Local conformational changes of proteins in DNA interfaces

DNA界面での蛋白質の局所的構造変化

角南 智子; 河野 秀俊

Sunami, Tomoko; Kono, Hidetoshi

To better understand the conformational changes of proteins upon DNA binding, we carried out quantitative analyses. We first described the proteins using a structural alphabet library of backbone geometries created by Kolodony et al. and then detected the conformational changes as changes in alphabets between DNA-free and bound forms. We first divided protein surface into two regions, DNA interface and protein surface which exclude the DNA interface and carried out the analyses. The results show that (1) the conformational changes at DNA interfaces are more frequent than those at the other surfaces; (2) DNA interfaces have more conformational variation even in the DNA-free form. The latter suggests that intrinsic, conformational flexibility of DNA interface seems to be important to adjust their conformations to DNA. In amino acid propensities, the conformationally changed regions in DNA interfaces as well as those in the other protein surfaces show that hydrophilic and glycine residues are more preferred compared with the conformation-unchanged regions. This trend is also found in the propensity for disordered regions, suggesting that the intrinsic flexibility be of importance not only for DNA binding but also for interacting with other molecules. Comparison of distributions of the structural alphabets between DNA interfaces and the other surfaces shows that some specific alphabets appear more often in DNA interfaces.