Creator/Principal investigator(s)
Elena Ambrosetti - Karolinska Institutet, Department of Medical Biochemistry and Biophysics - Biomaterials division
Description
Most proteins at the plasma membrane are not uniformly distributed but localize to dynamic domains of nanoscale dimensions. To investigate their functional relevance, there is a need for methods that enable comprehensive analysis of the compositions and spatial organizations of membrane protein nanodomains in cell populations. Here we describe the development of a non-microscopy based method for ensemble analysis of membrane protein nanodomains. The method, termed NANOscale DEciphEring of membrane Protein nanodomains (NanoDeep), is based on the use of DNA nanoassemblies to translate membrane protein organization information into a DNA sequencing readout. Using NanoDeep, we characterised the nanoenvironments of Her2, a membrane receptor of critical relevance in cancer. Importantly, we were able to modulate by design the inventory of proteins analysed by NanoDeep. NanoDeep has the potential to provide new insights into the roles of the composition and spatial organization of protein nanoenvironments in the regulation of membrane protein function.
The methodology is described in the preprint art
Language
English
Research principal
Responsible department/unit
Department of Medical Biochemistry and Biophysics - Biomaterials division
Data contains personal data
No
Population
cell membrane receptors
Study design
Experimental study
A DNA nanoassembly-based approach to map membrane protein nanoenvironments (preprint).
Elena Ambrosetti, Giulio Bernardinelli, Ian Hoffecker, Leonard Hartmanis, View ORCID ProfileRickard Sandberg, Björn Högberg, Ana I. Teixeira
doi: https://doi.org/10.1101/836049
DOI:
https://doi.org/10.1101/836049
“A DNA-nanoassembly-based approach to map membrane protein nanoenvironments” E. Ambrosetti, G. Bernardinelli, I. T. Hoffecker, L. Hartmanis, G. Kiriako, A. de Marco, R. Sandberg, B. Högberg, A. I. Teixeira. Nat. Nanotechnol. 2020.
DOI:
https://doi.org/10.1038/s41565-020-00785-0
If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.
Download data
Associated documentation
Description
The methodology for this dataset is available in the preprint (see publication list)Software for data collection:
Biacore T200 System Control software, NextSeq control software
Software for data analysis:
BIAevaluation v3.0, GraphPad Prism v8.2.1, Fiji ImageJ v1.0, Illumina Sequencing Analysis Viewer software, Python v3.8.0.
Version 1
https://doi.org/10.5878/jvvj-1688
Citation
Download citation
Data format / data structure
Numeric
Text
Still image
Other
Creator/Principal investigator(s)
Elena Ambrosetti - Karolinska Institutet, Department of Medical Biochemistry and Biophysics - Biomaterials division
Keywords