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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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ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.
Monod, J., Wyman, J., & Changeux, J. (1965) · Journal of Molecular Biology · doi:10.1016/s0022-2836(65)80285-6 · Cited by 7,681
Intrinsically unstructured proteins and their functions
Dyson, H. J., & Wright, P. E. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1589 · Cited by 3,871
Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits *
Koshland, D. E., Némethy, G., & Filmer, D. (1966) · Biochemistry · doi:10.1021/bi00865a047 · Cited by 3,019
Crystal Structure of a p53 Tumor Suppressor-DNA Complex: Understanding Tumorigenic Mutations
Cho, Y., Gorina, S., Jeffrey, P. D., & Pavletich, N. P. (1994) · Science · doi:10.1126/science.8023157 · Cited by 2,559
Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors
Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., Lahaye, T., Nickstadt, A., & Bonas, U. (2009) · Science · doi:10.1126/science.1178811 · Cited by 2,470
PROTEIN-DNA RECOGNITION
Pabo, C. O., & Sauer, R. T. (1984) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.53.070184.001453 · Cited by 1,585
The importance of intrinsic disorder for protein phosphorylation
Iakoucheva, L. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh253 · Cited by 1,429
Coupling of Local Folding to Site-Specific Binding of Proteins to DNA
Spolar, R. S., & Record, M. T. (1994) · Science · doi:10.1126/science.8303294 · Cited by 1,402
The role of DNA shape in protein–DNA recognition
Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., & Honig, B. (2009) · Nature · doi:10.1038/nature08473 · Cited by 1,096
Crystal structure of a yeast TBP/TATA-box complex
Kim, Y., Geiger, J. H., Hahn, S., & Sigler, P. B. (1993) · Nature · doi:10.1038/365512a0 · Cited by 1,085

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Self-citation

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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