Dynamic protein–DNA recognition: beyond what can be seen (Q22061739)

Trends in Biochemical Sciences

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published in

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volume

36

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issue

8

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page(s)

415-423

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cites work

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Dynamic behavior of an intrinsically unstructured linker domain is conserved in the face of negligible amino acid sequence conservation

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Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules

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Close encounters: why unstructured, polymeric domains can increase rates of specific macromolecular association

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Biophysical properties of regions flanking the bHLH-Zip motif in the p22 Max protein.

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A novel nucleolar transcriptional activator ApLLP for long-term memory formation is intrinsically unstructured but functionally active.

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Molecular flexibility in protein-DNA interactions

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Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker

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Essential role of coiled coils for aggregation and activity of Q/N-rich prions and PolyQ proteins

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The unstructured C-terminal extension of UvrD interacts with UvrB, but is dispensable for nucleotide excision repair

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Linear motifs: evolutionary interaction switches.

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Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

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Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation

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Flexibility and adaptability in binding of E. coli cytidine repressor to different operators suggests a role in differential gene regulation

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Mapping intramolecular interactions between domains in HMGB1 using a tail-truncation approach.

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Role of intrinsic flexibility in signal transduction mediated by the cell cycle regulator, p27 Kip1.

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The affinity of Ets-1 for DNA is modulated by phosphorylation through transient interactions of an unstructured region

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Internal regulatory interactions determine DNA binding specificity by a Hox transcription factor.

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Structure and disorder in an unfolded state under nondenaturing conditions from ensemble models consistent with a large number of experimental restraints

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Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails

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Tail-Mediated Collapse of HMGB1 Is Dynamic and Occurs via Differential Binding of the Acidic Tail to the A and B Domains

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Function and structure of inherently disordered proteins

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The extended arms of DNA-binding domains: a tale of tails

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Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions

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ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

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Recognition of specific DNA sequences.

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Biochemical characterization of the Oct-2 POU domain with implications for bipartite DNA recognition

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Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*

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Structural and thermodynamical characterization of the complete p21 gene product of Max

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The intrinsically unstructured domain of PC4 modulates the activity of the structured core through inter- and intramolecular interactions

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The thymine-DNA glycosylase regulatory domain: residual structure and DNA binding

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Chromatin condensing functions of the linker histone C-terminal domain are mediated by specific amino acid composition and intrinsic protein disorder

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Interactions of the acidic domain and SRF interacting motifs with the NKX3.1 homeodomain

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The basic helix-loop-helix region of human neurogenin 1 is a monomeric natively unfolded protein which forms a "fuzzy" complex upon DNA binding

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Dss1 regulates interaction of Brh2 with DNA.

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Unique physical properties and interactions of the domains of methylated DNA binding protein 2.

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pH-dependent enhancement of DNA binding by the ultrabithorax homeodomain

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Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition

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Conformational space of flexible biological macromolecules from average data

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Disordered tails of homeodomains facilitate DNA recognition by providing a trade-off between folding and specific binding

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Defining conformational ensembles of intrinsically disordered and partially folded proteins directly from chemical shifts.

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Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex

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Allosteric effects of DNA on transcriptional regulators

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Protein-DNA interaction. No code for recognition

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Crystal structure of a yeast TBP/TATA-box complex

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Determinants of repressor/operator recognition from the structure of the trp operator binding site.

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Structure of NF-kappa B p50 homodimer bound to a kappa B site

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Predicting intrinsic disorder in proteins: an overview

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Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA

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The role of DNA shape in protein-DNA recognition

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7 January 2021

Dynamic activation of an allosteric regulatory protein.

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Intrinsically unstructured proteins and their functions

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7 January 2021

How do transcription factors select specific binding sites in the genome?

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7 January 2021

Dynamically driven protein allostery.

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Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

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Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor

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Amplification of signaling via cellular allosteric relay and protein disorder

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DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail

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Speeding molecular recognition by using the folding funnel: the fly-casting mechanism

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Molecular basis for modulation of biological function by alternate splicing of the Wilms' tumor suppressor protein

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p300-mediated acetylation of human transcriptional coactivator PC4 is inhibited by phosphorylation

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Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements

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Determinants of histone H4 N-terminal domain function during nucleosomal array oligomerization: roles of amino acid sequence, domain length, and charge density

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Order and disorder in the domain organization of the plasmid partition protein KorB.

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Regulation of single-stranded DNA binding by the C termini of Escherichia coli single-stranded DNA-binding (SSB) protein

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Structural reorganization and the cooperative binding of single-stranded telomere DNA in Sterkiella nova.

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Intrinsic disorder and autonomous domain function in the multifunctional nuclear protein, MeCP2.

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Multiple intrinsically disordered sequences alter DNA binding by the homeodomain of the Drosophila hox protein ultrabithorax

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Intrinsic protein disorder, amino acid composition, and histone terminal domains.

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Secondary structure and dynamics of an intrinsically unstructured linker domain

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Local structural disorder imparts plasticity on linear motifs.

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Linker length and composition influence the flexibility of Oct-1 DNA binding

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Devoted to the lagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly

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The B-box dominates SAP-1-SRF interactions in the structure of the ternary complex

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DNA looping by the HMG-box domains of HMG1 and modulation of DNA binding by the acidic C-terminal domain

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Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level

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The importance of intrinsic disorder for protein phosphorylation

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NMR chemical shift and relaxation measurements provide evidence for the coupled folding and binding of the p53 transactivation domain

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The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA.

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Gradual phosphorylation regulates PC4 coactivator function

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Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.

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Variable control of Ets-1 DNA binding by multiple phosphates in an unstructured region

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Breaking the code of DNA binding specificity of TAL-type III effectors

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Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations

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Coupling of local folding to site-specific binding of proteins to DNA

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Protein-DNA recognition

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Origins of specificity in protein-DNA recognition.

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Evolutionarily conserved domains required for activation and repression functions of the Drosophila Hox protein Ultrabithorax.

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Prediction of protein binding regions in disordered proteins

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Alternative splicing modulates Ubx protein function in Drosophila melanogaster

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Understanding eukaryotic linear motifs and their role in cell signaling and regulation.

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