Data showing the lipid conformations and membrane binding behaviors of beta-amyloid fibrils in phase-separated cholesterol-enriched lipid domains with and without glycolipid and oxidized cholesterol from coarse-grained molecular dynamics simulations

Sara Y Cheng; Yiyi Cao; Marzieh Rouzbehani; Kwan H Cheng

doi:10.1016/j.dib.2020.105496

Data showing the lipid conformations and membrane binding behaviors of beta-amyloid fibrils in phase-separated cholesterol-enriched lipid domains with and without glycolipid and oxidized cholesterol from coarse-grained molecular dynamics simulations

Data Brief. 2020 Apr 19:30:105496. doi: 10.1016/j.dib.2020.105496. eCollection 2020 Jun.

Authors

Sara Y Cheng¹, Yiyi Cao², Marzieh Rouzbehani², Kwan H Cheng^{2

3}

Affiliations

¹ Department of Physics, University of Texas at Austin, Austin, TX, United States.
² Department of Neuroscience, Trinity University, San Antonio, TX, United States.
³ Department of Physics, Trinity University, San Antonio, TX, United States.

Abstract

The structural conformations of phospholipids and cholesterol in phase-separated lipid domains were determined by surface area, transverse density profile, and lipid acyl chain orientational parameter calculations. Binding kinetics and characterization of membrane-bound states of beta-amyloid fibrils of various sizes (dimer to pentamer), on those lipid domains, were determined using protein residue orientational parameter and fibril-residue-lipid minimum distance analysis methods. The energy of binding and characterization of annular lipid shells surrounding the surface-bound amyloid fibrils were also determined. The calculations described above support the article "Coarse-Grained MD simulations Reveal Diverse Membrane-Bound Conformational States of Beta-Amyloid Fibrils in the Liquid-ordered and Liquid-disordered Regions of Phase-Separated Lipid Rafts Containing Glycolipid, Cholesterol and Oxidized Cholesterol (Cheng et al., 2020 [1])". The reported data is valuable for the future design and analysis of any protein fibrils binding to phase-separated lipid domains in model multi-component lipids membranes using either atomistic or coarse-grained molecular dynamics simulations. Additionally, this data can guide or validate future single-molecule experiments on fibril/membrane interactions in model or cell membranes.

Keywords: Amyloid fibrils; Coarse-grained MD simulations; Lipid rafts; Membrane-bound protein orientation; Protein binding kinetics on membranes; Protein insertion.