DOI: 10.5061/dryad.cvdncjtfg
title: Data from: Examining the thermotropic properties of large, circularized nanodiscs

description: 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.
description: # Data from: Examining the thermotropic properties of large, circularized
 nanodiscs Dataset DOI: [10.5061/dryad.cvdncjtfg](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 associated with this repository as well as an archived version of the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