Dynamic protein–DNA recognition: beyond what can be seen

Fuxreiter, Monika; Simon, Istvan; Bondos, Sarah

doi:10.1016/j.tibs.2011.04.006

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

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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Some IDPs/IDRs may remain unfolded and dynamic even in the bound state, creating fuzzy complexes.
“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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pH-Dependent Enhancement of DNA Binding by the Ultrabithorax Homeodomain
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Biophysical properties of regions flanking the bHLH-Zip motif in the p22 Max protein
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Order and Disorder in the Domain Organization of the Plasmid Partition Protein KorB
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Molecular flexibility in protein–DNA interactions
Günther, S., Rother, K. M., & Frömmel, C. (2006) · Biosystems · doi:10.1016/j.biosystems.2005.12.007 · Cited by 11 · see citing works
Interactions of The Acidic Domain and SRF Interacting Motifs with the NKX3.1 Homeodomain
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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 2,155 · see citing works
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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 · see citing works
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 · see citing works
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Babu, M. M. (2016) · Biochemical Society Transactions · doi:10.1042/bst20160172 · Cited by 408 · see citing works
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 362 · see citing works
Structure, Function and Networks of Transcription Factors Involved in Abiotic Stress Responses
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Kim, H. J., Nam, H. G., & Lim, P. O. (2016) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2016.06.002 · Cited by 314 · see citing works
Fuzzy complexes: Specific binding without complete folding
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Intrinsically disordered proteins play diverse roles in cell signaling
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The new (dis)order in RNA regulation
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Allosteric post-translational modification codes
Nussinov, R., Tsai, C.-J., Xin, F., & Radivojac, P. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2012.07.001 · Cited by 211 · see citing works
Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling
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Intrinsically disordered regions as affinity tuners in protein–DNA interactions
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Protein disorder, prion propensities, and self-organizing macromolecular collectives
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Alternative splicing of intrinsically disordered regions and rewiring of protein interactions
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The Underappreciated Role of Allostery in the Cellular Network
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Principles of Allosteric Interactions in Cell Signaling
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Controlling entropy to tune the functions of intrinsically disordered regions
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Fuzziness in Protein Interactions—A Historical Perspective
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Eukaryotic transcription factors: paradigms of protein intrinsic disorder
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Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications
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Multiple conformational selection and induced fit events take place in allosteric propagation
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Biomolecular dynamics: order–disorder transitions and energy landscapes
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Sequence-Based Prediction of Fuzzy Protein Interactions
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Identification and expression of GRAS family genes in maize (Zea mays L.)
Guo, Y., Wu, H., Li, X., Li, Q., Zhao, X., Duan, X., An, Y., Lv, W., & An, H. (2017) · PLoS ONE · doi:10.1371/journal.pone.0185418 · Cited by 106 · see citing works
A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors inArabidopsis thaliana
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Wrecked regulation of intrinsically disordered proteins in diseases: pathogenicity of deregulated regulators
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Advances in the Determination of Nucleic Acid Conformational Ensembles
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Interactions via intrinsically disordered regions: What kind of motifs?
Pancsa, R., & Fuxreiter, M. (2012) · IUBMB Life · doi:10.1002/iub.1034 · Cited by 82 · see citing works
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Fuzziness enables context dependence of protein interactions
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The GRAS gene family in pine: transcript expression patterns associated with the maturation-related decline of competence to form adventitious roots
Abarca, D., Pizarro, A., Hernández, I., Sánchez, C., Solana, S. P., Amo, A. D., Carneros, E., & Díaz‐Sala, C. (2014) · BMC Plant Biology · doi:10.1186/s12870-014-0354-8 · Cited by 81 · see citing works
Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors
Smith, N. C., & Matthews, J. M. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.05.006 · Cited by 79 · see citing works
New insights into protein–DNA binding specificity from hydrogen bond based comparative study
Lin, M., & Guo, J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz963 · Cited by 76 · see citing works
Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding
Chen, T., Song, J., & Chan, H. S. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.12.002 · Cited by 74 · see citing works
Order by disorder in plant signaling
Kragelund, B. B., Jensen, M. K., & Skriver, K. (2012) · Trends in Plant Science · doi:10.1016/j.tplants.2012.06.010 · Cited by 71 · see citing works
Small-Angle X-Ray Scattering- and Nuclear Magnetic Resonance-Derived Conformational Ensemble of the Highly Flexible Antitoxin PaaA2
Sterckx, Y. G. ‐., Volkov, A. N., Vranken, W., Kragelj, J., Jensen, M. R., Buts, L., Garcia‐Pino, A., Jové, T., Melderen, L. V., Blackledge, M. J., et al. (2014) · Structure · doi:10.1016/j.str.2014.03.012 · Cited by 70 · see citing works
Evidence for a Strong Correlation Between Transcription Factor Protein Disorder and Organismic Complexity
Yruela, I., Oldfield, C. J., Niklas, K. J., & Dunker, A. K. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx073 · Cited by 67 · see citing works
Unstructured to structured transition of an intrinsically disordered protein peptide in coupling Ca 2+ -sensing and SK channel activation
Zhang, M., Pascal, J. M., & Zhang, J.-F. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1220253110 · Cited by 64 · see citing works
Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues
Gloaguen, E., Mons, M., Schwing, K., & Gerhards, M. (2020) · Chemical Reviews · doi:10.1021/acs.chemrev.0c00168 · Cited by 63 · see citing works
Dynamics and recognition within a protein–DNA complex: a molecular dynamics study of the SKN-1/DNA interaction
Éthève, L., Martin, J., & Lavery, R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1511 · Cited by 62 · see citing works
Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition
Schwing, K., & Gerhards, M. (2016) · International Reviews in Physical Chemistry · doi:10.1080/0144235x.2016.1229331 · Cited by 62 · see citing works
Allosteric Conformational Barcodes Direct Signaling in the Cell
Nussinov, R., Ma, B., Tsai, C.-J., & Csermely, P. (2013) · Structure · doi:10.1016/j.str.2013.06.002 · Cited by 55 · see citing works
Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors
Yesudhas, D., Batool, M., Anwar, M. A., Panneerselvam, S., & Choi, S. (2017) · Genes · doi:10.3390/genes8080192 · Cited by 57 · see citing works
Protein intrinsic disorder in Arabidopsis NAC transcription factors: transcriptional activation by ANAC013 and ANAC046 and their interactions with RCD1
O’Shea, C., Kryger, M., Stender, E. G. P., Kragelund, B. B., Willemoës, M., & Skriver, K. (2014) · Biochemical Journal · doi:10.1042/bj20141045 · Cited by 56 · see citing works
INTRINSIC DISORDER WITHIN AND FLANKING THE DNA-BINDING DOMAINS OF HUMAN TRANSCRIPTION FACTORS
Guo, X., Bulyk, M. L., & Hartemink, A. J. (2011) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789814366496_0011 · Cited by 48 · see citing works
Fuzzy regions in an intrinsically disordered protein impair protein–protein interactions
Gruet, A., Dosnon, M., Blocquel, D., Brunel, J., Gerlier, D., Das, R. K., Bonetti, D., Gianni, S., Fuxreiter, M., Longhi, S., et al. (2015) · FEBS Journal · doi:10.1111/febs.13631 · Cited by 52 · see citing works
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How do disordered regions achieve comparable functions to structured domains?
Latysheva, N. S., Flock, T., Weatheritt, R. J., Chavali, S., & Babu, M. M. (2015) · Protein Science · doi:10.1002/pro.2674 · Cited by 50 · see citing works
Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA
Chu, X., Liu, F., Maxwell, B. A., Wang, Y., Suo, Z., Wang, H., Han, W., & Wang, J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003804 · Cited by 50 · see citing works
The spatial structure of cell signaling systems
Nussinov, R. (2013) · Physical Biology · doi:10.1088/1478-3975/10/4/045004 · Cited by 49 · see citing works
Do Intrinsically Disordered Proteins Possess High Specificity in Protein–Protein Interactions?
