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Journal of Biomolecular NMR

, Volume 32, Issue 4, pp 273–280 | Cite as

Interpreting Dynamically-Averaged Scalar Couplings in Proteins

  • Kresten Lindorff-LarsenEmail author
  • Robert B. Best
  • Michele Vendruscolo
Article

Abstract

The experimental determination of scalar three-bond coupling constants represents a powerful method to probe both the structure and dynamics of proteins. The detailed structural interpretation of such coupling constants is usually based on Karplus relationships, which allow the measured couplings to be related to the torsion angles of the molecules. As the measured couplings are sensitive to thermal fluctuations, the parameters in the Karplus relationships are better derived from ensembles representing the distributions of dihedral angles present in solution, rather than from single conformations. We present a method to derive such parameters that uses ensembles of conformations determined through dynamic-ensemble refinement – a method that provides structural ensembles that simultaneously represent both the structure and the associated dynamics of a protein.

Key words

protein dynamics Karplus relationship protein structure scalar couplings 

Abbreviations

DER

dynamic-ensemble refinement

DFT

density functional theory

TNfn3

third fibronectin type III domain from human tenascin.

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Copyright information

© Springer 2005

Authors and Affiliations

  • Kresten Lindorff-Larsen
    • 1
    Email author
  • Robert B. Best
    • 2
  • Michele Vendruscolo
    • 3
  1. 1.Department of Biochemistry, Institute of Molecular Biology and PhysiologyUniversity of CopenhagenCopenhagen ØDenmark
  2. 2.Laboratory of Chemical Physics, NIDDKNational Institutes of HealthBethesdaU.S.A
  3. 3.Department of ChemistryUniversity of CambridgeCambridgeUnited Kingdom

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