Data · dataset · 2020
Beta-Amyloid Fibril Binding to Phase Separated Lipid Rafts from Solution to Membranes
Listed in Teesside University Research Data Repository
Description
Movies in animated GIF format showing the binding kinetics of human beta-amyloid fibrils of various sizes, derived from NMR structures (PDB: 2BEG), to phase separated lipid rafts consisting of saturated (DPPC) and unsaturated (DLPC) phospholipids, cholesterol (CHOL), head-group (C1-CHOL) or tail-group (P1-CHOL) modified cholesterol. These modified cholesterols mimic the oxidized cholesterols. The GM1 rafts contain asymmetrically distributed monosialotetrahexosylganglioside (GM1) clusters.
These movies show coarse-grained (CG) MD simulations of fibril/raft complexes as described in Cheng et al. "Coarse-Grained MD Simulations Reveal Beta-Amyloid Fibrils of Various Sizes Bind to Interfacial Liquid-Ordered and Liquid-Disordered Regions in Phase Separated Lipid Rafts with Diverse Membrane-Bound Conformational States" Biophysical Chemistry 2020 in press (DOI: 10.1016/j.bpc.2020.106355). Each movie contains 500 frames, with a time step of 40 ns, spanning 0 to 20 microseconds of CG MD simulations.
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Periodic membrane structures along the z-axis are shown. The lipid acyl chains are not shown for clarity. The membrane-bound states include: C, T, N, I and L, and these states refer to the segment of the fibril that binds to the lipid membrane via the C-terminal, C-and N-termini, N-terminal, transmembrane-insertion along the C- and N-terminals, and loop region, respectively. 1. 01-CO-ABCD-2-0to20us-hgrs.gif A movie of a tetramer fibril (4 chains - ABCD) binding to a lipid raft (DPPC/DLPC/CHOL).
The fibril starts from solution, binds to membrane at 4.2 microseconds, and establishes an equilibrated membrane-bound C-state. 2. 02-CO-ABCD-3-0to20us-hgrs.gif A movie of tetramer fibril (4 chains - ABCD) binding to a lipid raft (DPPC/DLPC/CHOL). The fibril starts from solution, binds to membrane at 0.4 microseconds, and establishes an equilibrated membrane-bound T-state. 3. 03-C1-ABC-3-0to20us-hgrs.gif A movie of a trimer fibril (3 chains - ABC) binding to a lipid raft (DPPC/DLPC/C1-CHOL).
The fibril starts from solution, binds to membrane at 0.7 microseconds, and establishes an equilibrated membrane-bound N-state. 4. 04-P1-ABC-2-0to20us-hgrs.gif A movie of trimer fibril (3 chain - ABC) binding to a lipid raft (DPPC/DLPC/P1-CHOL). The fibril starts from solution, binds to membrane at 0.3 microseconds, and establishes an equilibrated membrane-bound I-state. 5. 05-GM-ABCD-1-0to20us-hgrs.gif A movie of a tetramer (ABCD) fibril binding to an asymmetrical lipid raft (DPPC/DLPC/CHOL/GM1).
The fibril starts from solution, binds to membrane at 0.2 microseconds, and establishes an equilibrated membrane-bound C-state. 6. 06-GM-ABCD-2-0to2us-hgrs.gif A movie of a tetramer (ABCD) fibril binding to an asymmetrical lipid raft (DPPC/DLPC/CHOL/GM1). The fibril starts from solution, binds to asymmetric GM1 cluster at 1 microsecond, and establishes an equilibrated membrane-bound L-state.
Links
Where it is published
- DOI doi.org/10.17632/ktrspy2swx.1 ↗
DOI / persistent id · from researchdata tees ac uk
Catalogue records · 1
- OAI-PMH record data.mendeley.com/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Adata… ↗
metadata API · from researchdata tees ac uk
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Medicine & Health · Social Science
- Inferred from text
- Medical biochemistry and metabolomics 70%
Provenance · 1 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Teesside University Research Data Repository | oai:data.mendeley.com/ktrspy2swx.1 | 11 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].anzsrc:group:3205 | enrichment · researchdata tees ac uk | taxonomy-embedding@1.0.0 | title+keywords+description (70%) |
| concepts[field].local:field:earth-environmental | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:engineering | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:humanities | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| concepts[field].local:field:social-science | mapping · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| description | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/description |
| license | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/rights |
| publication_date | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | |
| title | source · researchdata tees ac uk | connector:researchdata_tees_ac_uk@1.0.0 | /metadata/dc/title |