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Dynamic protein–DNA recognition: beyond what can be seen
Open accessAbstract
Traditionally, specific DNA recognition is thought to rely on static contacts with the bases or phosphates. Recent results, however, indicate that residues far outside the binding context can crucially influence selectivity or binding affinity via transient, dynamic interactions with the DNA binding interface. These regions usually do not adopt a well-defined structure, even when bound to DNA, and thus form a fuzzy complex. Here, we propose the existence of a dynamic DNA readout mechanism, wherein distant segments modulate conformational preferences, flexibility or spacing of the DNA binding motifs or serve as competitive partners. Despite their low sequence similarity, these intrinsically disordered regions are often conserved at the structural level, and exploited for regulation of the transcription machinery via protein-protein interactions, post-translational modifications or alternative splicing.
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“Some IDPs/IDRs may remain unfolded and dynamic even in the bound state [19–23], creating fuzzy complexes (Fig. 1) [24, 25].”
From Intrinsically disordered proteins play diverse roles in cell signaling (2022) · cites this paper as [24]
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Metadata
- Authors
- Fuxreiter, M., Simon, I., & Bondos, S.
- Affiliations
- Texas A&M Health Science Center (US)
- ORCID
- Bondos, Sarah
- Venue
- Trends in Biochemical Sciences
- Publisher
- Elsevier BV
- Published
- 2011-08
- Volume
- 36
- Issue
- 8
- Pages
- 415-423
- ISSN
- 0968-0004 (ISSN-L)
- OpenAlex
- W2099650039
- Cited by
- 167
- References
- 99
- Citations by year
- 2026: 3 · 2025: 12 · 2024: 11 · 2023: 6 · 2022: 5 · 2021: 7 · 2020: 13 · 2019: 13 · 2018: 8 · 2017: 11 · 2016: 12 · 2015: 12 · 2014: 18 · 2013: 21 · 2012: 11
- FWCI
- 1.57
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- Locations
- Trends in Biochemical Sciences (publishedVersion)
- PubMed (publishedVersion)
- University of Debrecen Electronic Archive (University of Debrecen) (submittedVersion, other-oa)
- Padua Research Archive (University of Padova) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- protein-DNA recognition, intrinsically disordered regions, fuzzy complexes, DNA binding selectivity, protein flexibility, protein-protein interaction, post-translational modification, alternative splicing, transcriptional regulation, DNA-binding motifs
- MeSH terms
- DNA, DNA-Binding Proteins, Nucleic Acid Conformation, Protein Binding, Protein Conformation, Protein Processing, Post-Translational, Regulatory Sequences, Nucleic Acid, Alternative Splicing, Protein Interaction Domains and Motifs
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