Biology subjects

Bratek-Skicki, A.

Publications and source records attributed to Bratek-Skicki, A..

4 recordsLinked to original sources

bioRxiv2025

An Effective Method for Determining the Degree of Oligomerization of hnRNPA2 Low Complexity Domain

Theoretical calculations and various experimental techniques were applied to determine fundamental physicochemical characteristics of the RNA-binding protein low complexity domain (hnRNPA2 LCD), in sodium chloride solutions. The protein monomer size, cross-section area, the dependence of the nominal charge on pH, and its isoelectric point were predicted. These theoretical data allowed one to analyze and interpret the adsorption of hnRNPA2 LCD molecules on mica, which was investigated by the streaming potential technique, and on polymer particles, acquired by laser Doppler velocimetry. It was shown that the protein adsorbed in the form of oligomers whose size was resolved by atomic force microscopy. In the case of the adsorption on particles, the oligomer size and zeta potential were derived by applying the general electrokinetic model. Additionally, the electrokinetic properties of the hnRNPA2 LCD functionalized particles were determined and compared with the bulk protein properties. Using these results, a fast and easy method for quantifying the oligomerization kinetic of unstable protein solutions was developed.

biochemistry↗

bioRxiv2023

Application of polystyrene sulfonate (PSS) for inhibiting toxicity of ALS/FTD-linked dipeptide repeats

The GGGGCC (G4C2) expansion in the noncoding region of C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The repeat region is translated into five different dipeptide repeat proteins (DPRs), of which the arginine-rich DPRs (R-DPRs) poly- GR (GRn) and poly-PR (PRn) are highly neurotoxic. In this study, we characterized the protective effect against R- DPR toxicity of polystyrene sulfonate (PSS), an FDA-approved drug applied in hyperkalemia, in biochemical, cellular and iPSC-derived motor neuron (MN) models. We found that PSS, in a length-dependent manner, interacts very tightly with R-DPRs, and releases their bound RNA in R-DPR - RNA mixtures. PSS significantly influences the liquid- liquid phase separation (LLPS) of R-DPRs elicited by RNA and reduces their ensuing cell toxicity in Neuro-2a cells. PSS is cell penetrable, and it can effectively rescue the inhibitory effect R-DPRs on axonal mitochondrial transport in iPSC-derived MNs. Shorter (n < 340) variants of PSS are not toxic either to cells or to mice upon intracerebroventricular injection up to 1 mM concentration. Our results suggest that its polymeric nature endows PSS with an advantageous effect in C9-ALS providing a potential therapeutic tool against this debilitating neurodegenerative disease.

molecular biology↗

bioRxiv2022

Quantification of surface tension effects and nucleation-and-growth rates during self-assembly of biological condensates

Liquid-solid and liquid-liquid phase separation (PS) drives the formation of functional and disease-associated biological assemblies. Principles of phase equilibrium are here employed to derive a general kinetic solution that predicts the evolution of the mass and size of biological assemblies. Thermodynamically, protein PS is determined by two measurable concentration limits: the saturation concentration and the critical solubility. Due to surface tension effects, the critical solubility can be higher than the saturation concentration for small, curved nuclei. Kinetically, PS is characterized by the primary nucleation rate constant and a combined rate constant accounting for growth and secondary nucleation. It is demonstrated that the formation of a few number of large condensates is possible without active mechanisms of size control and in the absence of coalescence phenomena. Our exact analytical solution can be used to interrogate how the elementary steps of PS are affected by candidate drugs.

biophysics↗

bioRxiv2019

A generic approach for studying the kinetics of liquid-liquid phase separation under near-native conditions

Understanding the kinetics and underlying physicochemical forces of liquid-liquid phase separation (LLPS) is of paramount importance in cell biology, requiring reproducible methods for the analysis of often severely aggregation-prone proteins. Frequently applied approaches, such as dilution of the protein from an urea-containing solution or cleavage of its fused solubility tag, however, often lead to very different kinetic behaviors. Here we suggest that at extreme pH values even proteins such as the low-complexity domain (LCD) of hnRNPA2, TDP-43, and NUP-98 can be kept in solution, and then their LLPS can be induced by a jump to native pH, resulting in a system that can be easily controlled. This approach represents a generic method for studying LLPS under near native conditions, providing a platform for studying the phase-separation behavior of diverse proteins.

molecular biology↗