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

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.

Keywords: Crowding; Metabolic reaction network; Mycoplasma genitalium; Protein structure prediction.

Figure 1

Schematic view of Mycoplasma genitalium and the cytoplasmic subsection modeled here. The attachment organelle and its internal structure is schematically illustrated in brown.

Figure 2

Structures of cytoplasmic macromolecules. Coloring is by residue index. The labels correspond to the macromolecular tags in Tables S1-S3.

Figure 3

Predicted cytoplasmic metabolic reaction network. Compounds assumed to enter or exit the system with respect to the environment are highlighted in orange and red respectively. Colored sections represent major groups of metabolic pathways.

Figure 4

Complete cytoplasmic model system of Mycoplasma genitalium. The complete system is shown on the left, an enlarged cross-section on the right.