Local conformation changes of proteins in the 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

Using structural alphabets, we performed quantitative analyses of conformational changes of DNA binding proteins using the sets of proteins in DNA-free and DNA-bound forms. The results show that (1) the conformational changes in the DNA interfaces are more frequent than those in the non-interface; (2) DNA interfaces have more conformational variations even in the DNA-free forms. The latter suggests that the intrinsic, conformational flexibility of DNA interfaces seems to be important to adjust their conformations to DNA. In amino acid propensities, the conformation-changed regions in the DNA interfaces as well as those in the non-interface show that hydrophilic residues in addition to proline and glycine are more preferred compared with the conformation-unchanged regions. This trend is also found in the amino acid propensity for disordered regions, suggesting that the intrinsic flexibility be of importance not only for DNA binding but also for interactions with other molecules. Comparison of the distributions of the structural alphabets between the DNA interfaces and the non-interfaces shows that three specific alphabets appear more often in the DNA interfaces of DNA-bound forms. One of them is a helix-like structure. This is likely to consecutively show up to extend the helix that exists in the free form, which, as a result, will enhance the dipole moment of the helix. This may be why the alphabet is favored in the DNA interface.