Determining the structure and viscoelasticity of the cytosol in atomistic detail

Aleksei Aksimentiev, University of Illinois at Urbana-Champaign

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Aleksei Aksimentiev, Christopher Maffeo, Han-Yi Chou, David Winogradoff, Shidi Zhao, Himanshu IMANSHU Joshi, Kush Coshic, Jingqian Liu, Behzad Mehrafrooz

The interior of the cell is a highly complex and crowded environment. Biological macromolecules occupy a significant fraction of the cytoplasmic volume while performing all the processes fundamental to life. Experiments performed in vivo, including in–cell nuclearmagnetic resonance and in–cell fluorescence spectroscopy, hold promise to probe the intracellular milieu, but face considerable technical challenges and are limited in temporal and spatial resolution. Drawing from proteomics data, we have built a computational model of a eukaryotic cytoplasm at multiple resolutions. The endpoint of coarse-grained simulations has been mapped to an all-atom representation of the cytoplasm. Explicit-solvent molecular dynamics simulations of this system will provide the opportunity to investigate protein structure and dynamics in a biological setting and the quinary interactions between proteins. This work is an important advancement towards building an atomistic computational model of an entire cell.