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An Accurate and Efficient SAXS/SANS Implementation Including Solvation Layer Effects Suitable for Molecular Simulations.
Open accessPreprint — published as 10.1021/acs.jctc.3c00864 · Paper page
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.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Metadata
- Authors
- Ballabio, F., Paissoni, C., Bollati, M., de Rosa, M., Capelli, R., & Camilloni, C.
- Affiliations
- University of Milan (IT)
- Corresponding author
- de Rosa, Matteo
- Capelli, Riccardo
- Camilloni, Carlo
- ORCID
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2023-08-07
- Volume
- 19
- Issue
- 22
- Pages
- 8401-8413
- ISSN
- 1549-9618 (ISSN-L)
- PMC
- PMC10687869
- OpenAlex
- W4388314297
- Cited by
- 23
- References
- 1
- Citations by year
- 2026: 7 · 2025: 11 · 2024: 4 · 2023: 1
- FWCI
- 2.05
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Chemical Theory and Computation (publishedVersion, cc-by)
- ChemRxiv (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- Funders
- Diamond Light Source
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- small-angle X-ray scattering, small-angle neutron scattering, forward scattering model, coarse-grained representation, PLUMED, molecular dynamics simulation, gelsolin, protein structure refinement, solute-solvent interactions
- MeSH terms
- Protein Conformation, Proteins, X-Ray Diffraction, Scattering, Small Angle, Molecular Dynamics Simulation
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