jp311723a_si_001.pdf (3.63 MB)
Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme
journal contribution
posted on 2013-05-02, 00:00 authored by Shahidul
M. Islam, Richard A. Stein, Hassane S. Mchaourab, Benoît RouxDEER (double electron–electron
resonance) is a powerful
pulsed ESR (electron spin resonance) technique allowing the determination
of distance histograms between pairs of nitroxide spin-labels linked
to a protein in a native-like solution environment. However, exploiting
the huge amount of information provided by ESR/DEER histograms to
refine structural models is extremely challenging. In this study,
a restrained ensemble (RE) molecular dynamics (MD) simulation methodology
is developed to address this issue. In RE simulation, the spin–spin
distance distribution histograms calculated from a multiple-copy MD
simulation are enforced, via a global ensemble-based energy restraint,
to match those obtained from ESR/DEER experiments. The RE simulation
is applied to 51 ESR/DEER distance histogram data from spin-labels
inserted at 37 different positions in T4 lysozyme (T4L). The rotamer
population distribution along the five dihedral angles connecting
the nitroxide ring to the protein backbone is determined and shown
to be consistent with available information from X-ray crystallography.
For the purpose of structural refinement, the concept of a simplified
nitroxide dummy spin-label is designed and parametrized on the basis
of these all-atom RE simulations with explicit solvent. It is demonstrated
that RE simulations with the dummy nitroxide spin-labels imposing
the ESR/DEER experimental distance distribution data are able to systematically
correct and refine a series of distorted T4L structures, while simple
harmonic distance restraints are unsuccessful. This computationally
efficient approach allows experimental restraints from DEER experiments
to be incorporated into RE simulations for efficient structural refinement.