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research article

All-atom simulations of crowding effects on ubiquitin dynamics

Abriata, Luciano A.
•
Spiga, Enrico  
•
Dal Peraro, Matteo  
2013
Physical Biology

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 (similar to 0.5 mu s), 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.

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Type
research article
DOI
10.1088/1478-3975/10/4/045006
Web of Science ID

WOS:000322701100008

Author(s)
Abriata, Luciano A.
Spiga, Enrico  
Dal Peraro, Matteo  
Date Issued

2013

Publisher

Iop Publishing Ltd

Published in
Physical Biology
Volume

10

Issue

4

Article Number

045006

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
UPDALPE  
Available on Infoscience
October 1, 2013
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/95665
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