SAXS data fitting - restrained MD simulation

Objective

Fitting SAXS data to molecular structure - determine the structures of biomolecules in solution.

  • Small-angle X-ray scattering (SAXS) data of proteins - information on their structures in solution.
  • Difficulty in reconstruction of three-dimensional structures - small amount of information in the one-dimensional SAXS data - local mobility - conformational heterogeneity.
  • Modeling procedure for fitting the experimental data requires a priori assumptions about the specific factors characteristic of the solution condition.

Procedure

  • The structure of the DNA was first minimized using 2500 iterations of conjugate gradient algorithm. Then, the SAXS curve of the DNA structure and the SAXS data energy restraints are calculated.
  • A one femto second MD is carried out on the minimized DNA structure including the SAXS energy restraints. Next the SAXS curve of the new MD simulated DNA structure and the SAXS data energy restraints are calculated.
  • Using the new SAXS energy restraints and next step of MD is carried out and hence the new structure. These two steps are repeated to required number of iterations (using a shell script) till the calculated SAXS curve fits the experimental curve.

Inference

  • Restrained MD approach hence proves to be useful scattering data fitting especially in the SAXS region.