An official website of the United States government
An array of motor proteins consumes chemical energy in setting up the architectures of chromosomes. Here, we explore how the structure of ideal polymer chains is influenced by two classes of motors. The first class which we call “swimming motors” acts to propel the chromatin fiber through three-dimensional space. They represent a caricature of motors such as RNA polymerases. Previously, they have often been described by adding a persistent flow onto Brownian diffusion of the chain. The second class of motors, which we call “grappling motors” caricatures the loop extrusion processes in which segments of chromatin fibers some distance apart are brought together. We analyze these models using a self-consistent variational phonon approximation to a many-body Master equation incorporating motor activities. We show that whether the swimming motors lead to contraction or expansion depends on the susceptibility of the motors, that is, how their activity depends on the forces they must exert. Grappling motors in contrast to swimming motors lead to long-ranged correlations that resemble those first suggested for fractal globules and that are consistent with the effective interactions inferred by energy landscape analyses of Hi-C data on the interphase chromosome.
more »
« less
This content will become publicly available on December 14, 2025
Chromatin folding through nonuniform motorization by responsive motor proteins
Chromatin is partially structured through the effects of biological motors. “Swimming motors” such as RNA polymerases and chromatin remodelers are thought to act differentially on the active parts of the genome and the stored inactive part. By systematically expanding the many-body master equation for chromosomes driven by swimming motors, we show that this nonuniform aspect of motorization leads to heterogeneously folded conformations, thereby contributing to chromosome compartmentalization.
more »
« less
- Award ID(s):
- 2019745
- PAR ID:
- 10597746
- Publisher / Repository:
- AIP Publishing
- Date Published:
- Journal Name:
- The Journal of Chemical Physics
- Volume:
- 161
- Issue:
- 22
- ISSN:
- 0021-9606
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Fish locomotion emerges from diverse interactions among deformable structures, surrounding fluids and neuromuscular activations, i.e. fluid–structure interactions (FSI) controlled by fish's motor systems. Previous studies suggested that such motor-controlled FSI may possess embodied traits. However, their implications in motor learning, neuromuscular control, gait generation, and swimming performance remain to be uncovered. Using robot models, we studied the embodied traits in fish-inspired swimming. We developed modular robots with various designs and used central pattern generators (CPGs) to control the torque acting on robot body. We used reinforcement learning to learn CPG parameters for maximizing the swimming speed. The results showed that motor frequency converged faster than other parameters, and the emergent swimming gaits were robust against disruptions applied to motor control. For all robots and frequencies tested, swimming speed was proportional to the mean undulation velocity of body and caudal-fin combined, yielding an invariant, undulation-based Strouhal number. The Strouhal number also revealed two fundamental classes of undulatory swimming in both biological and robotic fishes. The robot actuators were also demonstrated to function as motors, virtual springs and virtual masses. These results provide novel insights in understanding fish-inspired locomotion.more » « less
-
The 3D spatiotemporal organization of the human genome inside the cell nucleus remains a major open question in cellular biology. In the time between two cell divisions, chromatin—the functional form of DNA in cells—fills the nucleus in its uncondensed polymeric form. Recent in vivo imaging experiments reveal that the chromatin moves coherently, having displacements with long-ranged correlations on the scale of micrometers and lasting for seconds. To elucidate the mechanism(s) behind these motions, we develop a coarse-grained active polymer model where chromatin is represented as a confined flexible chain acted upon by molecular motors that drive fluid flows by exerting dipolar forces on the system. Numerical simulations of this model account for steric and hydrodynamic interactions as well as internal chain mechanics. These demonstrate that coherent motions emerge in systems involving extensile dipoles and are accompanied by large-scale chain reconfigurations and nematic ordering. Comparisons with experiments show good qualitative agreement and support the hypothesis that self-organizing long-ranged hydrodynamic couplings between chromatin-associated active motor proteins are responsible for the observed coherent dynamics.more » « less
-
We present a mathematical model of lophotrichous bacteria, motivated by Pseudomonas putida, which swim through fluid by rotating a cluster of multiple flagella extended from near one pole of the cell body. Although the flagella rotate individually, they are typically bundled together, enabling the bacterium to exhibit three primary modes of motility: push, pull, and wrapping. One key determinant of these modes is the coordination between motor torque and rotational direction of motors. The computational variations in this coordination reveal a wide spectrum of dynamical motion regimes, which are modulated by hydrodynamic interactions between flagellar filaments. These dynamic modes can be categorized into two groups based on the collective behavior of flagella, i.e., bundled and unbundled configurations. For some of these configurations, experimental examples from fluorescence microscopy recordings of swimming P. putida cells are also presented. Furthermore, we analyze the characteristics of stable bundles, such as push and pull, and investigate the dependence of swimming behaviors on the elastic properties of the flagella.more » « less
-
Abstract Active dispersal of microorganisms is often attributed to the cells’ motile organelles. However, much less is known about whether sessile cells can access such motility through aggregation with motile counterparts. Here, we show that the rosette aggregates of the bacteriumCaulobacter crescentus, although predominantly sessile, can actively disperse through the flagellar motors of motile members. Comparisons in kinematics between the motile rosettes and solitary swimming cells indicate that the rosettes can be powered by as few as a single motor. We further reconstructed the 3D movements of the rosettes to reveal that their proximity to a solid-liquid interface promotes a wheel-like rolling, as powered by the flagellar torque. This rolling movement also features a sequence of sharp turns, a reorientation mechanism distinct from that of swimming cells. Overall, our study elucidates an unexplored regime of aggregation-based motility that can be widely applied to sessile-motile composites.more » « less
