Table 2: Summary of the results obtained for the porous medium model.

From: Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells

DrugD0 (μm2 s1)D (μm2 s1)R=D0/Dλ (μm)S/V (μm1)
Cytoplasm
 GFP169±630±42.3±0.20.8±0.26.3±1.3
 GFP329±19±13.2±0.11.5±0.24.0±0.4
  CYTD30±113±22.4±0.31.5±0.43.5±1.0
  WFA26±29±12.8±0.31.2±0.34.8±1.2
  NOC31±29±23.3±0.51.5±0.34.2±0.9
 GFP514±12±16.6±0.73.1±0.92.5±0.7
 CD51±211±22.3±0.21.3±0.33.9±0.9
 STAT224±16±13.8±0.82.0±0.83.3±1.3
Nucleus
 GFP166±629±32.3±0.20.8±0.26.3±1.4
 GFP325±28±13.1±0.31.6±0.33.9±0.7
  TSA30±211±32.8±0.72.0±0.82.9±1.2
  CQ28±113±22.1±0.31.7±0.72.8±1.2
 GFP513±1>1*<33*<5.51.6±0.2
 CD515±29.41.5±0.15.4,
  1. CD, chromodomain; CQ, chloroquine; CYTD, cytochalasin D; GFP, green fluorescent protein; NOC, nocodazole; STAT2, signal transducer and activator of transcription 2; WFA, withaferin A; TSA, trichostatin A.
  2. The parameters D0, D and λ were determined by least-squares fitting of the model function for diffusion in porous media21 to the measured time-dependent apparent diffusion coefficients of GFP1, GFP3, GFP5, the chromodomain (CD) of HP1β or STAT2 in human U2OS cells. CD and STAT2 were fluorescently labelled with GFP. The retardation R and the surface-to-volume ratio S/V=9/λ (1–1/R) were calculated from the fit results. The intracellular structure was perturbed by treatment of the cells with CYTD, WFA, NOC, TSA or CQ as indicated.
  3. *Since a significant fraction of GFP5 was trapped in the nucleus according to our FRAP analysis, these values apply only for the mobile GFP5 subpopulation.
  4. The microscopic diffusion coefficient of CD in the nucleus was fixed for least-squares fitting to that in the cytoplasm since these values should be similar in the short time-scale limit.
  5. This value corresponds to an effective surface-to-volume ratio including chromatin binding interactions.