Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
Protein-DNA Recognition Mechanism and Prediction
Protein-DNA interactions play a central role in gene regulation. DNA-binding proteins recognize their targets by direct base-amino acid interactions and indirect conformational energy contribution from DNA deformations and elasticity. In order to understand the recognition mechanism, it is important to analyze the relationship between the structure and specificity of protein-DNA recognition. Knowledge-based approach based on the statistical analysis of protein-DNA complex structures has been successfully used to calculate interaction energies and specificities of direct and indirect readouts in protein-DNA recognition. The quantification of specificity has enabled us to analyze the structure-specificity relationship in protein-DNA recognition. By using this method, it has been shown that both the direct and indirect readouts make important contributions to the specificity of protein-DNA recognition. We have also examined the cooperativity in protein-DNA recognition. In order to complement the knowledge-based approach, we have performed various kinds of computer simulations to derive energy potentials, which are equivalent to the statistical potentials, for direct and indirect readouts in protein-DNA recognition. These analyses provided insight into the molecular mechanism of protein-DNA recognition. By combining these methods, we have made some applications to drug-DNA interactions, chromosome positioning, and genome-scale target prediction of transcription factors.
Dept. Biochemical Engineering and Science