A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO).
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 cytoplasmic model (PD model) produced by CGCYTO with two other coarse-grained hard-sphere cytoplasmic models: 1), F70 model, macromolecules in the cytoplasm were modeled by homogeneous hard spheres with a radius of 55 Å, the size of Ficoll70 and 2), HS model, each macromolecule in the cytoplasm was modeled by a hard sphere of equal volume. It was found that the folding temperature T(f) of a test protein (apoazurin) in a PD model is ~5° greater than that in a F70 model. In addition, the deviation of T(f) in a PD model is twice as much as that in a HS model when an apoazurin is randomly placed at different voids formed by particle fluctuations in PD models.
Department of Physics, University of Houston, Houston, Texas, USA.
Qian
Q
Wang
Margaret S
MS
Cheung
D000465:Algorithms; D001059:Apoproteins / Q000378:metabolism; D001400:Azurin / Q000378:metabolism; D055592:Biophysical Phenomena; D003593:Cytoplasm / Q000378:metabolism*; D004926:Escherichia coli / Q000378:metabolism*; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D012985:Software Design; D013816:Thermodynamics
D001059:Apoproteins; C038778:apoazurin; D001400:Azurin