Related Experiment Video
Updated: Mar 3, 2026

Ubiquitin Chain Analysis by Parallel Reaction Monitoring
Published on: June 17, 2020
Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics
Yoshiharu Mori1, Yuko Okamoto1,2,3,4,5
1Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.
Abstract:
Molecular dynamics simulations for the system of ubiquitin were performed with pressure simulated tempering to study pressure-induced conformational changes of ubiquitin. The pressure dependence of ubiquitin was analyzed in a wide range of pressure from atmospheric pressure (0.1 MPa) to 1.0 GPa. The fluctuation of the distance between amino-acid residues and the distribution of a largely fluctuating distance were calculated. The large fluctuation of the L8-E34 distance induced by pressure means that the conformation of ubiquitin changes under high pressure conditions. There were more water molecules near the largely fluctuating region at high pressure than at low pressure. The pressure dependence of interaction energies among ubiquitin and water was also calculated to investigate the role of water for the pressure-induced conformational changes of ubiquitin. The protein-water interaction is important when the conformation of ubiquitin changes at high pressure. © 2017 Wiley Periodicals, Inc.
Related Concept Videos
Covalently Linked Protein Regulators
These groups modify specific amino acids in a protein....
The Proteasome Structure
The proteasome is an...
Molecular Chaperones and Protein Folding
The...
The Unfolded Protein Response
Regulated Protein Degradation
Protein degradation plays two important roles in the cells. It helps to protect cells from misfolded or damaged proteins before they lead to a...
The Proteasome
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. This involves participation of a series of enzymes including— E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...

