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Updated: Apr 16, 2026

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization
Published on: October 29, 2019
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
Michael Feig1, Ryuhei Harada2, Takaharu Mori3
1Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, United States; Department of Chemistry, Michigan State University, East Lansing, MI 48824, United States; Quantitative Biology Center, RIKEN, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
Abstract:
A model for the cytoplasm of Mycoplasma genitalium is presented that integrates data from a variety of sources into a physically and biochemically consistent model. Based on gene annotations, core genes expected to be present in the cytoplasm were determined and a metabolic reaction network was reconstructed. The set of cytoplasmic genes and metabolites from the predicted reactions were assembled into a comprehensive atomistic model consisting of proteins with predicted structures, RNA, protein/RNA complexes, metabolites, ions, and solvent. The resulting model bridges between atomistic and cellular scales, between physical and biochemical aspects, and between structural and systems views of cellular systems and is meant as a starting point for a variety of simulation studies.
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