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Data and Code for "Cholesterol Modulates Membrane Elasticity via Unified Biophysical Laws"

Version 3 2025-07-24, 16:37
Version 2 2025-07-22, 21:18
Version 1 2025-06-27, 21:11
dataset
posted on 2025-07-24, 16:37 authored by Rana AshkarRana Ashkar, Teshani Kumarage, Milka Doktorova, Michael Brown
<p dir="ltr">This data set contains data collected on lipid membranes consisting of phosphocholine lipids with varying amounts of cholesterol. The data files include:</p><ol><li>Neutron-spin echo (NSE) spectroscopy data on unilamellar vesicles for dynamic measurements of membrane bending fluctuations used to obtain the reported bending moduli.</li><li>Small-angle X-ray scattering (SAXS) data on unilamellar vesicles for measurements of structural membrane parameters used to obtain membrane thickness and lipid packing density.</li><li>Small-angle neutron scattering (SANS) data on unilamellar vesicles for measurements of structural membrane parameters used to obtain membrane thickness and lipid packing density.</li><li>Solid-state deuterium nuclear magnetic resonance (<sup>2</sup>H NMR) data on multilamellar lipid stacks for static measurements of the order parameter and dynamic measurements of the relaxation rates.</li><li>Trajectories for all-atom molecular dynamics (MD) simulations on all bilayers reported in this study (links to Zenodo repositories).</li><li>Code (.c and .py files) applied in fitting SAXS and SANS data in the form of a five-shell vesicle model (to be used as a plug-in model in the SasView data fitting package SasView 5.0.6), along with installation and data fitting instructions.</li><li>Code (.fdf file) applied in fitting the decays for NSE bending fluctuation spectra (to be used as a fitting function in Origin, Origin 2021b), along with installation and data fitting instructions.</li><li>Code (.m files) applied in processing and analyzing solid-state <sup>2</sup>H NMR data (to be used as MATLAB scripts, MATLAB 2021a), along with installation and run instructions.</li></ol><p dir="ltr">This dataset is supplement to the article "Cholesterol Modulates Membrane Elasticity via Unified Biophysical Laws" published by the Nature Communications journal DOI: <a href="https://doi.org/10.1038/s41467-025-62106-0" rel="noreferrer" target="_blank">https://doi.org/10.1038/s41467-025-62106-0</a> by the following authors: Kumarage, Teshani; Gupta, Sudipta; Morris, Nicholas B.; Doole, Fathima T.; Scott, Haden L.; Stingaciu; Laura-Roxana; Pingali, Sai Venkatesh; Katsaras, John; Khelashvili, George; Doktorova, Milka; Brown, Michael; Ashkar, Rana</p>

Funding

Collaborative Research: Emergent Dynamics and Scaling Laws in Bioinspired Lipid Membranes

Directorate for Mathematical & Physical Sciences

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Collaborative Research: Emergent Dynamics and Scaling Laws in Bioinspired Lipid Membranes

Directorate for Mathematical & Physical Sciences

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MEMBRANE BASIS OF VISUAL EXCITATION

National Eye Institute

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Essential Role of Water and Lipids in G-Protein-Coupled Receptor Chemistry

Directorate for Mathematical & Physical Sciences

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EAGER: Topographically Induced Lateral Organization in Biomimetic Lipid Membranes

Directorate for Biological Sciences

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Light-Induced Protein Quake of Visual Rhodopsin Investigated by Femtosecond Time-Resolved X-Ray Scattering

Directorate for Biological Sciences

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History

Publisher

University Libraries, Virginia Tech

Corresponding Author Name

Rana Ashkar

Corresponding Author E-mail Address

ashkar@vt.edu

Files/Folders in Dataset and Description

NSE data [Excel File] -- contains all NSE data as S(Q,t)/S(Q,0) vs. Fourier time t, as well as the relaxation rates Γ(Q) vs. Q^3 and associated error. SANS data [Excel File] -- contains all SANS data as I(Q) vs. Q and associated error. SAXS data [Excel File] -- contains all SAXS data as I(Q) vs. Q and associated error. NMR data [Excel File] -- contains all 2H NMR data as relaxation rates vs. squared order parameter. Links to MD Simulation Trajectories [PDF] -- contains links to Zenodo repositories of simulation trajectories. NSE Data Fitting Folder [ZIP File] -- contains the code used in fitting the NSE bending fluctuation spectra, in the form of an FDF Origin File, to be used as detailed in the accompanying instructions [PDF File]. SAXS-SANS Data Fitting Folder [ZIP File] -- contains the code used in the analysis of the SAXS/SANS data, in the form of a Five_Shell_Vesicle_Model with Python and C scripts, to be used as detailed in the accompanying instructions [PDF File]. NMR Data Processing and Fitting Folder [ZIP File] -- contains MATLAB scripts in the form M Files for processing and analyzing solid-state 2H NMR data, to be used as detailed in the accompanying instructions [PDF File]. license.txt - MIT license covering software files included with this dataset.

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