Huang, Y., & Liu, Z. (2013) · Chemistry - A European Journal · doi:10.1002/chem.201203100 · Cited by 48 · see citing works
A Comprehensive Survey of the Roles of Highly Disordered Proteins in Type 2 Diabetes
Du, Z., & Uversky, V. N. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18102010 · Cited by 44 · see citing works
High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants
Aditham, A. K., Markin, C. J., Mokhtari, D. A., DelRosso, N. V., & Fordyce, P. M. (2020) · Cell Systems · doi:10.1016/j.cels.2020.11.012 · Cited by 45 · see citing works
A broad view of scaffolding suggests that scaffolding proteins can actively control regulation and signaling of multienzyme complexes through allostery
Nussinov, R., Ma, B., & Tsai, C. (2013) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2012.12.014 · Cited by 45 · see citing works
An Adequate Account of Excluded Volume Is Necessary To Infer Compactness and Asphericity of Disordered Proteins by Förster Resonance Energy Transfer
Song, J., Gomes, G.-N. W., Gradinaru, C. C., & Chan, H. S. (2015) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5b09133 · Cited by 45 · see citing works
Deciphering the Binding between Nupr1 and MSL1 and Their DNA-Repairing Activity
Aguado‐Llera, D., Hamidi, T., Doménech, R., Pantoja‐Uceda, D., Gironella, M., Santoro, J., Velázquez‐Campoy, A., Neira, J. L., & Iovanna, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0078101 · Cited by 45 · see citing works
Interactions between the R2R3-MYB Transcription Factor, AtMYB61, and Target DNA Binding Sites
Prouse, M. B., & Campbell, M. M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065132 · Cited by 44 · see citing works
RAG2’s Acidic Hinge Restricts Repair-Pathway Choice and Promotes Genomic Stability
Coussens, M., Wendland, R. L., Deriano, L., Lindsay, C., Arnal, S. M., & Roth, D. B. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.07.041 · Cited by 44 · see citing works
Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture
Moriyama, K., Yoshizawa-Sugata, N., & Masai, H. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra117.000446 · Cited by 44 · see citing works
bHLH–PAS Proteins: Their Structure and Intrinsic Disorder
Kolonko, M., & Greb‐Markiewicz, B. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20153653 · Cited by 44 · see citing works
Aggregation and disaggregation features of the human proteome
Määttä, T. A., Rettel, M., Sridharan, S., Helm, D., Kurzawa, N., Stein, F., & Savitski, M. M. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209500 · Cited by 34 · see citing works
Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships
Jianhong, Z., Oldfield, C. J., Yan, W., Shen, B., & Dunker, A. K. (2019) · Protein Science · doi:10.1002/pro.3680 · Cited by 39 · see citing works
How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition
Battistini, F., Buitrago, D., Gallego, D., Dans, P. D., Gelpí, J. L., & Orozco, M. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.07.021 · Cited by 39 · see citing works
The functional diversity of structural disorder in plant proteins
Covarrubias, A. A., Romero-Perez, P. S., Cuevas‐Velazquez, C. L., & Rendón‐Luna, D. F. (2019) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2019.108229 · Cited by 39 · see citing works
Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins
Nagarajan, R., Ahmad, S., & Gromiha, M. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt544 · Cited by 36 · see citing works
A Tale of Loops and Tails: The Role of Intrinsically Disordered Protein Regions in R-Loop Recognition and Phase Separation
Dettori, L. G., Torrejon, D., Chakraborty, A., Dutta, A., Mohamed, M., Papp, C., Kuznetsov, V. A., Sung, P., Feng, W., & Bah, A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.691694 · Cited by 36 · see citing works
Statistical analysis of structural determinants for protein–DNA‐binding specificity
Corona, R. I., & Guo, J. (2016) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25061 · Cited by 35 · see citing works
Spatiotemporal and global profiling of DNA–protein interactions enables discovery of low-affinity transcription factors
Guo, A., Yan, K., Hu, H., Zhai, L., Hu, T., Su, H., Chi, Y., Zha, J., Xu, Y., Zhao, D., et al. (2023) · Nature Chemistry · doi:10.1038/s41557-023-01196-z · Cited by 35 · see citing works
Computational Approaches for Predicting the Binding Sites and Understanding the Recognition Mechanism of Protein–DNA Complexes
Gromiha, M. M., & Nagarajan, R. (2013) · Advances in protein chemistry and structural biology · doi:10.1016/b978-0-12-411637-5.00003-2 · Cited by 34 · see citing works
U-turn DNA bending by human mitochondrial transcription factor A
Rubio‐Cosials, A., & Solà, M. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.12.004 · Cited by 31 · see citing works
