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

Abstract

Small-angle X-ray and neutron scattering (SAXS/SANS) provide valuable information on biomolecules in solution and are particularly well-suited to complement a wide range of structural techniques, including molecular dynamics simulations. As contrast-based techniques, they are sensitive not only to structural properties but also to the solvent-solute interactions. Their use in molecular dynamics simulations requires a forward model that should be as fast and accurate as possible. Here we show that it is possible to calculate SAXS and SANS using a coarse-grained representation of one bead per amino acid and three beads for nucleic acid with form factors that can be corrected on-the-fly to account for their interaction with the solvent at no additional computational cost. We use SAXS data measured for the closed state of Gelsolin and previous data for a UP1-microRNA complex to show that such approach allows to refine the structure and dynamics of proteins and nucleic acids. Our hybrid resolution small angle scattering (hySAS) implementation, being distributed in PLUMED, is ready to be coupled with atomistic and coarse-grained simulations using diverse restraining strategies.

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

“…Plots were generated using the matplotlib 3.6.0 package, while the open-source software VMD and PyMOL were used for structural visualization of biomolecules. Relevant input files and trajectories are available on Zenodo and the PLUMED-NEST as plumID:23.029.…”