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All-atom simulations of crowding effects on ubiquitin dynamics.
Journal article

All-atom simulations of crowding effects on ubiquitin dynamics.

  • Abriata LA Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique F´ed´erale de Lausanne-EPFL, Lausanne, Switzerland.
  • Spiga E
  • Dal Peraro M
  • 2013-08-06
Published in:
  • Physical biology. - 2013
Crystallography, X-Ray
Glucose
Molecular Dynamics Simulation
Nuclear Magnetic Resonance, Biomolecular
Principal Component Analysis
Protein Binding
Protein Conformation
Solvents
Ubiquitin
Water
English It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to probe experimentally. Here we report on a simulation study aimed at evaluating the effects of crowding on internal protein dynamics, based on fully all-atom descriptions of the protein, the solvent and the crowder. Our model system consists of ubiquitin, a protein whose dynamic features are closely related to its ability to bind to multiple partners, in a 325 g L⁻¹ solution of glucose in water, a condition widely employed in in vitro studies of crowding effects. We observe a slight reduction in loop flexibility accompanied by a dramatic restriction of the conformational space explored in the timescale of the simulations (∼0.5 µs), indicating that crowding slows down collective motions and the rate of exploration of the conformational space. This effect is attributed to the extensive and long-lasting interactions observed between protein residues and glucose molecules throughout the entire protein surface. Potential implications of the observed effects are discussed.
Language
  • English
Open access status
closed
Identifiers
Persistent URL
https://folia.unifr.ch/global/documents/105508
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