Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse...

Area of Science:

• Structural Biology
• Biophysics
• Computational Biology

Background:

• X-ray diffraction yields Bragg peaks (mean electron density) and diffuse scattering (electron density correlations).
• Diffuse scattering contains crucial information about collective protein motions, but previous studies were limited by insufficient sampling in molecular dynamics (MD) simulations.
• Understanding protein dynamics is key to elucidating protein function.

Purpose of the Study:

• To overcome sampling limitations in MD simulations for modeling diffuse X-ray scattering.
• To investigate collective motions and conformational states of proteins using enhanced sampling.
• To correlate MD-derived diffuse scattering with experimental data for model validation.

Main Methods:

• Performed a 1.1-μs molecular dynamics (MD) simulation of crystalline staphylococcal nuclease, achieving 100-fold greater sampling than prior studies.
• Calculated diffuse X-ray scattering intensity from the extensive MD trajectory.
• Decomposed the MD model into protein and solvent components to analyze contributions to diffuse scattering.

Main Results:

• The calculated diffuse intensity from the MD model showed high correlation with experimental data.
• Excellent agreement was observed for the isotropic component, and substantial agreement for the anisotropic component of diffuse scattering.
• MD simulations predicted transitions among at least eight metastable states with distinct active-site geometries, highlighting functionally important motions.

Conclusions:

• Diffuse X-ray scattering can effectively validate predictions from MD simulations of protein dynamics.
• Enhanced MD sampling provides valuable insights into collective protein motions and protein-solvent interactions.
• Diffuse scattering data can be used to refine and improve MD models for studying protein dynamics.