Simulating the distance distribution between spin-labels attached to proteins

J Phys Chem B. 2015 Mar 12;119(10):3901-11. doi: 10.1021/jp510745d. Epub 2015 Feb 18.


EPR/DEER spectroscopy is playing an increasingly important role in the characterization of the conformational states of proteins. In this study, force field parameters for the bifunctional spin-label (RX) used in EPR/DEER are parametrized and tested with molecular dynamics (MD) simulations. The dihedral angles connecting the Cα atom of the backbone to the nitroxide ring moiety of the RX spin-label attached to i and i + 4 positions in a polyalanine α-helix agree very well with those observed in the X-ray crystallography. Both RXi,i+4 and RXi,i+3 are more rigid than the monofunctional spin-label (R1) commonly used in EPR/DEER, while RXi,i+4 is more rigid and causes less distortion in a protein backbone than RXi,i+3. Simplified dummy spin-label models with a single effective particle representing the RXi,i+3 and RXi,i+4 are also developed and parametrized from the all-atom simulations. MD simulations with dummy spin-labels (MDDS) provide distance distributions that can be directly compared to distance distributions obtained from EPR/DEER to rapidly assess if a hypothetical three-dimensional (3D) structural model is consistent with experiment. The dummy spin-labels can also be used in the restrained-ensemble MD (re-MD) simulations to carry out structural refinement of 3D models. Applications of this methodology to T4 lysozyme, KCNE1, and LeuT are shown to provide important insights about their conformational dynamics.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacteriophage T4 / enzymology
  • Crystallography, X-Ray
  • Electron Spin Resonance Spectroscopy
  • Molecular Dynamics Simulation
  • Muramidase / chemistry*
  • Potassium Channels, Voltage-Gated / chemistry*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Spin Labels*


  • Potassium Channels, Voltage-Gated
  • Spin Labels
  • Muramidase