ArticleBiophysical journal2015
Interpretation of solution x-ray scattering by explicit-solvent molecular dynamics.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Small-Angle X-ray Scattering (SAXS) Combined with SAXS-Driven Molecular Dynamics for Structural Analysis of Multistranded RNA Assemblies.ACS applied materials & interfaces · 2024Article
- A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria.Nature communications · 2024Article
- Fitting high-resolution electron density maps from atomic models to solution scattering data.Biophysical journal · 2023Article
- Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics.Nucleic acids research · 2023Article
- Upstream of N-Ras C-terminal cold shock domains mediate poly(A) specificity in a novel RNA recognition mode and bind poly(A) binding protein.Nucleic acids research · 2023Article
- Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MD.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Direct experimental observation of blue-light-induced conformational change and intermolecular interactions of cryptochrome.Communications biology · 2022Article
- Solution Structural Studies of Pre-amyloid Oligomer States of the Biofilm Protein Aap.Journal of molecular biology · 2022Article
- Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations.Cell reports. Physical science · 2022Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Visualizing RNA Structures by SAXS-Driven MD Simulations.Frontiers in bioinformatics · 2022Article
- Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations.The Journal of chemical physics · 2021Article
- Tracking Membrane Protein Dynamics in Real Time.The Journal of membrane biology · 2021Review
- Automatic Bayesian Weighting for SAXS Data.Frontiers in molecular biosciences · 2021Article
- Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering.IUCrJ · 2020Article
- Laterally Resolved Small-Angle Scattering Intensity from Lipid Bilayer Simulations: An Exact and a Limited-Range Treatment.Journal of chemical theory and computation · 2020Article
- Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data.The Journal of chemical physics · 2020Article
- Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics.Journal of chemical theory and computation · 2020Article
- Including residual contact information into replica-exchange MD simulations significantly enriches native-like conformations.PloS one · 2020Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Small- and wide-angle x-ray scattering (SWAXS) and molecular dynamics (MD) simulations are complementary approaches that probe conformational transitions of biomolecules in solution, even in a time-resolved manner. However, the structural interpretation of the scattering signals is challenging, while MD simulations frequently suffer from incomplete sampling or from a force-field bias. To combine the advantages of both techniques, we present a method that incorporates solution scattering data as a differentiable energetic restraint into explicit-solvent MD simulations, termed SWAXS-driven MD, with the aim to direct the simulation into conformations satisfying the experimental data. Because the calculations fully rely on explicit solvent, no fitting parameters associated with the solvation layer or excluded solvent are required, and the calculations remain valid at wide angles. The complementarity of SWAXS and MD is illustrated using three biological examples, namely a periplasmic binding protein, aspartate carbamoyltransferase, and a nuclear exportin. The examples suggest that SWAXS-driven MD is capable of refining structures against SWAXS data without foreknowledge of possible reaction paths. In turn, the SWAXS data accelerates conformational transitions in MD simulations and reduces the force-field bias.
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