ArticleProteins2023
Predicting molecular properties of α-synuclein using force fields for intrinsically disordered proteins.
Article in Proteins, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 27 citations in OpenAlex.
- Article
- Time-Resolved SAXS Reveals Distinct Millisecond Metal-Induced Conformational Dynamics of Monomeric α-Synuclein.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Molecular Dynamics of the Intrinsically Disordered Protein COR15A─A Force Field Validation on Structure and Dynamics.Journal of chemical theory and computation · 2025Article
- RNA Binding Mechanism of the FUS Zinc Finger in Concert with Its Flanking Intrinsically Disordered Region.Journal of chemical information and modeling · 2025Article
- Atomistic molecular dynamics simulations of intrinsically disordered proteins.Current opinion in structural biology · 2025Review
- Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations.Computational and structural biotechnology journal · 2025Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution.Journal of chemical information and modeling · 2024Article
- Advanced sampling simulations of coupled folding and binding of phage P22 N-peptide to boxB RNA.Biophysical journal · 2024Article
- Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study.Journal of chemical information and modeling · 2024Article
- Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4.Biophysical journal · 2024Article
- Development of a visual Adhesion/Invasion Inhibition Assay to assess the functionality ofFrontiers in immunology · 2024Article
- Benchmarking of force fields to characterize the intrinsically disordered R2-FUS-LC region.Scientific reports · 2023Article
- Predicting molecular properties of α-synuclein using force fields for intrinsically disordered proteins.Proteins · 2023Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Independent force field validation is an essential practice to keep track of developments and for performing meaningful Molecular Dynamics simulations. In this work, atomistic force fields for intrinsically disordered proteins (IDP) are tested by simulating the archetypical IDP α-synuclein in solution for 2.5 μs. Four combinations of protein and water force fields were tested: ff19SB/OPC, ff19SB/TIP4P-D, ff03CMAP/TIP4P-D, and a99SB-disp/TIP4P-disp, with four independent repeat simulations for each combination. We compare our simulations to the results of a 73 μs simulation using the a99SB-disp/TIP4P-disp combination, provided by D. E. Shaw Research. From the trajectories, we predict a range of experimental observations of α-synuclein and compare them to literature data. This includes protein radius of gyration and hydration, intramolecular distances, NMR chemical shifts, and
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