Universal glass-forming behavior of in vitro and living cytoplasm

Abstract

Physiological processes in cells are performed efficiently without getting jammed although cytoplasm is highly crowded with various macromolecules. Elucidating the physical machinery is challenging because the interior of a cell is so complex and driven far from equilibrium by metabolic activities. Here, we studied the mechanics of in vitro and living cytoplasm using the particle-tracking and manipulation technique. The molecular crowding effect on cytoplasmic mechanics was selectively studied by preparing simple in vitro models of cytoplasm from which both the metabolism and cytoskeletons were removed. We obtained direct evidence of the cytoplasmic glass transition; a dramatic increase in viscosity upon crowding quantitatively conformed to the super-Arrhenius formula, which is typical for fragile colloidal suspensions close to jamming. Furthermore, the glass-forming behaviors were found to be universally conserved in all the cytoplasm samples that originated from different species and developmental stages; they showed the same tendency for diverging at the macromolecule concentrations relevant for living cells. Notably, such fragile behavior disappeared in metabolically active living cells whose viscosity showed a genuine Arrhenius increase as in typical strong glass formers. Being actively driven by metabolism, the living cytoplasm forms glass that is fundamentally different from that of its non-living counterpart.

Glassy dynamics of a model of bacterial cytoplasm with metabolic activities

“…We introduce a model of bacterial cytoplasm focusing on the effect of non-SPP-type activity, in which proteins are modeled as particles under thermal agitation and their conformational change is taken into account as a change in the volume of the particles. 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].…”

Substrate Channelingviaa Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase

“…The transient GAPDH-LDH complex that forms in experiments with purified enzymes can be much more durable in concentrated protein solution in cytosol or in cell extracts 14,15,46 . The high protein concentrations can produce excluded volume effects that can increase the interaction energy (Δ G ) by favoring protein-protein interactions that can decrease the number of water molecules trapped in hydration shells 14,15,46 . It is also necessary to notice that in cytosol LDH-GAPDH complex can be a part of much larger glycolytic metabolon 8-10 .…”

The Evolution of the Cryopreservation Techniques in Reproductive Medicine—Exploring the Character of the Vitrified State Intra- and Extracellularly to Better Understand Cell Survival after Cryopreservation

“…An increase in the concentration of intracellular macromolecules is called "macromolecular crowding". In freezing studies on bacterial cytoplasm, glass-like properties have been reported to differ from those outside the cell [49,50]. In Lactobacillus and several other organisms, it has been described that osmotic dehydration emphasizes the intracellular macromolecular crowding.…”