Paper Info
Title
New computational strategy to analyze the interactions of ER alpha and ER beta with different ERE sequences
Abstract
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) alpha and beta and different estrogen responsive elements (ERE) near the estrogen-regulated genes. We used the crystallographic coordinates of the DNA binding domain of ER alpha 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 ER beta (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 ER alpha and ER beta 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. (C) 2007 Wiley Periodicals, Inc.
Year
DOI
Venue
2007
10.1002/jcc.20582
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
DocType
Volume
HINT,computational biology,modelling,binding affinity,protein-DNA interaction,estrogens
Journal
28.0
Issue
ISSN
Citations 
6
0192-8651
0
PageRank 
References 
Authors
0.34
0
3
Name
Order
Citations
PageRank
Anna Marabotti165.15
Giovanni Colonna243.38
Angelo M. Facchiano324.04