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Strange behavior in the crowded cellular environment

A group of researchers from RIKEN and Michigan State University have used the powerful K computer to show how molecules move within the extremely crowded interior of a bacterial cell.

Nov 2, 2016

In vitro studies—studies performed in test tubes—have given us great understanding of how molecules interact with one another. However, little is really known of how they interact in vivo—in actual cells—because due to the crowding, they can act based in ways that are difficult to model in test tubes. Approximately 70 percent of the cytosol is composed of water, and the remaining 30 percent is made up of macromolecules such as ribosomes, biomolecules such as proteins and DNA, metabolites such as ATP and amino acids, and ions.

For the study, published in eLife, the group modeled the inside of the smallest known bacteria—Mycoplasma genitalium—which has a length of approximately 400 nanometers—one nanometer being 1 billionth of a meter—and dynamically modeled approximately one trillion atoms within the cell, making this one of the largest molecular dynamic simulations performed to date. ...

  1. Isseki Yu, Takaharu Mori, Tadashi Ando, Ryuhei Harada, Jaewoon Jung, Yuji Sugita, Michael Feig, "Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm", eLife, doi: 10.7554/eLife.19274