Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. Free-energy landscape of protein oligomerization from atomistic simulations
 
Loading...
Thumbnail Image
research article

Free-energy landscape of protein oligomerization from atomistic simulations

Barducci, Alessandro  
•
Bonomi, Massimiliano
•
Prakash, Meher K.
Show more
2013
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS)

In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage.

  • Details
  • Metrics
Type
research article
DOI
10.1073/pnas.1320077110
Web of Science ID

WOS:000327744900002

Author(s)
Barducci, Alessandro  
•
Bonomi, Massimiliano
•
Prakash, Meher K.
•
Parrinello, Michele
Date Issued

2013

Publisher

National Academy of Sciences

Published in
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS)
Volume

110

Issue

49

Start page

E4708

End page

E4713

Subjects

molecular dynamics

•

enhanced sampling

•

fly-casting mechanism

•

conformational selection

Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LBS  
Available on Infoscience
January 9, 2014
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/99199
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés