BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION

G. Paciello, A. Acquaviva, E. Ficarra, M. A. Deriu, A. Grosso, E. Macii

2011

Abstract

In this paper we present a methodology to evaluate the binding free energy of a miRNA-mRNA complex through Molecular Dynamics-Thermodynamic Integration simulations. We applied our method on the C−elegans let-7 miRNA:lin-41 mRNA complex, known to be a validate miRNA:mRNA interaction, in order to evaluate the energetic stability of the structure. The methodology has been designed to face the various challenges of nucleic acid simulations and binding free energy computations and to allow an optimal trade-off between accuracy and computational cost.

References

  1. Bartel, D. P. (2004). MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell.
  2. Cevec, M., Thibaudeau, C., and Plavec, J. (2008). Soluctione structure of a let-7 miRNA:lin41 mRNA complex from C.elegans. Nucleic Acids Research.
  3. Cheatham, T. E. (2004). Simulation and modelling of nucleic acid structure, dynamics and interactions. Current Opinion in Structural Biology.
  4. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc.
  5. Lawrenz, M., Baron, R., and McCammon, J. A. (2009). Independent-trajectories thermodynamicintegration free-energy changes for biomolecular system: Determinants of N5HN1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. Journal of Chemical Theory and Computation.
  6. Pan, Y. and Mackerell, A. D. (2003). Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. Nucleic Acids Research.
  7. Schwarz, D. S. and Zamore, P. D. (2002). Why do miRNAs live in the miRNP? Genes e Development.
  8. Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., and Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of computational chemistry.
  9. Vella, M. C., Reinert, K., and Slack, F. J. (2004). Architecture of a validate microRNA::target interaction. Chemistry e Biology.
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Paper Citation


in Harvard Style

Paciello G., Acquaviva A., Ficarra E., A. Deriu M., Grosso A. and Macii E. (2011). BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 318-321. DOI: 10.5220/0003167703180321


in Bibtex Style

@conference{bioinformatics11,
author={G. Paciello and A. Acquaviva and E. Ficarra and M. A. Deriu and A. Grosso and E. Macii},
title={BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={318-321},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003167703180321},
isbn={978-989-8425-36-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - BINDING FREE ENERGY CALCULATION VIA MOLECULAR DYNAMICS SIMULATIONS FOR A miRNA:mRNA INTERACTION
SN - 978-989-8425-36-2
AU - Paciello G.
AU - Acquaviva A.
AU - Ficarra E.
AU - A. Deriu M.
AU - Grosso A.
AU - Macii E.
PY - 2011
SP - 318
EP - 321
DO - 10.5220/0003167703180321