ArticlePLoS computational biology2019
Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 72 citations in OpenAlex.
- Probing protein-lipid interactions by hydrogen/deuterium exchange-mass spectrometry: advances, challenges and future directions.Chemical science · 2026Review
- Cross-Linking and Covalent Labeling Mass Spectrometry Reveal Proteoform-Driven Conformational Changes in Alpha Synuclein.Analytical chemistry · 2026Article
- ZnJournal of the American Chemical Society · 2025Article
- Conformational Ensemble Dynamics of Intrinsically Disordered Full-Length α- and β-Synuclein Monomers.Journal of chemical information and modeling · 2025Article
- Experimental Evidence for Phosphorylation-Driven Allosteric Regulation of Alpha Synuclein Function.bioRxiv : the preprint server for biology · 2025Article
- Subtle concentration changes in zinc hold the key to fibrillation of α-synuclein: an updated insight on the micronutrient's role in prevention of neurodegenerative disorders.Frontiers in molecular biosciences · 2025Review
- Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution.Journal of chemical information and modeling · 2024Article
- Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping.Nature communications · 2024Article
- Structural Elucidation of Ubiquitin via Gas-Phase Ion/Ion Cross-Linking Reactions Using Sodium-Cationized Reagents Coupled with Infrared Multiphoton Dissociation.Analytical chemistry · 2024Article
- The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors.Mini reviews in medicinal chemistry · 2024Review
- The role of solvation on the conformational landscape of α-synuclein.The Analyst · 2023Article
- Saturation mutagenesis of α-synuclein reveals monomer fold that modulates aggregation.Science advances · 2023Article
- Exploring Intra- and Inter-Regional Interactions in the IDP α-Synuclein Using smFRET and MD Simulations.Biomacromolecules · 2023Article
- Big versus small: The impact of aggregate size in disease.Protein science : a publication of the Protein Society · 2023Review
- Dissecting the Self-assembly Dynamics of Imperfect Repeats in α-Synuclein.Journal of chemical information and modeling · 2023Article
- Structural and dynamic insights into α-synuclein dimer conformations.Structure (London, England : 1993) · 2023Article
- Taking Charge: Metal Ions Accelerate Amyloid Aggregation in Sequence Variants of α-Synuclein.Journal of the American Society for Mass Spectrometry · 2023Article
- Molecular Insights into the Misfolding and Dimerization Dynamics of the Full-Length α-Synuclein from Atomistic Discrete Molecular Dynamics Simulations.ACS chemical neuroscience · 2022Article
- Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2022Article
- Molecular insights into the oligomerization dynamics and conformations of amyloidogenic and non-amyloidogenic amylin from discrete molecular dynamics simulations.Physical chemistry chemical physics : PCCP · 2022Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Combining structural proteomics experimental data with computational methods is a powerful tool for protein structure prediction. Here, we apply a recently-developed approach for de novo protein structure determination based on the incorporation of short-distance crosslinking data as constraints in discrete molecular dynamics simulations (CL-DMD) for the determination of conformational ensemble of the intrinsically disordered protein α-synuclein in the solution. The predicted structures were in agreement with hydrogen-deuterium exchange, circular dichroism, surface modification, and long-distance crosslinking data. We found that α-synuclein is present in solution as an ensemble of rather compact globular conformations with distinct topology and inter-residue contacts, which is well-represented by movements of the large loops and formation of few transient secondary structure elements. Non-amyloid component and C-terminal regions were consistently found to contain β-structure elements and hairpins.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.