Cited by 167Protein Structure and DynamicsDiffusion and Search DynamicsGenomics and Chromatin Dynamics

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Dynamic protein–DNA recognition: beyond what can be seen

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Fuxreiter, Monika, Simon, Istvan, Bondos, Sarah·2011·Trends in Biochemical Sciences

DOI 10.1016/j.tibs.2011.04.006

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Abstract

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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Classification of Intrinsically Disordered Regions and Proteins
van der Lee, R., Buljan, M., Lang, B., Weatheritt, R. J., Daughdrill, G. W., Dunker, A. K., Fuxreiter, M., Gough, J., Gsponer, J., Jones, D. T., et al. (2014) · Chemical Reviews · doi:10.1021/cr400525m · Cited by 2,249
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Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell
Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436
Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks
Buljan, M., Chalancon, G., Eustermann, S., Wagner, G. P., Fuxreiter, M., Bateman, A., & Babu, M. M. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.039 · Cited by 396
“For instance, a change in the length of a disordered region can increase the conformational entropy and hence interfere with an interaction elsewhere on the protein (Fuxreiter et al., 2011; Hilser and Thompson, 2007).”
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The contribution of intrinsically disordered regions to protein function, cellular complexity, and human disease
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Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity
Brodsky, S., Jana, T., Mittelman, K., Chapal, M., Kumar, D. K., Carmi, M., & Barkai, N. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.05.032 · Cited by 376

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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)
DOI: 10.1016/j.tibs.2011.04.006
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: other-oa
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
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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Dynamic protein–DNA recognition: beyond what can be seen

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