Conformational Dynamics of a Crystalline Protein From Microsecond-Scale Molecular Dynamics Simulations and Diffuse X-ray Scattering

Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):17887-92. doi: 10.1073/pnas.1416744111. Epub 2014 Dec 1.

Abstract

X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

Keywords: diffuse scattering; molecular-dynamics simulation; protein crystallography; protein dynamics; staphylococcal nuclease.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Crystallography, X-Ray / methods*
  • Micrococcal Nuclease / chemistry*
  • Models, Molecular*
  • Molecular Dynamics Simulation
  • Principal Component Analysis
  • Protein Conformation
  • X-Ray Diffraction

Substances

  • Micrococcal Nuclease