ArticleBiophysical journal2019
Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data.
Article in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Elucidation of the Molecular Interaction Network Underlying Full-Length FUS Conformational Transitions and Its Phase Separation Using Atomistic Simulations.The journal of physical chemistry. B · 2025Article
- SAXS/MC studies of the mixed-folded protein Cdt1 reveal monomeric, folded over conformations.bioRxiv : the preprint server for biology · 2024Article
- Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology.Biomolecules · 2023Review
- Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Molecular Dynamics Simulations of Phosphorylated Intrinsically Disordered Proteins: A Force Field Comparison.International journal of molecular sciences · 2021Article
- Investigation into Early Steps of Actin Recognition by the Intrinsically Disordered N-WASP Domain V.International journal of molecular sciences · 2019Article
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Authors and funding
6 authors.
Funding
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Abstract
Because of their large conformational heterogeneity, structural characterization of intrinsically disordered proteins (IDPs) is very challenging using classical experimental methods alone. In this study, we use NMR and small-angle x-ray scattering (SAXS) data with multiple molecular dynamics (MD) simulations to describe the conformational ensemble of the fully disordered verprolin homology domain of the neural Aldrich syndrome protein involved in the regulation of actin polymerization. First, we studied several back-calculation software of SAXS scattering intensity and optimized the adjustable parameters to accurately calculate the SAXS intensity from an atomic structure. We also identified the most appropriate force fields for MD simulations of this IDP. Then, we analyzed four conformational ensembles of neural Aldrich syndrome protein verprolin homology domain, two generated with the program flexible-meccano with or without NMR-derived information as input and two others generated by MD simulations with two different force fields. These four conformational ensembles were compared to available NMR and SAXS data for validation. We found that MD simulations with the AMBER-03w force field and the TIP4P/2005s water model are able to correctly describe the conformational ensemble of this 67-residue IDP at both local and global level.
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