Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology

• Construction of a complete atomistic model of a bacterial cytoplasm.
• Genome-scale protein structure prediction.
• Correspondence between metabolic reaction network and physical composition of atomistic system.

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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