Biologistics—Diffusion coefficients for complete proteome of Escherichia coli

Abstract

Motivation: Biologistics provides data for quantitative analysis of transport (diffusion) processes and their spatio-temporal correlations in cells. Mobility of proteins is one of the few parameters necessary to describe reaction rates for gene regulation. Although understanding of diffusion-limited biochemical reactions in vivo requires mobility data for the largest possible number of proteins in their native forms, currently, there is no database that would contain the complete information about the diffusion coefficients (DCs) of proteins in a given cell type.Results: We demonstrate a method for the determination of in vivo DCs for any molecule—regardless of its molecular weight, size and structure—in any type of cell. We exemplify the method with the database of in vivo DC for all proteins (4302 records) from the proteome of K12 strain of Escherichia coli, together with examples of DC of amino acids, sugars, RNA and DNA. The database follows from the scale-dependent viscosity reference curve (sdVRC). Construction of sdVRC for prokaryotic or eukaryotic cell requires ~20 in vivo measurements using techniques such as fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), nuclear magnetic resonance (NMR) or particle tracking. The shape of the sdVRC would be different for each organism, but the mathematical form of the curve remains the same. The presented method has a high predictive power, as the measurements of DCs of several inert, properly chosen probes in a single cell type allows to determine the DCs of thousands of proteins. Additionally, obtained mobility data allow quantitative study of biochemical interactions in vivo.Contact: rholyst@ichf.edu.plSupplementary information: Supplementary data are available at Bioinformatics Online.

The effect of macromolecular crowding on mobility of biomolecules, association kinetics, and gene expression in living cells

“…Kalwarczyk et al [15] observed almost 10 fold decrease of ξ in E. coli with respect to HeLa and Swiss 3T3 cells. They collected literature data [12,13,[65][66][67][68][69][70][71][72][73][74][75][76][77] of diffusion coefficients in the cytoplasm of E. coli and used Equation 5 to fit the data.…”

“…The effective viscosity was calculated as the reciprocal of the relative diffusion coefficient provided in Seksek et al [40], Lukacs et al [42], Phair and Misteli [44], and Hinde et al [59]. Hydrodynamic radius of the DNA fragments was calculated from the relation taken from the work of Kalwarczyk et al [15]: r p = 0.024M 0.57 w ; where M w corresponded to molecular weight of the DNA. Hydrodynamic radius of dextran polymers was calculated from the relation obtained on the basis of experiments of Ioan et al [61]: r p = 0.072M 0.…”

“…The effect of macromolecular crowding on reaction rates and equilibrium constants may arise from: (i) change of reactants' mobility [12][13][14][15], (ii) depletion interaction (excluded volume effect) that results in attraction between reactants [1,8,[16][17][18], and (iii) non-specific chemical interaction with crowders [9,10,19,20]. Over three decades of studies of crowded systems, both at the theoretical and experimental level, contributed significantly to our understanding of these effects.…”

Molecular simulations of cellular processes

“…These interactions were refined in the subsequent phase, until the calculated diffusion coefficients of all macromolecules approached a cell-scale reference curve (Fig. 2c) (Kalwarczyk et al 2012;Sozański et al 2013;Feng et al 2016). The final nonspecific interactions, which accounted for the many body effects ignored in the first phase, were moderate enough to reduce aggregation and correlated strongly with binding energies between E. coli macromolecules.…”

Scanning X-ray nano-diffraction on eukaryotic cells

“…Therefore the damage sites will spread within a protein due to chemical reactions, which is determined by the rate constants of the specific chemical reaction and should not be further estimated here due to the high variability, or within the whole cell due to diffusion of more stable radical species. The mean squared displacement of a small protein with a diffusion constant of about 10 µm 2 /s (compare [147]) during one exposure of 0.5 s is about r 2 = 30 µm 2 or r 2 = 5.5 µm, which might contribute to the damage spreading. However, since the radiation damage will only reach observable magnitudes in regions with a (critically) high radical concentration, only regions close to the exposed position will be (visibly) destroyed within short time intervals after the exposure.…”