Journal of Biomolecular NMR

, Volume 53, Issue 4, pp 281–292 | Cite as

Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

  • Rinaldo W. Montalvao
  • Alfonso De Simone
  • Michele Vendruscolo
Article

Abstract

Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.

Keywords

Protein dynamics Protein conformational ensembles Molecular dynamics simulations 

Supplementary material

10858_2012_9644_MOESM1_ESM.pdf (2.6 mb)
Supplementary material 1 (PDF 2,705 kb)

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Rinaldo W. Montalvao
    • 1
  • Alfonso De Simone
    • 1
    • 2
  • Michele Vendruscolo
    • 1
  1. 1.Department of ChemistryUniversity of CambridgeCambridgeUK
  2. 2.Division of Molecular BiosciencesImperial CollegeLondonUK

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