A new view of the bacterial cytosol environment.
Bottom Line: In simulations containing ubiquitin, to represent a protein component, metabolite diffusion was reduced owing to long lasting protein-metabolite interactions.The dielectric constant of these simulations was found to differ from that of pure water only through a large contribution from ubiquitin as metabolite and monatomic ion effects cancel.We hope that future studies may be able to accurately predict how binding interactions differ in the cytosol relative to dilute aqueous solution.
Affiliation: Department of Life Science, Barcelona Supercomputer Center, Barcelona, Spain.Show MeSH
Related in: MedlinePlus
Mentions: Figure 2 shows a view through the 100 M box at the beginning of the production simulation and after 200 ns. It is clear that after equilibration there is a significant difference in structure. Within the 200 ns simulation of the 100 Å boxes many NIMS were formed which were stable over relatively long time periods. The most interesting of these NIMS were those with a stacking core of nucleotide base like groups (Figure 3 A). These stacks continuously gain and lose bases and persist as long as 50 ns. Some stack NIMS seem reminiscent of RNA and we speculate that these structures often show similarities with the elongation complex of RNA polymerases  in the way phosphates are aligned with ribose rings (Figure S3).
Affiliation: Department of Life Science, Barcelona Supercomputer Center, Barcelona, Spain.