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research article

Predicting internal protein dynamics from structures using coupled networks of hindered rotators

Abergel, Daniel
•
Bodenhausen, Geoffrey  
2005
The Journal of Chemical Physics

Internal motions in proteins, such as oscillations of internuclear vectors u(NiHiN) of amide bonds about their equil. position, can be characterized by a local order parameter. This dynamic parameter can be detd. exptl. by measuring the longitudinal and transverse relaxation rates of 15Ni nuclei by suitable NMR methods. In this paper, it is shown that local variations of order parameters Sii2 can be predicted from the knowledge of the structure. To this effect, the diffusive motion of the internuclear vector u(NiHiN) is described in a potential that takes into account the deviations of the angles qij between u(NiHiN) and neighboring vectors u(NjHjN) from their av. value and similarly of deviations of the angles subtended between u(NiHiN) and u(XjYj), where Xj and Yj are heavy atoms in the vicinity of the u(NiHiN) vector under investigation. It is shown how the concept of vicinity can be defined by a simple cutoff threshold, i.e., by neglecting vectors u(XjYj) with distances d(Ni,Xj)>7.5 A. The local order parameters Sii2 can be predicted from the structure using a limited set of coordinates of heavy atoms. The inclusion of a larger no. of heavy atoms does not improve the predictions. Applications to calmodulin, calbindin, and interleukin 4 illustrate the success and limitations of the predictions. [on SciFinder (R)]

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Type
research article
DOI
10.1063/1.2110028
Author(s)
Abergel, Daniel
Bodenhausen, Geoffrey  
Date Issued

2005

Published in
The Journal of Chemical Physics
Volume

123

Issue

20

Start page

204901/1

End page

204901/10

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LRMB  
Available on Infoscience
February 22, 2006
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/225687
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