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Josef Hamacek

Publications and source records attributed to Josef Hamacek.

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Physical Properties of Dextran Solutions as Model Crowding Media

The role of macromolecular crowding in living systems is widely appreciated, but artificial crowders used to model these effects in vitro are often inadequately characterized. In this work, we examine density, viscosity, polymer self-diffusion and water diffusion in crowded dextran systems. Dextran viscosity and self-diffusion follow size-dependent trends, collectively described by universal functions of the overlap concentration corresponding to a Flory exponent of 0.44, characteristic of branched polymers. Viscosity increases with concentration as a power law, with a crossover from dilute to semi-dilute behaviors. Dextran self-diffusion decays exponentially: this can be interpreted in light of Rosenfeld's excess entropy scaling hypothesis. Water self-diffusivity and specific volume decrease with concentration, but show no dependence on polymer size. We show how these results can be used to construct the true volume fraction of crowders, which takes into account bound water. Overall, our findings showcase the power of polymer physics concepts in macromolecular crowding studies in vitro.

cond-mat.soft

Kinetic theory of Hyaluronan cleavage by Bovine Testicular Hyaluronidase in Standard and Crowded Environments

${\bf Background}$ Details of the kinetic pathways governing enzymatic cleavage of hyaluronic acid (HA) by hyaluronidase are still widely uncharted. Capillary electrophoresis-based assays were used for accurate quantification of enzymatic products. A crowding agent was also employed to mimic excluded-volume constraints typical of in-vivo conditions. $ {\bf Scope}$ Introduce a comprehensive kinetic model describing the late-stage degradation of HA by hyaluronidase and identify the relevant kinetic pathways and the associated rates. ${\bf Major Conclusions}$ All relevant fragmentation and transglycosylation pathways and rates were identified. Two dimers forming a tetramer is the dominant recombination pathway. Macromolecular and self-crowding slow down the kinetics but do not alter the underlying mechanisms. ${\bf General Significance}$ Our results bring a novel and comprehensive quantitative insight into enzymatic HA degradation. Rationalizing the effect of crowding brings the intricate conditions of in-vivo settings a little closer, and also stands as a powerful tool to pinpoint relevant kinetic pathways in complex systems.

cond-mat.soft