Physiological environment induces quick response – slow exhaustion reactions

Abstract

In vivo environments are highly crowded and inhomogeneous, which may affect reaction processes in cells. In this study we examined the effects of intracellular crowding and an inhomogeneity on the behavior of in vivo reactions by calculating the spectral dimension (ds), which can be translated into the reaction rate function. We compared estimates of anomaly parameters obtained from fluorescence correlation spectroscopy (FCS) data with fractal dimensions derived from transmission electron microscopy (TEM) image analysis. FCS analysis indicated that the anomalous property was linked to physiological structure. Subsequent TEM analysis provided an in vivo illustration; soluble molecules likely percolate between intracellular clusters, which are constructed in a self-organizing manner. We estimated a cytoplasmic spectral dimension ds to be 1.39 ± 0.084. This result suggests that in vivo reactions initially run faster than the same reactions in a homogeneous space; this conclusion is consistent with the anomalous character indicated by FCS analysis. We further showed that these results were compatible with our Monte-Carlo simulation in which the anomalous behavior of mobile molecules correlates with the intracellular environment, leading to description as a percolation cluster, as demonstrated using TEM analysis. We confirmed by the simulation that the above-mentioned in vivo like properties are different from those of homogeneously concentrated environments. Additionally, simulation results indicated that crowding level of an environment might affect diffusion rate of reactant. Such knowledge of the spatial information enables us to construct realistic models for in vivo diffusion and reaction systems.

Hybrid spatial Gillespie and particle tracking simulation

“…At this scale [ l = 52nm, which is 3 pixel of the original binarized transmission electron microscopy (TEM) image of Hiroi et al (2011)] we see a reduction in diffusion (cf. Fig.…”

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Fig. 6. A Based on the statistics of binarized Transmission electron microscopy (TEM) images from (Hiroi et al , 2011) B realistically looking intracellular obstacle geometries were generated (Hiroi et al , 2012). C shows a 3D section of a generated volume, which looks similar like other 3D observations of membrane enclosed compartments like e.g.

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From microscopy data to in silico environments for in vivo-oriented simulations

“…The anomaly coefficient α =0.94 does not match the values observed in in vivo FCS measurements ( α =0.768±0.14) [4,5]. Especially, the molecular crowding by mobile NROs seems to have an important effect [9,34].…”

“…The difference may render actual in vivo reaction processes deviate from those in vitro or in silico . Lately, we showed the results of a combined investigation of Fluorescence Correlation Spectroscopy (FCS) and Transmission Electron Microscopy (TEM) [4,5]. We examined the effects of intracellular crowding and inhomogeneity on the mode of reactions in vivo by calculating the spectral dimension ( d s ) which can be translated into the reaction rate function.…”

“…In our former simulation, we used just one size of NRO, which could, e.g., represent single molecular obstacles [4,5]. But in a cell, many of those molecules representing the NRO exist as complexes or polymers, for instance cytoskeletal proteins.…”