# Marginal Stability of the YB1 Cold‐Shock Domain in Cells Enables Binding of Multiple Nucleic Acids

## TL;DR

The YB1 Cold-Shock Domain's marginal stability allows it to bind various nucleic acids, contributing to its multifunctionality in cells.

## Contribution

The study reveals that the CSDex's marginal stability in cells enables binding to multiple nucleic acids through a dynamic equilibrium of conformers.

## Key findings

- CSDex is 50% folded and 50% unfolded in cells, unlike the mostly unfolded CSD alone.
- Nucleic acid binding strongly increases CSD stability, with RNA having a stronger effect than DNA.
- CSDex's native ensemble comprises multiple conformers, allowing it to bind diverse ligands.

## Abstract

YB1 is an intrinsically disordered protein with a folded cold shock domain (CSD) required for translation, transcription, and RNA metabolism. This multifunctionality and cancer involvement make it a therapeutically attractive target. YB1‐CSD and nucleic acid interaction is essential for function. The CSD is marginally stable in vitro, with unknown implications for its function in the cell. In this study, the folding stability of the CSD in living cells is studied at the physiological levels of nucleic acids. The CSD is highly stabilized (increase in TM by 10 °C) by a disordered 11 amino acid tail encoded in the C‐terminal YB1‐domain (CSDex). Still, CSDex remains 50% folded and 50% unfolded inside cells, whereas CSD alone is mostly unfolded. The stability strongly increased upon nucleic acid binding, an effect that is sequence‐dependent and stronger for RNA than DNA. The thermodynamic and kinetic analysis revealed an ensemble of native state conformers for CSDex when probed in its native cellular environments. It is proposed that this allows the protein to retain its native fold upon binding to different ligands. The marginal stability can be a trade‐off for its high demand to bind efficiently to different ligands, mediating the multifunctionality of YB1.

This study suggests that the marginal stability of the YB1 Cold‐Shock Domain (CSDex) allows for a balance between multifunctionality and conformational changes under physiological conditions. This balance is driven by the dynamic equilibrium between the unfolded ensemble (UE) and the native ensemble (NE) of CSDex (PDB:6LMR). This NE comprises multiple conformers enabling binding to a diverse range of ligands (NB) in living cells.