and substrate-dependent virtual screening

“…Since MMP1 stabilized within ~5 ns ( Figure S2), we performed simulations for 20 ns. Previously, we reported a positive correlation between the catalytic pocket opening and interdomain separation for MMP1 dynamics on collagen [36] and fibrin [37]. Based on the criterion of positive correlation, it appears that binding pose 3 is likely to be one of the most appropriate binding poses.…”

“…The correlation decay rate of 0.08 s -1 on aSyn-induced aggregates for active MMP1 without ligand (Table S1). In comparison, the decay rates are 0.13 s -1 on collagen [36] and 0.08 s -1 on fibrin [37] for active MMP1 without ligand. In the presence of tetracycline, the two-state description still applies even though the two states and interconversion rates between them change compared to the dynamics without ligand (Table S1).…”

“…The two states are S1=0.46 and S2=0.52 on aSyn-induced aggregates for active MMP1 without ligand ( Table S1). In comparison, the two states are S1=0.44 and S2=0.55 on collagen [36] and S1=0.42 and S2=0.51 on fibrin [37] for active MMP1 without ligand. The correlation decay rate of 0.08 s -1 on aSyn-induced aggregates for active MMP1 without ligand (Table S1).…”

“…Recently, we published a quantitative analysis of MMP1 dynamics on collagen fibrils [36] and fibrin [37]. The histograms reveal conformations of MMP1, and the autocorrelations show the relation between conformations at different time points.…”

“…However, the hemopexin domain sequence varies [33,34], suggesting that differences in activity and substrate specificity among MMPs are due to allosteric (distant from the catalytic site) communications [17,35]. Recently, we reported activity-dependent MMP1 dynamics and allosteric communications on type-1 collagen fibrils [36] and fibrin [37]. We showed that functionally-relevant conformations have the catalytic and hemopexin domains of MMP1 well-separated.…”