Table 1. Simulation parameters.

The parameters of the simulation, organized by category, are listed along with their values as determined from minimizing the discrepancies between the experimental and simulation results. The uncertainties in the simulation parameters were estimated by varying the parameter and comparing the results with the experimental data, as described in experimental procedures.

PARAMETERS		Values and Significance
Collagen fibril structure
1	Cleavage site spacing	67 nm (either 67 or 300 nm)
2	Stagger	0 nm (either 0 or 67 nm)
3	Hot spot spacing	1.2 µm, defines the peak in DPDs at ~1.3 µm
4	Hot spot spacing std. dev.	335 nm
5	Pre-cleaved sites	1.35%, determines downward curvature of MSD, only for active WT enzyme
6	adjacent track lateral spacing	3 nm (not varied)
Diffusion constants
7	1-D diffusion constant (D)	7.5 ± 1 µm2 s−1, intrinsic diffusion constant
8	Lateral jump rate (Pj)	0.5 s−1, rate of jumping to adjacent tracks
MMP1 binding properties
9	Binding to regular sites	150 s−1
10	Binding to hot spots	30000 s−1
11	Type I pause escape rate	5 s−1
12	Number of kinetic steps in type II (Gamma) pause	11 ± 3 steps
13	Rate of kinetic steps in type II pause	11 ± 3 s−1 (the average lifetime of the type II pauses is ~1 s)
14	Fraction of class II pauses at hot-spots	40 ± 15% (WT), 5 ± 5% (mutant), fraction of hot spot pauses that escape via gamma distribution
	MMP1 cleavage properties
15	Percentage of cleavage after long dwells	5 ± 2%
16	Number of successive cuts after initial cut	15 ± 4, determines upward curvature of MSD and average motion after a long pause
17	Std. dev. of number of cuts	3, Reflects intrinsic variability in the number of successive cuts, which is a Gaussian distribution centered at 15 cuts with a standard deviation of 3.
	Additional simulation parameters
18	Noise (σx)	170 nm, determines y-intercept of MSDs
19	Time step (Δt)	1 µs, simulation time step (not varied)