Geometrical and Mechanical Properties Control Actin Filament Organization

Abstract

TRIOBP is an actin-bundling protein. Mutations of TRIOBP are associated with human deafness DFNB28. TRIOBP has three isoforms, named TRIOBP-1, TRIOBP-4, and TRIOBP-5. In vitro, TRIOBP isoform 4 (TRI-OBP-4) forms dense F-actin bundles resembling the inner ear hair cell rootlet structure. Deletion of TRIOBP isoforms 4 and 5 leads to hearing loss in mice due to the absence of stereocilia rootlets. The mechanism of actin bundle formation by TRIOBP is not fully understood. The amino acid sequences of TRI-OBP isoforms 4 and 5 contain two repeated motifs, referred to here as R1 and R2. Recent our study demonstrated that R1 motif is the major actin-binding domain of TRIOBP-4, and the binding of R2 motif with actin filaments is nonspecific. Structural analysis of TRIOBP by amino acid sequence showed ID proteins. Thus the second structure of TRIOBP may not have. To investigate the structural property of TRIOBP-4, we analyzed the structure of TRIOBP-4 by using circular dichroism, dynamic light scattering, and fluorescence correlation spectroscopy. Our analysis show that TRIOBP has a beta-sheet, but not alpha-helix. To investigate the structure of tight F-actin bundle structure with TRIOBP, we analyzed 3-D structure of the bundle by using 3-D image analysis from transmitted electron microscope images.

Active cargo positioning in antiparallel transport networks

“…1). Inclusion of methylcellulose as a depleting agent ensured that most of the network remained within ∼200 nm of the glass surface (20), thus forming an actin sheet.…”

Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling

“…Actin bundles are important for cellular stability, growth and mechanosensing. While prior experimental and modeling research has primarily focused on bundle formation processes [40,72,95,96], in this work we have addressed the stability and temporal evolution of various bundle configurations. We used MEDYAN, a mechano-chemical forcefield based on molecular principles, to simulate bundle dynamics in 3D.…”

“…Filaments that polymerize towards the boundary experience a reduction in polymerization rate based on the Brownian ratchet model [71]. In MEDYAN, the growth propensity for an actin filamentous tip is based on the local, instantaneous concentration of diffusing G-actin in the tip’s neighborhood [58], while, in comparison, actin filaments grow/shrink at a constant rate in Cytosim, [72]. Furthermore, MEDYAN can explicitly account for ATP, ADP.Pi, and ADP bound actin monomeric states, enabling more elaborate simulations of F-actin polymerization dynamics [73,74].…”

A Mechanistic View of Collective Filament Motion in Active Nematic Networks

“…In an analogous manner, we assessed the number of microtubules in our one-dimensional representation of the experimental chamber of length 400 mm to be $400. Those filaments are placed randomly as described below (In Silico Study: Random Polarity Field) and experience a drag coefficient of g ¼ 0.5 pN s/mm (30)(31)(32). As motor parameters, we use V m ¼ 20 nm/s ( 6), F m $ 1 pN ( 5), and N m ¼ 25 as the average number of motors per filament (18).…”