ArticlePhysical chemistry chemical physics : PCCP2016
Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region.
Article in Physical chemistry chemical physics : PCCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
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- Fine-Tuning of ATF4 DNA Binding Activity by a Secondary Basic Motif Unique to the ATF-X Subfamily of bZip Transcription Factors.Biochemistry · 2025Article
- Breaking down walls: Continuous potential models for internal motions in NMR spin relaxation.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2024Article
- Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins.Protein science : a publication of the Protein Society · 2024Article
- Liquid-Liquid Phase Separation Modifies the Dynamic Properties of Intrinsically Disordered Proteins.Journal of the American Chemical Society · 2023Article
- Convergent views on disordered protein dynamics from NMR and computational approaches.Biophysical journal · 2022Article
- Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2022Article
- NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins.Chemical reviews · 2022Review
- Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry.Chemical reviews · 2022Review
- A systematic genome-wide account of binding sites for the model transcription factor Gcn4.Genome research · 2022Article
- Dynamics in natural and designed elastins and their relation to elastic fiber structure and recoil.Biophysical journal · 2021Article
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- Bootstrap Aggregation for Model Selection in the Model-free Formalism.Magnetic resonance (Gottingen, Germany) · 2021Article
- Model-Free or Not?Frontiers in molecular biosciences · 2021Review
- Sequence-Dependent Correlated Segments in the Intrinsically Disordered Region of ChiZ.Biomolecules · 2020Article
- Protein Dynamics revealed by NMR Relaxation Methods.Emerging topics in life sciences · 2020Article
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Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) are known to play important roles in regulatory and signaling pathways. A critical aspect of these functions is the ability of IDP/IDRs to form highly specific complexes with target molecules. However, elucidation of the contributions of conformational dynamics to function has been limited by challenges associated with structural heterogeneity of IDP/IDRs. Using NMR spin relaxation parameters ((15)N R1, (15)N R2, and {(1)H}-(15)N heteronuclear NOE) collected at four static magnetic fields ranging from 14.1 to 21.1 T, we have analyzed the backbone dynamics of the basic leucine-zipper (bZip) domain of the Saccharomyces cerevisiae transcription factor GCN4, whose DNA binding domain is intrinsically disordered in the absence of DNA substrate. We demonstrate that the extended model-free analysis can be applied to proteins with IDRs such as apo GCN4 and that these results significantly extend previous NMR studies of GCN4 dynamics performed using a single static magnetic field of 11.74 T [Bracken, et al., J. Mol. Biol., 1999, 285, 2133-2146] and correlate well with molecular dynamics simulations [Robustelli, et al., J. Chem. Theory Comput., 2013, 9, 5190-5200]. In contrast to the earlier work, data at multiple static fields allows the time scales of internal dynamics of GCN4 to be reliably quantified. Large amplitude dynamic fluctuations in the DNA-binding region have correlation times (τs ≈ 1.4-2.5 ns) consistent with a two-step mechanism in which partially ordered bZip conformations of GCN4 form initial encounter complexes with DNA and then rapidly rearrange to the high affinity state with fully formed basic region recognition helices.
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