James Magee, School of Chemical Engineering and Analytical Science, University of Manchester, PO Box 88, Sackville Street, Manchester M60 1QD, United Kingdom and Jim Warwicker, Faculty of Life Sciences, University of Manchester, PO Box 88, Sackville Street, Manchester M60 1QD, United Kingdom.
To understand binding between mRNA and the eukaryotic translation initiation factor complex eIF4F, we must consider interactions which are not specific to mRNA sequence. We report simulation results examining the contribution of these non-specific interactions, predicting nucleic acid paths around protein surfaces, and giving binding constant differences for changes in the protein scaffold. Results from two systems are presented, suggesting a role for non-specific inteRactions in modulating translation initiation (in formation of the capped mRNA - eIF4E - eIF4G complex), and examining the competition for mRNA binding between two S. Pombe eIF4E isoforms under common stress conditions (temperature and salt concentration).