ArticleBiophysical journal2018
Using a FRET Library with Multiple Probe Pairs To Drive Monte Carlo Simulations of α-Synuclein.
Article in Biophysical journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 29 citations in OpenAlex.
- Genetic Code Expansion for Site-Specific Encoding of a Switchable, Intrinsic Fluorophore-Quencher Pair to Monitor Protein Dynamics.bioRxiv : the preprint server for biology · 2026Article
- Interactions of Neurodegenerative Disease Positron Emission Tomography Imaging Probe Candidates with the C-Terminus of α-Synuclein Fibrils.Chembiochem : a European journal of chemical biology · 2025Article
- Strategic Modulation of Polarity and Viscosity Sensitivity of Bimane Molecular Rotor-Based Fluorophores for Imaging α-Synuclein.Journal of the American Chemical Society · 2025Article
- Highly tunable bimane-based fluorescent probes: design, synthesis, and application as a selective amyloid binding dye.Chemical science · 2024Article
- Semi-Synthetic CoA-α-Synuclein Constructs Trap N-Terminal Acetyltransferase NatB for Binding Mechanism Studies.Journal of the American Chemical Society · 2023Article
- Illuminating Intrinsically Disordered Proteins with Integrative Structural Biology.Biomolecules · 2023Review
- Cysteine-Based Mimic of Arginylation Reproduces Neuroprotective Effects of the Authentic Post-Translational Modification on α-Synuclein.Journal of the American Chemical Society · 2022Article
- New strategies for fluorescently labeling proteins in the study of amyloids.Current opinion in chemical biology · 2021Review
- Genetic encoding of a highly photostable, long lifetime fluorescent amino acid for imaging in mammalian cells.Chemical science · 2021Article
- The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds.Structure (London, England : 1993) · 2021Article
- Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.Chemical reviews · 2021Review
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins.The journal of physical chemistry. B · 2020Article
- Protein labeling for FRET with methoxycoumarin and acridonylalanine.Methods in enzymology · 2020Article
- Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation.Biochimica et biophysica acta. Proteins and proteomics · 2019Review
- Measuring Intrinsic Disorder and Tracking Conformational Transitions Using Rosetta ResidueDisorder.The journal of physical chemistry. B · 2019Article
- Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins.Biomolecules · 2019Review
- Cyclized NDGA modifies dynamic α-synuclein monomers preventing aggregation and toxicity.Scientific reports · 2019Article
- Monitoring metal-amyloid-β complexation by a FRET-based probe: design, detection, and inhibitor screening.Chemical science · 2019Article
- A Chemical Chaperone Decouples TDP-43 Disordered Domain Phase Separation from Fibrillation.Biochemistry · 2018Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
We describe a strategy for experimentally-constraining computational simulations of intrinsically disordered proteins (IDPs), using α-synuclein, an IDP with a central role in Parkinson's disease pathology, as an example. Previously, data from single-molecule Förster Resonance Energy Transfer (FRET) experiments have been effectively utilized to generate experimentally constrained computational models of IDPs. However, the fluorophores required for single-molecule FRET experiments are not amenable to the study of short-range (<30 Å) interactions. Using ensemble FRET measurements allows one to acquire data from probes with multiple distance ranges, which can be used to constrain Monte Carlo simulations in PyRosetta. To appropriately employ ensemble FRET data as constraints, we optimized the shape and weight of constraining potentials to afford ensembles of structures that are consistent with experimental data. We also used this approach to examine the structure of α-synuclein in the presence of the compacting osmolyte trimethylamine-N-oxide. Despite significant compaction imparted by 2 M trimethylamine-N-oxide, the underlying ensemble of α-synuclein remains largely disordered and capable of aggregation, also in agreement with experimental data. These proof-of-concept experiments demonstrate that our modeling protocol enables one to efficiently generate experimentally constrained models of IDPs that incorporate atomic-scale detail, allowing one to study an IDP under a variety of conditions.
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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.