title: 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.
authors.affiliation: Department 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. Electronic address: feig@msu.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Feig
authors.affiliation: Advanced Institute for Computational Science, RIKEN, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Quantitative Biology Center, RIKEN, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Ryuhei
authors.initials: R
authors.lastname: Harada
authors.affiliation: Quantitative Biology Center, RIKEN, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Theoretical Molecular Science Laboratory and iTHES, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
authors.forename: Takaharu
authors.initials: T
authors.lastname: Mori
authors.affiliation: Theoretical Molecular Science Laboratory and iTHES, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
authors.forename: Isseki
authors.initials: I
authors.lastname: Yu
authors.affiliation: Quantitative Biology Center, RIKEN, Laboratory for Biochemical Simulation, Suita, Osaka 565-0874, Japan; Institute for Advanced Biosciences, Keio University, Fujisawa 252-8520, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Takahashi
authors.affiliation: Advanced Institute for Computational Science, RIKEN, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Quantitative Biology Center, RIKEN, International Medical Device Alliance (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Theoretical Molecular Science Laboratory and iTHES, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sugita
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D003593:Cytoplasm / Q000737:chemistry / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D045704:Mycoplasma genitalium / Q000166:cytology* / Q000235:genetics
chemical_list: D001426:Bacterial Proteins
keywords: Crowding; Metabolic reaction network; Mycoplasma genitalium; Protein structure prediction