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

SND-ID: 2020-90

Description Data and documentation

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

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Language

English

Research principal, contributors, and funding
Protection and ethical review

Data contains personal data

No

Method

Population

cell membrane receptors

Study design

Experimental study

Geographic coverage
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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Dataset
A DNA-nanoassembly-based approach to map membrane protein nanoenvironments

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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

Citation

Elena Ambrosetti. Karolinska Institutet, Department of Medical Biochemistry and Biophysics - Biomaterials division (2021). <em>A DNA-nanoassembly-based approach to map membrane protein nanoenvironments</em>. Swedish National Data Service. Version 1. <a href="https://doi.org/10.5878/jvvj-1688">https://doi.org/10.5878/jvvj-1688</a>

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Creator/Principal investigator(s)

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

Keywords

nanodeep

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
Published: 2021-06-24