A DNA-nanoassembly-based approach to map membrane protein nanoenvironments

SND-ID: 2020-90-1. Version: 1. DOI: https://doi.org/10.5878/jvvj-1688

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Creator/Principal investigator(s)

Elena Ambrosetti - Karolinska Institutet, Department of Medical Biochemistry and Biophysics - Biomaterials division

Research principal

Karolinska Institutet - Department of Medical Biochemistry and Biophysics - Biomaterials division rorId

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

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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 article (see publications list).

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. Show less..

Data contains personal data

No

Language

Method and outcome

Population

cell membrane receptors

Study design

Experimental study

Data format / data structure

Data collection
  • Mode of collection: Measurements and tests
  • Time period(s) for data collection: 2017-05-01 – 2020-07-15
  • Source of the data: Biological samples
Geographic coverage
Administrative information

Responsible department/unit

Department of Medical Biochemistry and Biophysics - Biomaterials division

Topic and keywords

Research area

Biochemistry and molecular biology (Standard för svensk indelning av forskningsämnen 2011)

Biophysics (Standard för svensk indelning av forskningsämnen 2011)

Publications

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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

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Published: 2021-06-24