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Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations.

Federico Ballabio1, Cristina Paissoni1, Michela Bollati1,2

  • 1Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy.

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Summary

This study introduces a fast, accurate method for calculating small-angle scattering (SAS) intensities from molecular dynamics simulations. The hybrid-resolution small-angle scattering (hySAS) approach refines biomolecular structure and dynamics using experimental data.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Small-angle X-ray and neutron scattering (SAXS/SANS) are crucial for studying biomolecular structure and dynamics in solution.
  • These contrast-based methods offer insights into both structural properties and solvent-solute interactions.
  • Integrating SAXS/SANS with molecular dynamics (MD) simulations requires efficient and accurate forward models.

Purpose of the Study:

  • To develop and validate a novel method for calculating SAXS/SANS intensities from coarse-grained molecular dynamics simulations.
  • To enable on-the-fly correction for solvation effects without increasing computational cost.
  • To demonstrate the utility of this method for refining biomolecular structure and dynamics using experimental SAS data.

Main Methods:

  • Developed a coarse-grained model with one bead per amino acid and three beads per nucleic acid.
  • Implemented a forward model for calculating SAXS/SANS intensities with on-the-fly solvation corrections.
  • Coupled the forward model with MD simulations, using experimental SAS data for restraints.
  • Applied the hybrid-resolution small-angle scattering (hySAS) implementation in PLUMED to gelsolin and a UP1-microRNA complex.

Main Results:

  • Demonstrated the feasibility of calculating SAXS/SANS intensities using the described coarse-grained approach.
  • Showcased the ability to refine conformational ensembles and structures of proteins and nucleic acids.
  • Validated the approach using experimental SAXS data for gelsolin and a microRNA complex.

Conclusions:

  • The hySAS implementation provides a computationally efficient and accurate method for integrating SAS data with MD simulations.
  • This approach facilitates the determination of biomolecular structure and dynamics in solution.
  • The method is versatile, applicable to both atomistic and coarse-grained simulations with various restraining strategies.