Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates

DNA-binding proteins trigger various cellular functions and determine cellular fate. Before performing functions such as transcription, DNA repair, and DNA recombination, DNA-binding proteins need to search for and bind to their target sites in genomic DNA. Under evolutionary pressure, DNA-binding p...

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Autor principal:	Kiyoto Kamagata
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	single-molecule molecular dynamics sliding target search diffusion intrinsically disordered protein Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/3c59b84edf114ccd8f26e0b3d725820b
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spelling	oai:doaj.org-article:3c59b84edf114ccd8f26e0b3d725820b2021-11-19T05:36:31ZSingle-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates2296-889X10.3389/fmolb.2021.795367https://doaj.org/article/3c59b84edf114ccd8f26e0b3d725820b2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmolb.2021.795367/fullhttps://doaj.org/toc/2296-889XDNA-binding proteins trigger various cellular functions and determine cellular fate. Before performing functions such as transcription, DNA repair, and DNA recombination, DNA-binding proteins need to search for and bind to their target sites in genomic DNA. Under evolutionary pressure, DNA-binding proteins have gained accurate and rapid target search and binding strategies that combine three-dimensional search in solution, one-dimensional sliding along DNA, hopping and jumping on DNA, and intersegmental transfer between two DNA molecules. These mechanisms can be achieved by the unique structural and dynamic properties of these proteins. Single-molecule fluorescence microscopy and molecular dynamics simulations have characterized the molecular actions of DNA-binding proteins in detail. Furthermore, these methodologies have begun to characterize liquid condensates induced by liquid-liquid phase separation, e.g., molecular principles of uptake and dynamics in droplets. This review discusses the molecular action of DNA-binding proteins on DNA and in liquid condensate based on the latest studies that mainly focused on the model protein p53.Kiyoto KamagataFrontiers Media S.A.articlesingle-moleculemolecular dynamicsslidingtarget searchdiffusionintrinsically disordered proteinBiology (General)QH301-705.5ENFrontiers in Molecular Biosciences, Vol 8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	single-molecule molecular dynamics sliding target search diffusion intrinsically disordered protein Biology (General) QH301-705.5
spellingShingle	single-molecule molecular dynamics sliding target search diffusion intrinsically disordered protein Biology (General) QH301-705.5 Kiyoto Kamagata Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates
description	DNA-binding proteins trigger various cellular functions and determine cellular fate. Before performing functions such as transcription, DNA repair, and DNA recombination, DNA-binding proteins need to search for and bind to their target sites in genomic DNA. Under evolutionary pressure, DNA-binding proteins have gained accurate and rapid target search and binding strategies that combine three-dimensional search in solution, one-dimensional sliding along DNA, hopping and jumping on DNA, and intersegmental transfer between two DNA molecules. These mechanisms can be achieved by the unique structural and dynamic properties of these proteins. Single-molecule fluorescence microscopy and molecular dynamics simulations have characterized the molecular actions of DNA-binding proteins in detail. Furthermore, these methodologies have begun to characterize liquid condensates induced by liquid-liquid phase separation, e.g., molecular principles of uptake and dynamics in droplets. This review discusses the molecular action of DNA-binding proteins on DNA and in liquid condensate based on the latest studies that mainly focused on the model protein p53.
format	article
author	Kiyoto Kamagata
author_facet	Kiyoto Kamagata
author_sort	Kiyoto Kamagata
title	Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates
title_short	Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates
title_full	Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates
title_fullStr	Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates
title_full_unstemmed	Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates
title_sort	single-molecule microscopy meets molecular dynamics simulations for characterizing the molecular action of proteins on dna and in liquid condensates
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/3c59b84edf114ccd8f26e0b3d725820b
work_keys_str_mv	AT kiyotokamagata singlemoleculemicroscopymeetsmoleculardynamicssimulationsforcharacterizingthemolecularactionofproteinsondnaandinliquidcondensates
_version_	1718420368643850240

Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates

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