A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO).

ABSTRACT: We have investigated protein stability in an environment of Escherichia coli cytoplasm using coarse-grained computer simulations. To coarse-grain a small slide of E. coli's cytoplasm consisting of over 16 million atoms, we have developed a self-assembled clustering algorithm (CGCYTO). CGCYTO uses the shape parameter and asphericity as well as a parameter λ (ranging from 0 to 1) that measures the covolume of a test protein and a macromolecule against the covolume of a test protein and a sphere of equal volume as that of a macromolecule for the criteria of coarse-graining a cytoplasmic model. A cutoff λ(c) = 0.8 was chosen based on the size of a test protein and computational resources and it determined the resolution of a coarse-grained cytoplasm. We compared the results from a polydisperse

SUBMITTER: Wang Q 

PROVIDER: S-EPMC3353097 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature