Biology subjects

Lisicki, M.

Publications and source records attributed to Lisicki, M..

3 recordsLinked to original sources

bioRxiv2024

Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation

The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation. To estimate the hydrodynamic radius, we rely on the minimum dissipation approximation recently introduced by Cichocki et al. Using a large set of experimentally measured hydrodynamic radii of IDPs over a wide range of chain lengths and domain contributions, we demonstrate that our predictions are more accurate than the Kirkwood approximation and phenomenological approaches. Our technique may prove valuable in predicting the hydrodynamic properties of both fully unstructured and multidomain disordered proteins. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/578612v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1e2943aorg.highwire.dtl.DTLVardef@7193c8org.highwire.dtl.DTLVardef@9d5bceorg.highwire.dtl.DTLVardef@f64f72_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Topological evolution of sprouting vascular networks: from day-by-day analysis to general growth rules.

Engineering tissues with an embedded vasculature of well-controlled topology remains one of the basic problems in biofabrication. Still, little is known about the evolution of topological characteristics of vascular networks over time. Here, we perform a high-throughput day-by-day analysis of tens of microvasculatures that sprout from endothelial-cell coated micrometric beads embedded in an external fibrin gel. We use the bead-assays to systematically analyze (i) macroscopic observables such as the overall length and area of the sprouts, (ii) microscopic observables such as the lengths of segments or the branching angles and their distributions, as well as (iii) general measures of network complexity such as the average number of bifurcations per branch. We develop a custom angiogenic image analysis toolkit and track the evolution of the networks for at least 14 days of culture under various conditions, e.g., in the presence of fibroblasts or with added endothelial growth factor (VEGF). We find that the evolution always consists of three stages: (i) an inactive stage in which cells remain bound to the beads, (ii) a sprouting stage in which the sprouts rapidly elongate and bifurcate, and (iii) the maturation stage in which the growth slows down. We show that higher concentrations of VEGF lead to an earlier onset of sprouting and to a higher number of primary branches, yet without significantly affecting the speed of growth of the individual sprouts. We find that the mean branching angle is weakly dependent on VEGF and typically in the range of 60-75 degrees suggesting that, by comparison with the available Laplacian growth models, the sprouts tend to follow local VEGF gradients. Finally, we observe an exponential distribution of segment lengths, which we interpret as a signature of stochastic branching at a constant bifurcation rate (per unit branch length). Our results, due to high statistical relevance, may serve as a benchmark for predictive models and reveal how the external means of control, such as VEGF concentration, could be used to control the morphology of the vascular networks. We provide guidelines for the fabrication of optimized microvasculatures with potential applications in drug testing or regenerative medicine.

bioengineering↗

bioRxiv2023

DNA supercoiling-induced shapes alter minicircle hydrodynamic properties

DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.

biophysics↗