Order and disorder in intermediate filament proteins

AbstractIntermediate filaments (IFs), important components of the cytoskeleton, provide a versatile, tunable network of self-assembled proteins. IF proteins contain three distinct domains: an α-helical structured rod domain, flanked by intrinsically disordered head and tail domains. Recent studies demonstrated the functional importance of the disordered domains, which differ in length and amino-acid sequence among the 70 different human IF genes. Here, we investigate the biophysical properties of the disordered domains, and review recent findings on the interactions between them. Our analysis highlights key components governing IF functional roles in the cytoskeleton, where the intrinsically disordered domains dictate protein–protein interactions, supramolecular assembly, and macro-scale order

Toward Task Capable Active Matter: Learning to Avoid Clogging in Confined Collectives via Collisions

Social organisms which construct nests consisting of tunnels and chambers necessarily navigate confined and crowded conditions. Unlike low density collectives like bird flocks and insect swarms in which hydrodynamic and statistical phenomena dominate, the physics of glasses and supercooled fluids is important to understand clogging behaviors in high density collectives. Our previous work revealed that fire ants flowing in confined tunnels utilize diverse behaviors like unequal workload distributions, spontaneous direction reversals and limited interaction times to mitigate clogging and jamming and thus maintain functional flow; implementation of similar rules in a small robophysical swarm led to high performance through spontaneous dissolution of clogs and clusters. However, how the insects learn such behaviors and how we can develop &ldquo;task capable&rdquo; active matter in such regimes remains a challenge in part because interaction dynamics are dominated by local, potentially time-consuming collisions and no single agent can survey and guide the entire collective. Here, hypothesizing that effective flow and clog mitigation could be generated purely by collisional learning dynamics, we challenged small groups of robots to transport pellets through a narrow tunnel, and allowed them to modify their excavation probabilities over time. Robots began excavation with equal probabilities to excavate and without probability modification, clogs and clusters were common. Allowing the robots to perform a &ldquo;reversal&rdquo; and exit the tunnel when they encountered another robot which prevented forward progress improved performance. When robots were allowed to change their reversal probabilities via both a collision and a self-measured (and noisy) estimate of tunnel length, unequal workload distributions comparable to our previous work emerged and excavation performance improved. Our robophysical study of an excavating swarm shows that despite the seeming complexity and difficulty of the task, simple learning rules can mitigate or leverage unavoidable features in task capable dense active matter, leading to hypotheses for dense biological and robotic swarms. &nbsp;</p

Forces underlying the conformational selection of myelin basic protein

Myelin Basic Protein (MBP) has important biological role in stabilizing and compacting the myelin sheath. Previous evidence suggest that MBP adopts a compact structure when adsorbed to negatively charged membrane and gains flexibility and expands in solution. This inherent flexibility in solution, unlike most proteins, is termed intrinsic disorder. Being highly disordered, MBP adopts a wide variety of conformations simultaneously in solution. Small angle x-ray scattering and analysis using ensemble modelling are used to quantify the conformatioal diversity under varying pH and salt conditions.MBP is a polyampholyte, having both positively and negatively charged monomers with a high excess of positive charge. At pH 7.4 the mean radius of gyration (R_g) of MBP decreases with increasing salts, with a local minimum encountered around 100mM followed by re-swelling and then re-compaction. At pH 10 MBP displays a size minimum near 100mM yet no re-compaction is observed up to 500mM salt concentration. MBP in pH 4 displays R_g trend highly similar to pH 7.4, though always with slightly larger R_g as expected with its increased net charge. Underlying forces are discussed through free energy estimates calculated using polymer physics derivations.MBP’s size minimum at 100mM salt concentration is not entirely consistent with simplistic polyampholyte view, and more likely secondary structure changes are involved. Calculations indicate that salt concentration strongly affects secondary structure selection of MBP by modulating an interplay between electrostatic interaction and polymer chain entropy. The results imply a strategy for designing structural stabilization upon adsorption to a surface

Gliders in shape-changing active matter

We report in experiment and simulation the spontaneous formation of dynamically bound pairs of shape changing smarticle robots undergoing locally repulsive collisions. Borrowing terminology from Conway's simulated Game of Life, these physical `gliders' robustly emerge from an ensemble of individually undulating three-link two-motor smarticles and can remain bound for hundreds of undulations and travel for multiple robot dimensions. Gliders occur in two distinct binding symmetries and form over a wide range of angular flapping extent. This parameter sets the maximal concavity which influences formation probability and translation characteristics. Analysis of dynamics in simulation reveals the mechanism of effective dynamical attraction -- a result of the emergent interplay of appropriately oriented and timed repulsive interactions