Glu mutations, or vice versa, of the acidic residues suggested to be important for cooperativity may alter the subtle balance of intermolecular and intramolecular interactions contribut- ing to the cooperativity. In addition, mutation of any of the charged residues discussed above to neutral species would be expected to impact cooperativity. Asp110 and Glu111 may be the most interesting as their impact on CBFb binding would be expected to be minimal while their impact on cooperativity should be large. CONCLUSION MD simulations of RD along with its binding partners CBFb and DNA, as well as the CBFb–RD and RD–DNA binary complexes and the CBFb–RD–DNA ternary complex have been performed to better understand the cooperative nature of the binding of these residues. In accordance with the experi- ment, the simulation data show cooperative binding of DNA in the presence of CBFb as well as predict that binding of DNA to RD facilitates RD–CBFb binding, indicating cooper- ativity for this interaction. These observations are consistent with the experimental data (16,18), supporting that ability of the applied simulation models to represent the experimental regimen. Energetic and structural analysis allow for contributions to the binding and cooperativity to be understood in terms of different regions of the RD protein as well as the contribution of individual residues. Of note is the balance of intermolecular and intramolecular interactions that result in the cooperative binding. These interactions are, to a large extent, dominated by charged residues suggesting that long-range interactions may contribute to cooperativity. From these results a number of residues of interest for mutational analysis are suggested. SUPPLEMENTARY MATERIAL Supplementary Material is available at NAR Online. ACKNOWLEDGEMENTS The National Institutes of Health is acknowledged for financial support (GM 51501 and CA 95350) and the National Science Foundation Partnerships for Advanced Computational Infrastructure Program, Department of Defense Aeronautical Systems Center Major Shared Resource Computing, and the Pittsburgh Supercomputing Center Terascale Computing for computational support. Funding to pay the Open Access publication charges for this article was provided by NIH GM51501. Conflict of interest statement. None declared. REFERENCES 1. Ogawa,E., Maruyama,M., Kagoshima,H., Inuzuka,M., Lu,J., Satake,M., Shigesada,K. and Ito,Y. (1993) PEBP2/PEA2 represents a family of transcription factors homologous to the products of the Drosophila runt gene and the human AML1 gene. Proc. Natl Acad. Sci. USA, 90, 6859–6863. 2. Okuda,T., van Deursen,J., Hiebert,S.W., Grosveld,G. and Downing,J.R. 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