Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.

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ID: 47943
2018
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Abstract
Transcription factors bind to their binding sites over a wide range of affinities, yet how differences in affinity are encoded in DNA sequences is not well understood. Here, we report X-ray crystal structures of four heterodimers of the Hox protein AbdominalB bound with its cofactor Extradenticle to four target DNA molecules that differ in affinity by up to ∼20-fold. Remarkably, despite large differences in affinity, the overall structures are very similar in all four complexes. In contrast, the predicted shapes of the DNA binding sites (i.e., the intrinsic DNA shape) in the absence of bound protein are strikingly different from each other and correlate with affinity: binding sites that must change conformations upon protein binding have lower affinities than binding sites that have more optimal conformations prior to binding. Together, these observations suggest that intrinsic differences in DNA shape provide a robust mechanism for modulating affinity without affecting other protein-DNA interactions.
Reference Key
zeiske2018intrinsiccell Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Zeiske, Tim;Baburajendran, Nithya;Kaczynska, Anna;Brasch, Julia;Palmer, Arthur G;Shapiro, Lawrence;Honig, Barry;Mann, Richard S;
Journal Cell reports
Year 2018
DOI
S2211-1247(18)31233-6
URL
Keywords
dna binding specificity dna shape extradenticle hox proteins pbx abdominal b cooperative binding homeodomain low-affinity binding sites

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