Data from: Examining the thermotropic properties of large, circularized nanodiscs
Data files
Oct 23, 2025 version files 2.99 MB
-
PaperData.tar.gz
2.99 MB
-
README.md
3.02 KB
Abstract
Nanodiscs, soluble membrane mimetics composed of an amphipathic membrane scaffold protein encircling a lipid bilayer, are widely used in biophysical and structural studies of membrane proteins. Because many membrane proteins are responsive to their membrane environment, through specific protein–lipid interactions and bulk membrane shape and structure, it is important to understand the properties of lipid bilayers contained within nanodiscs in order to interpret studies using this technology. Nanodiscs are known to alter lipid properties, such as membrane thickness and melting temperature, and interactions with the nanodisc rim have been hypothesized to produce local perturbations in lipid structure and dynamics. Larger nanodiscs should compensate for this effect with a larger unperturbed area. To test this hypothesis, we examined the lipid bilayer properties of several lipids (DMPC, DPPC, POPC, DSPC) and soy polar lipid in circularized nanodiscs of 11 nm to 50 nm diameter using the environmentally-sensitive fluorophore, Laurdan. In nanodiscs containing a single lipid type, as nanodisc size increased, lipid packing, melting temperature, and cooperativity better approximated the properties of that lipid in large unilamellar vesicles (LUVs). In spNW50 (50 nm nanodisc), the lipid packing and melting temperature were indistinguishable from LUVs. However, nanodiscs containing soy polar lipids did not follow this trend, suggesting that complex lipid mixtures may produce preferential incorporation of lipids into the nanodisc or nonhomogeneous distribution of lipids within the nanodisc.
Dataset DOI: 10.5061/dryad.cvdncjtfg
Description of the data and file structure
This repository contains raw fluorescence spectrum data for all samples included in the study associated with this repository as well as an archived version of the Python-based script used for data analysis of the raw fluorescence spectra and plotting scripts used in the study. The raw data were acquired on a Fluoromax+ spectrophotometer. The output was directly copied from the spectrophotometer software into CSV tables (raw data presented here). The data analysis script was run using Python 3.6.8.
Shortly, to assess how the incorporation of different lipid types into large, circularized nanodiscs was affected by nanodisc size, we measured the emission spectrum of different lipid types (asolectin, DMPC, DPPC, DSPC, and POPC) in nanodiscs ranging from 11 nm to 50 nm. Laurdan, a lipophilic, environmentally-sensitive fluorophore, was incorporated at a ratio of 1:200 Laurdan: lipids to report on membrane packing/fluidity. This deposit contains the raw Laurdan emission spectra measured for each sample presented in the paper.
Files and variables
File: PaperData.tar.gz
Description: This tarball directory (PaperData.tar.gz) contains all of the raw data and analysis scripts used in this paper. Each lipid type (asolection, DMPC, DPPC, DSPC, and POPC) has its own directory with its own raw data and analysis script to be able to exactly reproduce the figures displayed in this manuscript. Within each directory, there are three (3) Excel files labeled 'Nanodisc_Spectra_{Lipid Type}_{Run Number}.xlsx' coinciding with the sample number for each nanodisc size presented in the paper. These files contain the raw spectral data gathered from the Fluoromax+ instrument. The top row of each Excel file contains the temperature at which the spectrum was obtained. The leftmost column contains the emission wavelength measured by the instrument. The data in the sheet contains the counts per second measured by the instrument at the emission wavelength.
The data can be analyzed using the included 'extract_data.{Lipid Type}.py' script by running Python3 (either using "python extract_data.{Lipid Type}.py" or "python3 extract_data.{Lipid Type}.py") depending on your system. This will extract the data from all Excel files in the directory and output graphs of the measured spectrum for each sample, the generalized polarization of each spectrum, the average generalized polarization across all samples, as well as the derivative plot to determine the transition temperature for the lipid type.
Code/software
Excel or any other program that can read Excel-style files is needed to view the raw data. Python (version 3.6.8) was used for all data analysis.
Access information
Other publicly accessible locations of the data:
- None
Data was derived from the following sources:
- None