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Updated: Feb 11, 2026
10:26
Profiling Ubiquitin and Ubiquitin-like Dependent Post-translational Modifications and Identification of Significant Alterations
Published on: November 7, 2019
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Atomic-level description of ubiquitin folding
Stefano Piana1, Kresten Lindorff-Larsen, David E Shaw
1D. E. Shaw Research, New York, NY 10036, USA. Stefano.Piana-Agostinetti@DEShawResearch.com
Summary
Equilibrium molecular dynamics simulations reveal the folding mechanism, thermodynamics, and kinetics of ubiquitin. These findings suggest general principles for protein folding applicable beyond fast-folding proteins.
Area of Science:
- Biophysics
- Computational Biology
- Protein Dynamics
Background:
- Fast-folding protein mechanisms are elucidated by equilibrium molecular dynamics (EMD) simulations.
- Applicability of EMD findings to slower-folding, naturally occurring proteins remains unclear.
Purpose of the Study:
- To investigate the folding mechanism, thermodynamics, and kinetics of ubiquitin, a slow-folding protein.
- To assess the generalizability of folding principles derived from fast-folding proteins.
Main Methods:
- Utilized equilibrium atomistic simulations to study ubiquitin folding.
- Analyzed folding pathways, energy landscapes, and folding rates.
Main Results:
- Determined the mechanism, thermodynamics, and kinetics of ubiquitin folding.
- Observed simulation results align with experimental data on ubiquitin folding.
- Identified consistency with folding principles from fast-folding protein simulations.
Conclusions:
- EMD simulations can characterize the folding of slow-folding proteins like ubiquitin.
- Folding principles derived from fast-folding proteins appear applicable to a broader range of proteins.
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