Type species designation for Archaebranchinecta Rogers &amp;amp; Coronel (Branchiopoda: Anostraca)

Rogers, D. Christopher

doi:10.11646/zootaxa.4700.2.9

Cited by 2 publications

(1 citation statement)

References 4 publications

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“…For example, nucleosomes bend DNA, and preferentially bind to DNA sequences where particular dinucleotides are located at specific positions relative to the direction of the DNA bending (Reviewed in 10 ). Some transcription factors can also affect the conformation of the DNA backbone [11][12][13][14][15][16][17][18] , and their specificity towards dinucleotides could similarly be explained by the contribution of the dinucleotides to the structure and flexibility of the DNA backbone. However, the structural distortion caused by histone octamer or DNA-bending TFs is expected to result in relatively weak dinucleotide preferences, and thus cannot account for highly specific recognition of dinucleotides observed for TFs.…”

Section: Introductionmentioning

confidence: 99%

Interfacial water confers transcription factors with dinucleotide specificity

Morgunova,

Yin,

Zhu

et al. 2023

Preprint

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Transcription factors bind to DNA by recognizing specific bases within their binding motifs. Binding to each DNA mononucleotide within the motif often contributes independently to total binding energy. However, some transcription factors (TFs) can bind to DNA more specifically than predicted by this model, by directly recognizing DNA dinucleotides. To understand this process, we have solved the structures of the basic helix-loop-helix protein MYF5, and the homeodomain protein BARHL2 together with DNA containing a set of dinucleotides that have different affinities to the proteins at high resolution (< 1 Å). We observe that dinucleotides can be recognized either enthalpically by an extensive water network that connects the adjacent bases to the TF, or entropically by formation of a hydrophobic patch that maintains water mobility at the protein-DNA interface. The two distinct thermodynamic signatures of the two equally optimal sites also confer differential temperature sensitivity to the optimal sites, with implications for thermal regulation of gene expression. Our results uncover the enigma of how TFs can recognize more complex local features than mononucleotides, and demonstrate that water-mediated recognition is important in predicting affinities of macromolecules from their sequence.

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