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2015 ; 58
(ä): 1-9
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Complete atomistic model of a bacterial cytoplasm for integrating physics,
biochemistry, and systems biology
#MMPMID25765281
Feig M
; Harada R
; Mori T
; Yu I
; Takahashi K
; Sugita Y
J Mol Graph Model
2015[May]; 58
(ä): 1-9
PMID25765281
show ga
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.