Protein-DNA binding specificity predictions with structural models.

ABSTRACT: Protein-DNA interactions play a central role in transcriptional regulation and other biological processes. Investigating the mechanism of binding affinity and specificity in protein-DNA complexes is thus an important goal. Here we develop a simple physical energy function, which uses electrostatics, solvation, hydrogen bonds and atom-packing terms to model direct readout and sequence-specific DNA conformational energy to model indirect readout of DNA sequence by the bound protein. The predictive capability of the model is tested against another model based only on the knowledge of the consensus sequence and the number of contacts between amino acids and DNA bases. Both models are used to carry out predictions of protein-DNA binding affinities which are then compared with experimental measu

SUBMITTER: Morozov AV 

PROVIDER: S-EPMC1270944 | biostudies-literature | 2005

REPOSITORIES: biostudies-literature