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

J Mol Graph Model. 2015 May:58:1-9. doi: 10.1016/j.jmgm.2015.02.004. Epub 2015 Feb 28.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / chemistry
  • Cytoplasm* / chemistry
  • Cytoplasm* / metabolism
  • Metabolic Networks and Pathways
  • Models, Biological*
  • Mycoplasma genitalium / cytology*
  • Mycoplasma genitalium / genetics

Substances

  • Bacterial Proteins