Kluza, A. | bioRxiv Science

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

First crystal structure of double knotted protein TrmD-Tm1570 - inside from degradation perspective

Herein, we present the first crystal structure of a double knotted protein TrmD-Tm1570 from Calditerrivibrio nitroreducens, as well the X-ray structure of each sub-domain. The protein consists of two domains TrmD and Tm1570, each embedding a single trefoil knot, which can function on their own. TrmD-Tm1570 forms a compact homodimeric complex. This protein represents one of 296 possible doubly knotted proteins from SPOUT family. Based on TrmD-Tm1570 from Calditerrivibrio nitroreducens we show that a double knotted protein can be fully degraded by the ClpXP degradation system, as well as its individual domains. We used numerical simulations to explain the difference in the speed of degradation. The derived kinetic parameters for the degradation process are comparable to the experimental data found for unknotted polypeptide chains.

biophysics↗