# General information

Authors: Ragaller, F.; Andronico, L.; Sykora, J.; Kulig, W.; Rog, T.; Urem, Y.B.; Abhinav; Danylchuk, D.I.; Hof, M.; Klymchenko, A.; Amaro, M.;  Vattulainen, I.; Sezgin, E.
Publisher: Karolinska Institute, Stockholm, Sweden [https://ki.se/]
DOI: https://doi.org/10.17044/scilifelab.20509362
Contact e-mail: erdinc.sezgin@ki.se

This item contains datasets from Ragaller et al, Open Biology, 2022 (https://doi.org/10.1098/rsob.220175). 
It contains excel data of Generalized Polarization (GP) values, GP profiles, GP maps, raw spectral images, MD Simulation snapshots, excel data of Tilt angle distributions, Partial density profiles, Relaxation time and Stokes Shift



This readme file was last updated: 13.09.2022
Licence: CC BY 4.0

Please cite as: Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties. 
DOI: 10.17044/scilifelab.20509362




#Data set description

This dataset is connected to a research article, https://doi.org/10.1098/rsob.220175 

Ragaller, F.; Andronico, L.; Sykora, J.; Kulig, W.; Rog, T.; Urem, Y.B.; Abhinav; Danylchuk, D.I.; Hof, M.; Klymchenko, A.; Amaro, M.; Vattulainen, I.; Sezgin, E.Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties. Open Biology 2022, 12, 220175  



## Abstract
The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (cis vs. trans), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question. 


## Dataset items

### Figure 1b-d
Spectral Images:
Pro12A
GUV: [GP_GUV_Pro12A_10-2_n2.tif]
GPMV: [GP_GPMV_Pro12A_10-2_n3.tif]

NR12S
GUV: [GP_GUV_NR12S_8.tif]
GPMV: [GP_GPMV_NR12S_5-2_n3.tif]

NR12A
GUV: [GP_GUV_NR12A_5-2_n3.tif]
GPMV: [GP_GPMV_NR12A_20-2_n3.tif]

### Figure 1e-g
Normalized intensity spectra [Spectral_Shift.xlsx; Sheet: Normalised intensity Spectra]


### Figure 1h-j
GP Images: 
Pro12A 
GUV [GP_GUV_Pro12A_10-2_n2_GP_MAP.png]
GPMV [GP_GPMV_Pro12A_10-2_n3_GP_MAP_.png]

NR12S
GUV [GP_GUV_NR12S_8_GP_MAP.png]
GPMV [GP_GPMV_NR12S_5-2_n3_GP_MAP.png]

NR12A 
GUV [GP_GUV_NR12A_5-2_n3_GP_MAP.png]
GPMV [GP_GPMV_NR12A_20-2_n3_GP_MAP.png]

Linearised GP profiles [Spectral_Shift.xlsx; Sheet: linearised GP profiles]


### Figure 1k-m
GP box plots
Phase-separated GUVs [Spectral_Shift.xlsx; Sheet: Phase-separated GUVs]
Phase-separated GPMVs [Spectral_Shift.xlsx; Sheet: Phase-separated GPMVs]


### Figure 2b-e
GP box plots [GP_lipidcompositions.xlsx; Sheet: GP_GUVs]
GP delta values [GP_lipidcompositions.xlsx; Sheet: GP_delta]
Raw spectral image example Pro12A in POPC [POPC_Pro12A.lsm]
Raw spectral image example NR12S in POPC [POPC_NR12S.lsm]
Raw spectral image example NR12A in POPC [POPC_NR12A.lsm]


### Figure 3a
Simulation snapshots
NR12A [NR12A-POPC_v2.png; NR12A-POPC-CHOL_v2.png]
NR12S [NR12S-POPC_v2.png; NR12S-POPC-CHOL_v2.png]
Pro12A [PRO12A-POPC_v2.png; PRO12A-POPC-CHOL_v2.png]


### Figure 3b-c
Tilt angle distributions [MD_simulation_data.xlsx; Sheet: Tilt angles]
Partial density profiles [MD_simulation_data.xlsx; Sheet: Partial density profiles]


### Figure 4a-b
Relaxation time [TDFS_data.xlsx; Sheet: Relaxation time vs. GP]
Stokes Shift [TDFS_data.xlsx; Sheet:Stokes Shift vs. GP]



Researchers are welcome to use the data contained in the dataset for any projects. Please cite this item upon use or when published.



# Software to open files:
.xlsx - Microsoft Excel
.tif, .png, .lsm - Fiji (https://imagej.net/Fiji.html#Downloads)