Biology subjects

Akenuwa, O. H.

Publications and source records attributed to Akenuwa, O. H..

3 recordsLinked to original sources

bioRxiv2024

Polarity sorting of actin filaments by motor-driven cargo transport

During the active transport of cellular cargo, forces generated by cargo-associated molecular motors propel the cargo along cytoskeletal tracks. However, the forces impact not only the cargo, but also the underlying cytoskeletal filaments. To better understand the interplay between cargo transport and the organization of cytoskeletal filaments, we employ coarse-grained computer simulations to study actin filaments interacting with cargo-anchored myosin motors in a confined domain. We show that cargo transport can lead to the segregation of filaments into domains of preferred filament polarity separated by clusters of aggregated cargoes. The formation of polarity-sorted filament domains is enhanced by larger numbers of cargoes, more motors per cargo, and longer filaments. Analysis of individual trajectories reveals dynamic and heterogeneous behavior, including locally stable aggregates of cargoes that undergo rapid coalescence into larger clusters when sufficiently close. Our results provide insight into the impact of motor-driven organelle transport on actin filaments, which is relevant both in cells and in synthetic environments. O_TEXTBOXSIGNIFICANCE The actin cytoskeleton is vital for intracellular transport, and there is an intricate interplay between the organization of the actin network and cargo transport by molecular motors. In this work, we use computer simulations to demonstrate that the transport of cargoes by teams of molecular motors can lead to the emergence of filament domains, separated by clusters of cargoes, that are sorted by the polarity of filaments. The results, which highlight feedback between transport and filament organization, provide insight into mechanisms influencing the cytoskeleton in cells and in reconstituted systems. C_TEXTBOX

biophysics↗

bioRxiv2024

Morphometric analysis of actin networks

The organization of cytoskeletal elements is pivotal for coordinating intracellular transport in eukaryotic cells. Several quantitative measures based on image analysis have been proposed to characterize morphometric features of fluorescently labeled actin networks. While helpful in detecting differences in actin organization between treatments or genotypes, the accuracy of these measures could not be rigorously assessed due to a lack of ground-truth data to which they could be compared. To overcome this limitation, we utilized coarse-grained computer simulations of actin filaments and crosslinkers to generate synthetic actin networks with varying levels of bundling. We converted the simulated networks into pseudo-fluorescence images similar to images obtained using confocal microscopy. Using both published and novel analysis procedures, we extracted a series of morphometric parameters and benchmarked them against analogous measures based on the ground-truth actin configurations. Our analysis revealed a set of parameters that reliably reports on actin network density, orientation, ordering, and bundling. Application of these morphometric parameters to root epidermal cells of Arabidopsis thaliana revealed subtle changes in network organization between wild-type and mutant cells. This work provides robust measures that can be used to quantify features of actin networks and characterize changes in actin organization for different experimental conditions.

biophysics↗

bioRxiv2022

Organization and Dynamics of Crosslinked Actin Filaments in Confined Environments

The organization of the actin cytoskeleton is impacted by the interplay between physical confinement, features of crosslinking proteins, and deformations of semiflexible actin filaments. Some crosslinking proteins preferentially bind filaments in parallel, while others bind more indiscriminately. However, a quantitative understanding of how the mode of binding influences the assembly of actin networks in confined environments is lacking. Here we employ coarse-grained computer simulations to study the dynamics and organization of semiflexible actin filaments in confined regions upon the addition of crosslinkers. We characterize how the emergent behavior is influenced by the system shape, the number and type of crosslinking proteins, and the length of filaments. Structures include isolated clusters of filaments, highly connected filament bundles, and networks of interconnected bundles and loops. Elongation of one dimension of the system promotes the formation of long bundles that align with the elongated axis. Dynamics are governed by rapid crosslinking into aggregates, followed by a slower change in their shape and connectivity. Crosslinking decreases the average bending energy of short or sparsely connected filaments by suppressing shape fluctuations. However, it increases the average bending energy in highly connected networks because filament bundles become deformed and small numbers of filaments exhibit long-lived, highly unfavorable configurations. Indiscriminate crosslinking promotes the formation of high-energy configurations due to the increased likelihood of unfavorable, difficult-to-relax configurations at early times. Taken together, this work demonstrates physical mechanisms by which crosslinker binding and physical confinement impact the emergent behavior of actin networks, which is relevant both in cells and in synthetic environments. SIGNIFICANCEThe actin cytoskeleton is vital for intracellular transport, yet it remains challenging to understand how its organization is impacted by the interplay between physical confinement and the crosslinking of semiflexible actin filaments. In this study, we explore how the mode of crosslinker binding and the shape of the confining region impact the assembly and organization of actin filaments. The dynamics are governed by rapid crosslinking of spatially proximal filaments into aggregates, followed by slower relaxation of their shape and connectivity. Indiscriminate crosslinking promotes more highly connected networks, greater curvature of long filament bundles, and a subset of filaments in highly unfavorable configurations. The results provide insight into mechanisms influencing the cytoskeleton in cells and in reconstituted systems.

biophysics↗