Abstract
When a protein binds to DNA, a conformational change is often induced so that the protein will fit into the DNA structure. Therefore, quantitative analyses were conducted to understand the conformational changes in proteins. The results showed that conformational changes in DNA interfaces are more frequent than in non-interfaces, and DNA interfaces have more conformational variations in the DNA-free form. As expected, the former indicates that interaction with DNA has some influence on protein structure. The latter suggests that the intrinsic conformational flexibility of DNA interfaces is important for adjusting their conformation for DNA. The amino acid propensities of the conformationally changed regions in DNA interfaces indicate that hydrophilic residues are preferred over the amino acids that appear in the conformationally unchanged regions. This trend is true for disordered regions, suggesting again that intrinsic flexibility is of importance not only for DNA binding but also for interactions with other molecules. These results demonstrate that fragments destined to be DNA interfaces have an intrinsic flexibility and are composed of amino acids with the capability of binding to DNA. This information suggests that the prediction of DNA binding sites may be improved by the integration of amino acid preference for DNA and one for disordered regions.
Highlights
Protein–DNA interaction plays an essential role in many cellular functions such as transcription, replication, recombination, and DNA packaging
The b2/b3 connecting loop of the papillomavirus E2 protein, which is unstructured in the free form, adopts a b-hairpin conformation in order to form electrostatic contacts with DNA backbone phosphates in the complex form [4,6]
The conformational change in the loop has been observed in molecular dynamics simulations [7,8]
Summary
Protein–DNA interaction plays an essential role in many cellular functions such as transcription, replication, recombination, and DNA packaging. The conformational change in the loop has been observed in molecular dynamics simulations [7,8]. Another example of conformational change was observed in the linker region of MATa2 [5]. In this case, two independent copies of the complex were found in the asymmetric unit. The sequence of the region is coined as a chameleon sequence This conformational transition at the sequence is thought to be important for DNA recognition [10]
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