New computational strategy to analyze the interactions of ERα and ERβ with different ERE sequences

Anna Marabotti, Giovanni Colonna, Angelo Facchiano

Research output: Contribution to journalArticlepeer-review


The importance of computational methods for the simulation and analysis of biological systems has increased during the last years. In particular, methods to predict binding energies are developing not only with the aim of ranking the affinities between two or more complexes, but also to quantify the contribution of different types of interaction. In this work, we present the application of HINT, a non Newtonian force field, to rank the affinities of complexes formed by estrogen receptors (ER) α and β and different estrogen responsive elements (ERE) near the estrogen-regulated genes. We used the crystallographic coordinates of the DNA binding domain of ERα complexed to a consensus ERE as a starting point to simulate several complexes in which some nucleotides in the ERE sequence were mutated. Moreover, we used homology modeling methods to create the structure of the complexes between the DNA binding domain of ERβ (for which no experimental structures are currently available) and the same ERE sequences. Our results show that HINT is able to rank the affinities of ERα and ERβ for different ERE sequences, and to correctly identify the positions on the DNA sequence that are most important for binding affinity. Moreover, the HINT output gives us the opportunity to identify and quantify the role played by each single atom of amino acids and nucleotides in the binding event, as well as to predict the effect on the binding affinity for other nucleotide mutations.

Original languageEnglish
Pages (from-to)1031-1041
Number of pages11
JournalJournal of Computational Chemistry
Issue number6
Publication statusPublished - Apr 30 2007


  • Binding affinity
  • Computational biology
  • Estrogens
  • HINT
  • Modelling
  • Protein-DNA interaction

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality


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