Structural analysis of conserved base pairs in protein-DNA complexes.

ABSTRACT: Understanding of protein-DNA interactions is crucial for prediction of DNA-binding specificity of transcription factors and design of novel DNA-binding proteins. In this paper we develop a novel approach to analysis of protein-DNA interactions. We bring together two sources of information: (i) structures of protein-DNA complexes (PDB/NDB database) and (ii) experimentally obtained sites recognized by DNA-binding proteins. Sites are used to compute conservation (information content) of each base pair, which indicates relative importance of the base pair in specific recognition. The main result of this study is that conservation of base pairs in a site exhibits significant correlation with the number of contacts the base pairs have with the protein. In particular, base pairs that have more co

SUBMITTER: Mirny LA 

PROVIDER: S-EPMC101836 | biostudies-literature | 2002 Apr

REPOSITORIES: biostudies-literature