Essential Dynamics of Ubiquitin in Water and in a Natural Deep Eutectic Solvent

11 June 2024, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Natural deep eutectic solvents (NADESs) comprised of osmolytes are of interest as potential biomolecular (cryo)protectants. However, the way these solvents influence the structure and dynamics of biomolecules as well as the role of water remains poorly understood. We carried out principal component analysis of various secondary structure elements of ubiquitin in water and a betaine:glycerol:water (1:2:;z = 0, 1, 2, 5, 10, 20, 45) NADES, from molecular dynamics trajectories, to gain insight into the protein dynamics as it undergoes a transition from a highly viscous anhydrous to an aqueous environment. A crossover of the protein’s essential dynamics at z ~ 5, induced by solvent-shell coupled fluctuations, is observed, indicating that ubiquitin should (re)fold in the NADES upon water addition at z > ~ 5. Further, in contrast to water, the anhydrous NADES preserves ubiquitin’s essential modes at high temperatures explaining the protein’s enhanced thermal stability.

Supplementary materials

Title
Description
Actions
Title
Supporting Information
Description
Figures S1 to S12
Actions

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.