Abstract
Recent experiments have revealed that cytoplasms become glassy when their metabolism is suppressed, while they maintain fluidity in a living state. The mechanism of this active fluidization is not clear, especially for bacterial cytoplasms, since they lack traditional motor proteins, which can cause directed motions. We introduce a model of bacterial cytoplasm focusing on the impact of conformational change in proteins due to metabolism. In the model, proteins are treated as particles under thermal agitation, and conformation changes are treated as changes in particle volume. Simulations revealed that a small change in volume fluidizes the glassy state, accompanied by a change in fragility, as observed experimentally.
Highlights
Active matter [1,2] encompasses a vast range of nonequilibrium systems such as living organisms [3,4,5,6] and artificial objects including active Janus particles [7,8] and anisotropic vibrated rods [9] or disks [10]
We introduce a model of bacterial cytoplasm focusing on the impact of conformational change in proteins due to metabolism
By means of a molecular dynamics (MD) simulation of the model, we show that small changes in particle volume drastically accelerate the dynamics and alter the fragility from fragile to strong, as observed in previous experiments [19]
Summary
Active matter [1,2] encompasses a vast range of nonequilibrium systems such as living organisms [3,4,5,6] and artificial objects including active Janus particles [7,8] and anisotropic vibrated rods [9] or disks [10]. Recent experimental measurements of diffusivity and viscosity revealed that bacterial cytoplasm behaves to glass when adenosine triphosphate (ATP), the biological energy source, is depleted, while the dynamics is dramatically accelerated and the system behaves to a fluid when ATP is supplied [17,19,20] This activeness was shown to alter the fragility of the system: The system becomes stronger when ATP is supplied [19]. Bacterial cytoplasm is different from dense SPPs in that the former does not have traditional motor proteins, which undergo directed motion and can be modeled as SPPs. Instead, as Parry et al discussed, the metabolism of bacteria can cause non-SPP-type active perturbations, such as conformational changes in proteins, which may result in the fluidization of the glassy state [17]. By means of a molecular dynamics (MD) simulation of the model, we show that small changes in particle volume drastically accelerate the dynamics and alter the fragility from fragile to strong, as observed in previous experiments [19]
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