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Nucleic Acids Research 2005 33(21):6694-6699; doi:10.1093/nar/gki981
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Published online 27 November 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Simulation of non-specific protein–mRNA interactions

James Magee and Jim Warwicker1,*

School of Chemical Engineering and Analytical Science, University of Manchester Jackson's Mill, PO Box 88, Sackville Street, Manchester M60 1QD, UK 1Faculty of Life Sciences, University of Manchester Michael Smith Building, Oxford Road, Manchester M13 9PT, UK

*To whom correspondence should be addressed. Tel: +44 0 161 200 4490; Fax: +44 0 161 275 5082; Email: jim.warwicker{at}manchester.ac.uk

Received September 9, 2005. Revised November 8, 2005. Accepted November 8, 2005.

Protein–nucleic acid interactions exhibit varying degrees of specificity. Relatively high affinity, sequence-specific interactions, can be studied with structure determination, but lower affinity, non-specific interactions are also of biological importance. We report simulations that predict the population of nucleic acid paths around protein surfaces, and give binding constant differences for changes in the protein scaffold. The method is applied to the non-specific component of interactions between eIF4Es and messenger RNAs that are bound tightly at the cap site. Adding a fragment of eIF4G to the system changes both the population of mRNA paths and the protein–mRNA binding affinity, suggesting a potential role for non-specific interactions in modulating translational properties. Generally, the free energy simulation technique could work in harness with characterized tethering points to extend analysis of nucleic acid conformation, and its modulation by protein scaffolds.


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