10.5878/jvvj-1688
Ambrosetti, Elena
Elena
Ambrosetti
Department of Medical Biochemistry and Biophysics - Biomaterials division, Karolinska Institutet
A DNA-nanoassembly-based approach to map membrane protein nanoenvironments
A DNA-nanoassembly-based approach to map membrane protein nanoenvironments
Karolinska Institutet
2021
Amino Acids, Peptides, and Proteins
Aminosyror, peptider och proteiner
Cell Membrane
Cellmembran
Cellular Structures
Cellstrukturer
Cells
Celler
NanoDeep
NanoDeep
Biochemistry and Molecular Biology
Biokemi och molekylärbiologi
Biophysics
Biofysik
Biological Sciences
Biologi
Natural Sciences
Naturvetenskap
2021-06-24
2017-05-01/2020-07-15
eng
10.5878/nkjg-zk79
10.1101/836049
10.1038/s41565-020-00785-0
31.58 GiB
1
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.
De flesta proteiner vid plasmamembranet är inte jämnt fördelade men lokaliseras till dynamiska nanodomäner. För att undersöka deras funktionella relevans finns det ett behov av metoder som möjliggör omfattande analys av kompositionerna och rumsliga organisationerna av membranprotein-nanodomäner i cellpopulationer. Här beskriver vi utvecklingen av en icke-mikroskopibaserad metod för ensembleanalys av membranprotein-nanodomäner. Metoden, benämnd NANOscale DEciphEring of membrane Protein nanodomains (NanoDeep), baseras på användningen av DNA-nano assemblies för att översätta information om membranproteinorganisation till en DNA-sekvenseringsavläsning. Med hjälp av NanoDeep karakteriserade vi nano-miljöerna hos Her2, en membranreceptor av kritisk relevans vid cancer. NanoDeep har potential att ge nya insikter om rollerna för sammansättningen och den rumsliga organisationen av proteinnanomiljöer i regleringen av membranproteinfunktionen.
Metoden finns beskriven i preprint (se publikationer).
Metoden finns beskriven i preprint (se publikationer).
Mjukvaror för datainsamling:
Biacore T200 System Control software, NextSeq control software
Mjukvaror för dataanalys:
BIAevaluation v3.0, GraphPad Prism v8.2.1, Fiji ImageJ v1.0, Illumina Sequencing Analysis Viewer software, Python v3.8.0.