In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy

Abstract Obtaining (dynamic) structure related information on proteins is key for understanding their function. Methods as single-molecule Förster Resonance Energy Transfer (smFRET) and Electron Paramagnetic Resonance (EPR) that measure distances between labeled residues to obtain dynamic informatio...

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Autores principales:	Hendrik R. Sikkema, Bert Poolman
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f682c8ad8bc643c5971b3fe417631ebd
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spelling	oai:doaj.org-article:f682c8ad8bc643c5971b3fe417631ebd2021-12-02T13:30:11ZIn silico method for selecting residue pairs for single-molecule microscopy and spectroscopy10.1038/s41598-021-85003-02045-2322https://doaj.org/article/f682c8ad8bc643c5971b3fe417631ebd2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85003-0https://doaj.org/toc/2045-2322Abstract Obtaining (dynamic) structure related information on proteins is key for understanding their function. Methods as single-molecule Förster Resonance Energy Transfer (smFRET) and Electron Paramagnetic Resonance (EPR) that measure distances between labeled residues to obtain dynamic information rely on selection of suitable residue pairs for chemical modification. Selection of pairs of amino acids, that show sufficient distance changes upon activity of the protein, can be a tedious process. Here we present an in silico approach that makes use of two or more structures (or structure models) to filter suitable residue pairs for FRET or EPR from all possible pairs within the protein. We apply the method for the study of the conformational dynamics of the substrate-binding domain of the osmoregulatory ATP-Binding Cassette transporter OpuA. This method speeds up the process of designing mutants, and because of its systematic nature, the chances of missing promising candidates are reduced.Hendrik R. SikkemaBert PoolmanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hendrik R. Sikkema Bert Poolman In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy
description	Abstract Obtaining (dynamic) structure related information on proteins is key for understanding their function. Methods as single-molecule Förster Resonance Energy Transfer (smFRET) and Electron Paramagnetic Resonance (EPR) that measure distances between labeled residues to obtain dynamic information rely on selection of suitable residue pairs for chemical modification. Selection of pairs of amino acids, that show sufficient distance changes upon activity of the protein, can be a tedious process. Here we present an in silico approach that makes use of two or more structures (or structure models) to filter suitable residue pairs for FRET or EPR from all possible pairs within the protein. We apply the method for the study of the conformational dynamics of the substrate-binding domain of the osmoregulatory ATP-Binding Cassette transporter OpuA. This method speeds up the process of designing mutants, and because of its systematic nature, the chances of missing promising candidates are reduced.
format	article
author	Hendrik R. Sikkema Bert Poolman
author_facet	Hendrik R. Sikkema Bert Poolman
author_sort	Hendrik R. Sikkema
title	In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy
title_short	In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy
title_full	In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy
title_fullStr	In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy
title_full_unstemmed	In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy
title_sort	in silico method for selecting residue pairs for single-molecule microscopy and spectroscopy
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/f682c8ad8bc643c5971b3fe417631ebd
work_keys_str_mv	AT hendrikrsikkema insilicomethodforselectingresiduepairsforsinglemoleculemicroscopyandspectroscopy AT bertpoolman insilicomethodforselectingresiduepairsforsinglemoleculemicroscopyandspectroscopy
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In silico method for selecting residue pairs for single-molecule microscopy and spectroscopy

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