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Istituto di scienza dell'alimentazione

Torna all'elenco Contributi in rivista anno 2007

Contributo in rivista

Tipo: Articolo in rivista

Titolo: A new computational strategy to analyze the interactions of ERalpha and ERbeta with Different ERE Sequences.

Anno di pubblicazione: 2007

Autori: Marabotti A, Colonna G, Facchiano A

Affiliazioni autori: Istituto di Scienza dell'Alimentazione, CNR, Avellino Seconda UniversitÓ di Napoli

Autori CNR:


Lingua: inglese

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 ERalpha 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 ERbeta (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 ERalpha and ERbeta 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.

Lingua abstract: inglese

Pagine da: 1031

Pagine a: 1041


Journal of computational chemistry Wiley.
Paese di pubblicazione: Stati Uniti d'America
Lingua: inglese
ISSN: 0192-8651

Numero volume: 28

DOI: 10.1002/jcc.20582

Indicizzato da: PubMed [17269124]

URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20582/abstract;jsessionid=1C543675A570E917CF0FCB3A0D9D33DC.d01t01

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