Organization of associating or crosslinked actin filaments in confinement

Abstract

A key factor of actin cytoskeleton organization in cells is the interplay between the dynamical properties of actin filaments and cell geometry, which restricts, confines and directs their orientation. Crosslinking interactions among actin filaments, together with geometrical cues and regulatory proteins can give rise to contractile rings in dividing cells and actin rings in neurons. Motivated by recent in vitro experiments, in this work we performed computer simulations to study basic aspects of the interplay between confinement and attractive interactions between actin filaments. We used a spring-bead model and Brownian dynamics to simulate semiflexible actin filaments that polymerize in a confining sphere with a rate proportional to the monomer concentration. We model crosslinking, or attraction through the depletion interaction, implicitly as an attractive short-range potential between filament beads. In confining geometries smaller than the persistence length of actin filaments, we show rings can form by curving of filaments of length comparable to, or longer than the confinement diameter. Rings form for optimal ranges of attractive interactions that exist in between open bundles, irregular loops, aggregated and unbundled morphologies. The probability of ring formation is promoted by attraction to the confining sphere boundary and decreases for large radii and initial monomer concentrations, in agreement with prior experimental data. The model reproduces ring formation along the flat plane of oblate ellipsoids.

Reconstitution of contractile actomyosin rings in vesicles

“…Theoretical predictions by Adeli Koudehi et al have suggested that actin organization depends crucially on confinement and surface attachment. 46 In order to explore the agreement of our experimental results with these simulations, we adopted their theoretical model. As such, we performed numerical simulations of interacting actin filaments under spherical confinement using Brownian dynamics (see Supplementary Methods).…”

“…As such, we performed numerical simulations of interacting actin filaments under spherical confinement using Brownian dynamics (see Supplementary Methods). 46 Semi-flexible actin filaments were modeled as beads connected by springs, with cross-linking represented by a short-range attraction with spring constant k atr . Polymerization from an initial number of filament seeds was simulated by addition of beads at one of the filament ends (representing the barbed end).…”

Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture

“…The formation of complex structures with actin aggregates in the absence of motor proteins was surprising, as motor-driven dynamics is required for F-actin clustering 33,34 . However, simulations have shown that confined actin and crosslinkers can form rings, open bundles, irregular loops or aggregates depending on crosslinker type and concentration, and confinement geometry 35 . Although α-actinin and fascin have similar bundling affinities, α-actinin has a higher binding affinity to single filaments and forms antiparallel bundle with large spacing and mixed polarity as opposed to unidirectional packed parallel bundling by fascin.…”

“…These properties enables α-actinin to form more complex structures in bulk including bundle clusters at high α-actinin concentrations 36,37 . In vitro reconstitution and simulation studies have also shown that the actin contractile machinery in eukaryotes is a result of one or a combination of three distinct coordinating mechanisms, F-actin buckling in disordered actomyosin networks, sliding (sarcomere-like contraction), and polarity sorting 35,38,39,40,41,42,43 . All three mechanisms are promoted by α-actinin and the polarity sorting and buckling mechanisms can result in myosindriven clustering and the formation of large star-like structures 39,40,41 .…”

“…These signify ring formation near GUV midplane. Experimental and numerical evidence shows that upon compression, rings can assemble in the equatorial plane perpendicular to the direction of compression 28,35 . As the GUV size increased, we found more complex actin network geometries ( Fig.…”