Abstract
Members of the ADF/cofilin family of regulatory proteins bind actin filaments cooperatively, locally change actin subunit conformation and orientation, and sever filaments at “boundaries” between bare and cofilin-occupied segments. A cluster of bound cofilin introduces two distinct classes of boundaries due to the intrinsic polarity of actin filaments, one at the “pointed” end side and the other at the “barbed” end-side of the cluster; severing occurs more readily at the pointed end side of the cluster (“fast-severing” boundary) than the barbed end side (“slow-severing” boundary). A recent electron-cryomicroscopy (cryo-EM) model of the slow-severing boundary revealed structural “defects” at the interface that potentially contribute to severing. However, the structure of the fast-severing boundary remains uncertain. Here, we use extensive molecular dynamics simulations to produce atomic resolution models of both severing boundaries. Our equilibrated simulation model of the slow-severing boundary is consistent with the cryo-EM structural model. Simulations indicate that actin subunits at both boundaries adopt structures intermediate between those of bare and cofilin-bound actin subunits. These “intermediate” states have compromised intersubunit contacts, but those at the slow-severing boundary are stabilized by cofilin bridging interactions, accounting for its lower fragmentation probability. Simulations where cofilin proteins are removed from cofilactin filaments favor a mechanism in which a cluster of two contiguously bound cofilins is needed to fully stabilize the cofilactin conformation, promote cooperative binding interactions, and accelerate filament severing. Together, these studies provide a molecular-scale foundation for developing coarse-grained and theoretical descriptions of cofilin-mediated actin filament severing.
Highlights
Which are filament severing proteins that accelerate network turnover by increasing the concentration of polymer ends where subunits can add and dissociate [1]
Molecular dynamics (MD) simulations have been successful in capturing the molecular details and dynamics of actin filaments, including cofilin-linked changes to structure and filament rigidity [5, 7, 12, 13, 30]
The resulting, equilibrated structures (Fig. 1A) were joined end to end in a head-to-tail manner through alignment of two subunits from each structure, yielding starting models for the slow- and fast-severing boundaries (Fig. 1A)
Summary
Which are filament severing proteins that accelerate network turnover by increasing the concentration of polymer ends where subunits can add and dissociate [1]. Filament severing proteins in the cofilin/ADF family ( referred to as cofilin) bind actin filaments between longitudinally adjacent actin subunits [2]. Cofilin binding displaces a stabilizing intersubunit contact formed by the actin “D-loop” of one subunit and the “target binding cleft” of its longitudinally adjacent, pointed end neighbor (Fig. 1A) [11,12,13,14]. We employ MD simulations to predict structures of these two boundaries starting from the bare actin and cofilactin filament structures. Further simulations of synthetic boundaries generated by removal of cofilin from cofilactin structures allow us to assess stability of cofilin clusters of varying size
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