The University of Southampton
University of Southampton Institutional Repository

Molecular dynamics of mouse and syrian hamster PrP: Implications for activity

Parchment, O. G. and Essex, J. W. (2000) Molecular dynamics of mouse and syrian hamster PrP: Implications for activity Proteins-Structure Function and Genetics, 38, (3), pp. 327-340. (doi:10.1002/(SICI)1097-0134(20000215)38:3<327::AID-PROT8>3.0.CO;2-G).

Record type: Article


Molecular dynamics computer simulations have been performed on Mouse (Mo) and Syrian Hamster (SHa) prion proteins. These proteins differ, primarily, in that the SHa form incorporates additional residues at the C-terminus and also includes a segment of the unstructured N-terminal region that is required for infectivity, The 1-ns simulations have been analyzed by using a combination of dynamical cross-correlation maps, residue-residue contact plots, digital filtering, and residue-based root-mean-square deviations. The results show that the extra residues present in the SHa form at the C- and N-termini produce changes in the stability of key regions of the protein. The loop region between strand S2 and helix B that contains part of the proposed discontinuous binding site for the chaperone, protein X, is found to be more stable in SHa than in the Mo protein; these results are consistent with the NMR data of James et al, (James et al, Proc Natl Acad Sci USA 1997;94:10086-10091), In addition, a degree of flexibility within the region between and including strand S1 and helix A is also shown in SHa, which is not present in the Mo form; the cross-correlation maps suggest that this is a consequence of the additional unstructured N-terminal region. Furthermore, the extra residues in the N-terminal region of SHa are found to form a beta-bridge with the beta-sheet, within which critical point mutations associated with prion diseases lie. The implications of these results for the conformational interconversion pathway of the prion protein are discussed.

Full text not available from this repository.

More information

Published date: 15 February 2000
Keywords: computer simulation, prion, conformational flexibility, digital filter, mutantscreutzfeldt-jakob-disease, prion protein, scrapie prion, collectivemotions, trajectories, simulations, conversion, isoform


Local EPrints ID: 18962
PURE UUID: 15165286-64e3-486b-9a07-8058be435195

Catalogue record

Date deposited: 19 Jan 2006
Last modified: 17 Jul 2017 16:34

Export record



Author: O. G. Parchment
Author: J. W. Essex

University divisions

Download statistics

Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.

View more statistics

Atom RSS 1.0 RSS 2.0

Contact ePrints Soton:

ePrints Soton supports OAI 2.0 with a base URL of

This repository has been built using EPrints software, developed at the University of Southampton, but available to everyone to use.

We use cookies to ensure that we give you the best experience on our website. If you continue without changing your settings, we will assume that you are happy to receive cookies on the University of Southampton website.