Diffusion coefficient of Venus YFP in cytoplasm

Value 8 µm^2/s Range: +4/-2 µm^2/s
Organism Bacteria Escherichia coli
Reference Elf J, Li G, Xie XS. 2007. Probing transcription factor dynamics at the single-molecule level in a living cell. Science May 25 316:1191–94 Supporting Online Material pp 5PubMed ID17525339
Method P.1194 left column 2nd paragraph: "[Investigators] next determine the apparent diffusion constant. The mean square displacement (MSD) of IPTG-bound LacI measured at various time intervals follows a linear dependence at the time scale >10 ms (Fig. 4C) and does not exhibit anomalous diffusion, as was observed for mRNA in E. coli cytoplasm at longer time scales (ref 26). The apparent diffusion constant, Deff = 0.4 ± 0.02 μm^2/s, is one order of magnitude higher than the 1D diffusion constant (D1) of LacI dimers on DNA. Therefore, [they] attribute apparent diffusion to the contribution from 3D diffusion in between nonspecific bindings. Using fluorescence correlation spectroscopy (FCS) (ref 27), [they] measured the in vivo diffusion constant of LacI-Venus without its DNA binding domain to be D3 = 3 ± 0.3 μm^2/s (SOM=Supporting Online Material). This suggests that the Lac I dimer spends ∼87% of the time nonspecifically bound and diffusing along DNA (SOM). This fraction is consistent with the previous population-averaged estimate (>90%) on the basis of the LacI tetramer concentration in minicells (ref 28)."
Comments Supporting Online Material p.5 bottom paragraph: "[Investigators] also measured the diffusion constant of free Venus in E. coli. As shown in Fig. S7, the diffusion constant of free Venus is estimated to be D3=8(+4)(-2)µm^2/s. This is also in good agreement with Elowitz et al. (ref 5 BNID 100193)." Free author manuscript available at PUBMED. For diffusion rate of 40kDa dextran in cytoplasm see BNID 100198.
Entered by Uri M
ID 105477