Evaluation of FRET X for single-molecule protein fingerprinting

Summary: Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between excha...

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Autores principales:	Carlos Victor de Lannoy, Mike Filius, Raman van Wee, Chirlmin Joo, Dick de Ridder
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Structural biology Biophysics Mathematical biosciences Proteomics Science Q
Acceso en línea:	https://doaj.org/article/0318f720399348acb2e17a402c51e526
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id	oai:doaj.org-article:0318f720399348acb2e17a402c51e526
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spelling	oai:doaj.org-article:0318f720399348acb2e17a402c51e5262021-11-20T05:08:45ZEvaluation of FRET X for single-molecule protein fingerprinting2589-004210.1016/j.isci.2021.103239https://doaj.org/article/0318f720399348acb2e17a402c51e5262021-11-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2589004221012074https://doaj.org/toc/2589-0042Summary: Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and accumulated FRET efficiencies constitute the fingerprint for a protein. To evaluate the feasibility of this approach, we simulated fingerprints for hundreds of proteins using a coarse-grained lattice model and experimentally demonstrated FRET X fingerprinting on model peptides. Measured fingerprints are in agreement with our simulations, corroborating the validity of our modeling approach. In a simulated complex mixture of >300 human proteins of which only cysteines, lysines, and arginines were labeled, a support vector machine was able to identify constituents with 95% accuracy. We anticipate that our FRET X fingerprinting approach will form the basis of an analysis tool for targeted proteomics.Carlos Victor de LannoyMike FiliusRaman van WeeChirlmin JooDick de RidderElsevierarticleStructural biologyBiophysicsMathematical biosciencesProteomicsScienceQENiScience, Vol 24, Iss 11, Pp 103239- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Structural biology Biophysics Mathematical biosciences Proteomics Science Q
spellingShingle	Structural biology Biophysics Mathematical biosciences Proteomics Science Q Carlos Victor de Lannoy Mike Filius Raman van Wee Chirlmin Joo Dick de Ridder Evaluation of FRET X for single-molecule protein fingerprinting
description	Summary: Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and accumulated FRET efficiencies constitute the fingerprint for a protein. To evaluate the feasibility of this approach, we simulated fingerprints for hundreds of proteins using a coarse-grained lattice model and experimentally demonstrated FRET X fingerprinting on model peptides. Measured fingerprints are in agreement with our simulations, corroborating the validity of our modeling approach. In a simulated complex mixture of >300 human proteins of which only cysteines, lysines, and arginines were labeled, a support vector machine was able to identify constituents with 95% accuracy. We anticipate that our FRET X fingerprinting approach will form the basis of an analysis tool for targeted proteomics.
format	article
author	Carlos Victor de Lannoy Mike Filius Raman van Wee Chirlmin Joo Dick de Ridder
author_facet	Carlos Victor de Lannoy Mike Filius Raman van Wee Chirlmin Joo Dick de Ridder
author_sort	Carlos Victor de Lannoy
title	Evaluation of FRET X for single-molecule protein fingerprinting
title_short	Evaluation of FRET X for single-molecule protein fingerprinting
title_full	Evaluation of FRET X for single-molecule protein fingerprinting
title_fullStr	Evaluation of FRET X for single-molecule protein fingerprinting
title_full_unstemmed	Evaluation of FRET X for single-molecule protein fingerprinting
title_sort	evaluation of fret x for single-molecule protein fingerprinting
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/0318f720399348acb2e17a402c51e526
work_keys_str_mv	AT carlosvictordelannoy evaluationoffretxforsinglemoleculeproteinfingerprinting AT mikefilius evaluationoffretxforsinglemoleculeproteinfingerprinting AT ramanvanwee evaluationoffretxforsinglemoleculeproteinfingerprinting AT chirlminjoo evaluationoffretxforsinglemoleculeproteinfingerprinting AT dickderidder evaluationoffretxforsinglemoleculeproteinfingerprinting
_version_	1718419520527269888

Evaluation of FRET X for single-molecule protein fingerprinting

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