ArticleBiophysical journal2014
Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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82 citing papers in PubMed, 164 citations in OpenAlex.
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- Depletion of the Protein Hydration Shell with Increasing Temperature Observed by Small-Angle X-ray Scattering and Molecular Simulations.Journal of the American Chemical Society · 2025Article
- Rapid and Reliable Conformational Analysis of Glycans by Small Angle X-Ray Scattering Guided Molecular Dynamics Simulations.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Evaluation and refinement of all-atom force fields for reproducing collagen structure and dynamics.Biophysical journal · 2025Article
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- Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold.PLoS computational biology · 2025Article
- Revealing the Solution Conformation and Hydration Structure of Type I Tropocollagen Using X-ray Scattering and Molecular Dynamics Simulation.Biomacromolecules · 2025Article
- Investigating the quaternary structure of a homomultimeric catechol 1,2-dioxygenase: An integrative structural biology study.PloS one · 2025Article
- Small-Angle X-ray Scattering (SAXS) Combined with SAXS-Driven Molecular Dynamics for Structural Analysis of Multistranded RNA Assemblies.ACS applied materials & interfaces · 2024Article
- Sequence-dependent conformational preferences of disordered single-stranded RNA.Cell reports. Physical science · 2024Article
- On the use of dioxane as reference for determination of the hydrodynamic radius by NMR spectroscopy.Biophysical journal · 2024Article
- Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications.Journal of applied crystallography · 2024Article
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- Mechanism of Cationic Lipid Induced DNA Condensation: Lipid-DNA Coordination and Divalent Cation Charge Fluctuations.Biomacromolecules · 2024Article
22 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Wide-angle x-ray scattering (WAXS) experiments of biomolecules in solution have become increasingly popular because of technical advances in light sources and detectors. However, the structural interpretation of WAXS profiles is problematic, partly because accurate calculations of WAXS profiles from structural models have remained challenging. In this work, we present the calculation of WAXS profiles from explicit-solvent molecular dynamics (MD) simulations of five different proteins. Using only a single fitting parameter that accounts for experimental uncertainties because of the buffer subtraction and dark currents, we find excellent agreement to experimental profiles both at small and wide angles. Because explicit solvation eliminates free parameters associated with the solvation layer or the excluded solvent, which would require fitting to experimental data, we minimize the risk of overfitting. We further find that the influence from water models and protein force fields on calculated profiles are insignificant up to q≈15nm(-1). Using a series of simulations that allow increasing flexibility of the proteins, we show that incorporating thermal fluctuations into the calculations significantly improves agreement with experimental data, demonstrating the importance of protein dynamics in the interpretation of WAXS profiles. In addition, free MD simulations up to one microsecond suggest that the calculated profiles are highly sensitive with respect to minor conformational rearrangements of proteins, such as an increased flexibility of a loop or an increase of the radius of gyration by < 1%. The present study suggests that quantitative comparison between MD simulations and experimental WAXS profiles emerges as an accurate tool to validate solution ensembles of biomolecules.
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