Resolving the contributions of two cooperative mechanisms to the DNA Binding of AGT

Manana Melikishvili, Michael G. Fried

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


The O6-alkylguanine DNA alkyltransferase (AGT) is a DNA repair enzyme that binds DNA with moderate cooperativity. This cooperativity is important for its search for alkylated bases. A structural model of the cooperative complex of AGT with DNA predicts short-range interactions between nearest protein neighbors and long-range interactions between proteins separated in the array. DNA substrates ranging from 11bp to 30bp allowed us to use differences in binding stoichiometry to resolve short- and long-range protein contributions to the stability of AGT complexes. We found that the short-range component of ΔG°coop was nearly independent of DNA length and protein packing density. In contrast the long-range component oscillated with DNA length, with a period equal to the occluded binding site size (4bp). The amplitude of the long-range component decayed from ∼-4 kcal/mole of interaction to ∼-1.2 kcal/mol of interaction as the size of cooperative unit increased from 4 to 7 proteins, suggesting a mechanism to limit the size of cooperative clusters. These features allow us to make testable predictions about AGT distributions and interactions with chromatin structures in vivo.

Original languageEnglish
Pages (from-to)509-516
Number of pages8
Issue number9
StatePublished - Sep 1 2015

Bibliographical note

Publisher Copyright:
© 2015 The Authors Biopolymers Published by Wiley Periodicals, Inc.


  • DNA repair
  • O6-alkylguanine
  • binding cooperativity
  • protein-DNA interaction

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry


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