The DOI matches its Crossref record; 99 of the 99 references it cites were found in a registry or an index.
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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Cites
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
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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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
Self-citationWei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436
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).”
Self-citationBabu, M. M. (2016) · Biochemical Society Transactions · doi:10.1042/bst20160172 · Cited by 431
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
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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