Novel peptide binds EWS-FLI1 and reduces the oncogenic potential in Ewing tumors
Erkizan, H. V., Scher, L., Gamble, S. E., Barber-Rotenberg, J. S., Sajwan, K. P., Üren, A., & Toretsky, J. A. (2011) · Cell Cycle · doi:10.4161/cc.10.19.17734 · Cited by 29 · see citing works
Roles of conformational disorder and downhill folding in modulating protein–DNA recognition
Chu, X., & Muñoz, V. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp04380e · Cited by 29 · see citing works
Context-dependent, fuzzy protein interactions: Towards sequence-based insights
Fuxreiter, M. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102834 · Cited by 31 · see citing works
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Origins of Myc Proteins – Using Intrinsic Protein Disorder to Trace Distant Relatives
Mahani, A., Henriksson, J., & Wright, A. P. H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075057 · Cited by 28 · see citing works
Interactions of p53 with poly(ADP-ribose) and DNA induce distinct changes in protein structure as revealed by ATR-FTIR spectroscopy
Krüger, A., Stier, A., Fischbach, A., Bürkle, A., Hauser, K., & Mangerich, A. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz175 · Cited by 28 · see citing works
Mechanistic regulation of FOXO transcription factors in the nucleus
Guo, X., Peng, K., He, Y., & Xue, L. (2024) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2024.189083 · Cited by 27 · see citing works
How acidic amino acid residues facilitate DNA target site selection
Hossain, K. A., Kogut, M., Słabońska, J., Sappati, S., Wieczór, M., & Czub, J. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2212501120 · Cited by 29 · see citing works
Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions
Fuxreiter, M. (2018) · Molecules · doi:10.3390/molecules23113008 · Cited by 27 · see citing works
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A low-complexity region in the YTH domain protein Mmi1 enhances RNA binding
Stowell, J. A. W., Wagstaff, J. L., Hill, C. H., Yu, M., McLaughlin, S. H., Freund, S. M. V., & Passmore, L. A. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.002291 · Cited by 25 · see citing works
Structural Fuzziness of the RNA-Organizing Protein SERF Determines a Toxic Gain-of-interaction
Meyer, N. H., Dellago, H., Tam‐Amersdorfer, C., Merle, D. A., Parlato, R., Gesslbauer, B., Almer, J., Gschwandtner, M., Leon, A., Franzmann, T. M., et al. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.11.014 · Cited by 24 · see citing works
Probing Surfaces in Dynamic Protein Interactions
Spreitzer, E., Usluer, S., & Madl, T. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.02.032 · Cited by 23 · see citing works
Determination of helix orientations in a flexible DNA by multi-frequency EPR spectroscopy
Grytz, C. M., Kazemi, S., Marko, A., Čekan, P., Güntert, P., Sigurdsson, S. T., & Prisner, T. F. (2017) · Physical Chemistry Chemical Physics · doi:10.1039/c7cp04997h · Cited by 21 · see citing works
The Intrinsically Disordered Regions of the Drosophila melanogaster Hox Protein Ultrabithorax Select Interacting Proteins Based on Partner Topology
Hsiao, H., Gonzalez, K. L., Catanese, D. J., Jordy, K. E., Matthews, K. S., & Bondos, S. E. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108217 · Cited by 21 · see citing works
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Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins
Chu, X., & Wang, J. (2019) · Physical Chemistry Chemical Physics · doi:10.1039/c8cp06803h · Cited by 21 · see citing works
The neglected functions of intrinsically disordered proteins and the origin of life
Jaeken, L. (2017) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2017.03.002 · Cited by 21 · see citing works
Combining Rational Design and Continuous Evolution on Minimalist Proteins That Target the E-box DNA Site
Inamoto, I., Sheoran, I. S., Popa, S. C., Hussain, M., & Shin, J. A. (2020) · ACS Chemical Biology · doi:10.1021/acschembio.0c00684 · Cited by 20 · see citing works
Capturing the Conformational Ensemble of the Mixed Folded Polyglutamine Protein Ataxin-3
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TIBS-844; No. of Pages 9 Review Dynamic protein–DNA recognition: beyond
Fuxreiter, M., Simon, I., & Bondos, S. (2013)
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Mondol, T., Batabyal, S., & Roy, S. (2016)
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Fuzzy protein-DNA interactions and beyond: A common theme in transcription?
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Self-citation
Intrinsically disordered regions as affinity tuners in protein–DNA interactions
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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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