Berlin 2008 – scientific programme
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BP: Fachverband Biologische Physik
BP 28: Molecular Recognition
BP 28.2: Talk
Friday, February 29, 2008, 11:00–11:15, PC 203
Structure based prediction of protein-DNA recognition — Sahand Jamal Rahi1, •Peter Virnau2, Mehran Kardar1, and Leonid A. Mirny1,3 — 1Massachusetts Institute of Technology — 2Johannes Gutenberg-Universität Mainz — 3Harvard-MIT Division of Health Sciences and Technology
Binding of proteins to specific DNA sites is central for several vital biological processes, such as regulation of genes, replication of DNA and repair of DNA damage. The challenge can be formulated as follows: Given the structure of a protein-DNA binding complex, predict sites in the genome which the protein recognizes, i.e., to which it binds with significant affinity. In this talk, we will discuss the predictive quality of atomistic force-fields in conjunction with molecular mechanics calculations and compare results with predictions from bioinformatics for the PurR protein-DNA complex. We will also compare binding energies derived from simulations with experimental binding energies for several amino acid and DNA point mutations.