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  4. Enhanced Sampling Molecular Dynamics Identifies PrPSc Structures Harboring a C-Terminal beta-Core
 
research article

Enhanced Sampling Molecular Dynamics Identifies PrPSc Structures Harboring a C-Terminal beta-Core

Baillod, Pascal
•
Garrec, Julian  
•
Colombo, Maria-Carola  
Show more
2012
Biochemistry

We perform a replica exchange molecular dynamics simulation corresponding to a 2.8 mu s total time for the extensive enhanced sampling of the conformational space of the C-terminal part (residues 124-226) of the mouse prion protein (PrP); 1.3% of the conformations sampled display a high level of beta-structure (>= 19 residues), allowing the assessment of beta-propensities along the sequence and high-lighting the roost structurally labile hot spots. A clustering algorithm is applied to sort the structures of this pool according to their fold. Ten beta-rich folds are thus defined and analyzed with regard to their topology, accumulation temperatures, and structural characteristics. In contrast to the so-called spiral and beta-helix models suggesting that the beta-rich core of the scrapie isoform (PrPSc) comprises the N-terminal tail and part of the C-terminal domain up to helix 1 (H1), we present putative structural models for monomeric precursors of PrPSc and PrP beta-oligomers that are characterized by a C-terminal beta-rich core, in agreement with the suggestions of a series of recent experiments.

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Type
research article
DOI
10.1021/bi301091x
Web of Science ID

WOS:000312122700014

Author(s)
Baillod, Pascal
Garrec, Julian  
Colombo, Maria-Carola  
Tavernelli, Ivano  
Rothlisberger, Ursula  
Date Issued

2012

Publisher

Amer Chemical Soc

Published in
Biochemistry
Volume

51

Issue

49

Start page

9891

End page

9899

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCBC  
Available on Infoscience
March 28, 2013
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/91119
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