Local conformational changes of proteins in DNA interfaces

Sunami, Tomoko; Kono, Hidetoshi

DNA-protein interaction plays a key role in many cellular functions such as transcription and replication. Understanding the mechanisms by which the protein recognizes DNA sequences is necessary. With increased amount of crystal structures, conformational changes of proteins in DNA interfaces are suggested to be one of important factors in DNA recognition. To better understand a role of the deformation of the proteins, we carried out quantitative analyses of local conformational changes observed in DNA interfaces using pre-defined 4-residue-length 7-letter structural-codes. We found (1) larger number of fragments in DNA interface undergo conformational change upon DNA binding, (2) conformational variation in DNA interface is high in DNA-unbound state and less in DNA-bound state, (3) amino acid composition of conformationally variable regions in DNA interfaces is different from that in other region, but structural characteristics of DNA interface are similar to that of other region.