Impact of crowded environments on binding between protein and single-stranded DNA

Abstract The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structu...

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Autores principales:	Birgit Köhn, Patricia Schwarz, Pernilla Wittung-Stafshede, Michael Kovermann
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8a50fd7795844c2d80b2f7d036f8616f
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spelling	oai:doaj.org-article:8a50fd7795844c2d80b2f7d036f8616f2021-12-02T16:37:38ZImpact of crowded environments on binding between protein and single-stranded DNA10.1038/s41598-021-97219-12045-2322https://doaj.org/article/8a50fd7795844c2d80b2f7d036f8616f2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97219-1https://doaj.org/toc/2045-2322Abstract The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structural features of ssDNA-bound CspB are fully conserved in crowded environments as probed by high-resolution NMR spectroscopy, intrinsic fluorescence quenching experiments reveal subtle changes in equilibrium affinity. Kinetic stopped-flow data showed that DNA-to-protein association is significantly retarded independent of choice of the molecule that is added to the solution, but dissociation depends in a nontrivial way on its size and chemical characteristics. Thus, for this DNA–protein interaction, excluded volume effect does not play the dominant role but instead observed effects are dictated by the chemical properties of the crowder. We propose that surrounding molecules are capable of specific modification of the protein’s hydration shell via soft interactions that, in turn, tune protein–ligand binding dynamics and affinity.Birgit KöhnPatricia SchwarzPernilla Wittung-StafshedeMichael KovermannNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Birgit Köhn Patricia Schwarz Pernilla Wittung-Stafshede Michael Kovermann Impact of crowded environments on binding between protein and single-stranded DNA
description	Abstract The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structural features of ssDNA-bound CspB are fully conserved in crowded environments as probed by high-resolution NMR spectroscopy, intrinsic fluorescence quenching experiments reveal subtle changes in equilibrium affinity. Kinetic stopped-flow data showed that DNA-to-protein association is significantly retarded independent of choice of the molecule that is added to the solution, but dissociation depends in a nontrivial way on its size and chemical characteristics. Thus, for this DNA–protein interaction, excluded volume effect does not play the dominant role but instead observed effects are dictated by the chemical properties of the crowder. We propose that surrounding molecules are capable of specific modification of the protein’s hydration shell via soft interactions that, in turn, tune protein–ligand binding dynamics and affinity.
format	article
author	Birgit Köhn Patricia Schwarz Pernilla Wittung-Stafshede Michael Kovermann
author_facet	Birgit Köhn Patricia Schwarz Pernilla Wittung-Stafshede Michael Kovermann
author_sort	Birgit Köhn
title	Impact of crowded environments on binding between protein and single-stranded DNA
title_short	Impact of crowded environments on binding between protein and single-stranded DNA
title_full	Impact of crowded environments on binding between protein and single-stranded DNA
title_fullStr	Impact of crowded environments on binding between protein and single-stranded DNA
title_full_unstemmed	Impact of crowded environments on binding between protein and single-stranded DNA
title_sort	impact of crowded environments on binding between protein and single-stranded dna
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8a50fd7795844c2d80b2f7d036f8616f
work_keys_str_mv	AT birgitkohn impactofcrowdedenvironmentsonbindingbetweenproteinandsinglestrandeddna AT patriciaschwarz impactofcrowdedenvironmentsonbindingbetweenproteinandsinglestrandeddna AT pernillawittungstafshede impactofcrowdedenvironmentsonbindingbetweenproteinandsinglestrandeddna AT michaelkovermann impactofcrowdedenvironmentsonbindingbetweenproteinandsinglestrandeddna
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Impact of crowded environments on binding between protein and single-stranded DNA

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