## General information

Authors: Gurdap, C. O.; Wedemann, L.; Sych, T.; Sezgin, E.
Publisher: Karolinska Institute, Stockholm, Sweden (https://ki.se/)
DOI: 10.17044/scilifelab.21102061
Contact e-mail: erdinc.sezgin@ki.se

This item contains datasets from Gurdap et al, Biophysical Journal, 2022. 
This includes confocal images of vesicles for partitioning, Fluorescence Correlation Spectroscopy curves, excel and Prism files for all graphs for diffusion and partitoning and svg files of figures.


This readme file was last updated: 16-09-2022
License: CC BY 4.0	

Please cite as: Gurdap, C. O.; Wedemann, L.; Sych, T.; Sezgin, E. Influence of the extracellular domain size on the dynamic behavior of membrane proteins.
DOI: 10.17044/scilifelab.21102061

## Dataset description

This dataset is connected to a research article Gurdap et al, Biophysical Journal, 2022, https://doi.org/10.1016/j.bpj.2022.09.010
Gurdap, C. O.; Wedemann, L.; Sych, T.; Sezgin, E. Influence of the extracellular domain size on the dynamic behavior of membrane proteins.

## Abstract
The dynamic behavior of membrane proteins (MPs) mediates various cellular processes such as cellular motility, communication, and signaling. It is widely accepted that the dynamics of the MPs is determined either by the interactions of the transmembrane domain with the surrounding lipids or by the interactions of the intracellular domain with cytosolic components such as cortical actin. Although initiation of different cellular signaling events at the PM has been attributed to the extracellular domain (ECD) properties recently, the impact of ECDs on the dynamic behavior of MPs is rather unexplored. Here, we investigate how the ECD properties influence protein dynamics in the lipid bilayer by reconstituting ECDs of different sizes or glycosylation in model membrane systems and analyzing ECD-driven protein sorting in lipid domains as well as protein mobility. Our data shows that increasing the ECD mass or glycosylation leads to a decrease in ordered domain partitioning and diffusivity. Our data reconciles different mechanisms proposed for the initiation of cellular signaling by linking the ECD size of MPs with their localization and diffusion dynamics in the PM.


## Abbreviations 
GUV - giant unilamellar vesicle
GPMV- giant plasna membrane vesicle
DO- di-oleyl
DP- di-palmitol
CD- cluster of differentiation
PODXL- Podocalyxin-like protein
FCS- fluroescence correlation spectroscopy
A488- Alexa 488
ICAM- Intercellular Adhesion Molecule 

## Dataset items

# Figure 1B
Images:
GUV DO Ni-NTA .czi
GUV DP Ni-NTA.lsm

# Figure 1D
Images:
GPMV DO Ni-NTA .lsm
GPMV DP Ni-NTA.lsm

# Figure 2A
Images:
GUV DO Ni-NTA.lsm
GUV DP Ni-NTA.lsm
Prism:
Line profile.pzfx

# Figure 2B-C
Excel:
GUVs DO Ni-NTA.xlsx
GUVs DP Ni-NTA.xlsx
Prism:
GUVs partitioning.pzfx

# Figure 3C-D
Images:
CD34.czi
PODXL.czi
PODXL2.czi
Excel:
Glycoproteins partitioning.xlsx
Prism:
Glycoproteins partitioning.pzfx

# Figure 4A
Excel:
FCS curves.xlsx
Prism:
FCS curves.pzfx

# Figure 4B
Excel:
FCS on ECDs.xlsx
Prism:
FCS on GUVs ECDs.pzfx

# Figure 4D-E
Excel:
FCS on glycoproteins.xlsx
FCS on glycoproteins enzyme treatment.xlsx
Prism:
FCS on glycoproteins.pzfx
FCS:
CD34.fcs
PODXL.fcs
PODXL2.fcs

# Figure 5B
Excel:
GPMVs diffusion.xlsx
Prism:
GPMVs diffusion.pzfx
FCS:
A488-6xHis.fcs
CD2.fcs
CD45.fcs
CD59.fcs
ICAM-1.fcs

# Composed figures:
Figure1.svg
Figure2.svg
Figure3.svg
Figure4.svg
Figure5.svg

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

## Software to open files:
.csv - Microsoft Excel
.czi, .lsm - Fiji (https://imagej.net/Fiji.html#Downloads)
.pzfx - GraphPad Prism
.svg - Inkscape (https://inkscape.org/)
.fcs - FoCuS_point (https://academic.oup.com/bioinformatics/article/32/6/958/1744608)