Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA

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2023_RSCchembio_rodriguez_molecular.pdf (2.8 MB)
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URI: http://hdl.handle.net/10347/30838
E-ISSN: 2633-0679
DOI: 10.1039/D3CB00053B

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2023

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Springer
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We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these types of complexes, dissecting interactions that are key to modulate their stability. The relevance of these interactions was validated experimentally. These results confirm the potential of this type of computational approach for studying peptide–DNA complexes and suggest that they could be very useful for the rational design of non-natural, DNA binding miniproteins

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RSC Chem. Biol., 2023, 4, 486

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This work has received financial support from Spanish grants (IJC2019-040358-I funded by MCIN/AEI/10.13039/501100011033 to J. R., PID2019-108624RB-I00 funded by MCIN/AEI/10.13039/501100011033 to J. L. M. and RTI2018-096704-B-100 and PID2021-122478NB-I00 to M. O.), the Consellería de Cultura, Educación e Ordenación Universitaria (Grants 2015-CP082, ED431C-2017/19, ED431C-2021/ 25 and ED431G 2019/03: Centro Singular de Investigación de Galicia accreditation 2019–2022 to J. L. M.) and the European Union (European Regional Development Fund-ERDF corresponding to the multiannual financial framework 2014–2020 to J. L. M.). This work was also supported by the BioExcel-2. Centre of Excellence for Computational Biomolecular Research” (823830, M. O.) and the Instituto de Salud Carlos III–Instituto Nacional de Bioinformática (ISCIII PT 17/0009/0007 co-funded by the Fondo Europeo de Desarrollo Regional, M. O.)

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© The Royal Society of Chemistry 2023. This article is licensed under a Creative Commons Attribution-NonComercial 3.0 Unported Licence
Atribución-NoComercial 4.0 Internacional

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Centro de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)