Dynamics of water molecules and proteins interacting with DNA

DNAと相互作用する水とタンパク質のダイナミクス

米谷 佳晃; 河野 秀俊

Yonetani, Yoshiteru; Kono, Hidetoshi

Molecular behavior of hydration water of DNA, in particular the DNA sequence dependence, has not been fully understood, in spite of many 3D complex structures determined by crystallography and NMR. Recently, we present that the sequence dependence of minor groove hydration is clearly correlated with that of DNA deformability based on the molecular dynamics analysis of 136 DNA sequences that differ from each other in their central tetramer [Yonetani, Kono, Biophys. J. 97, 1138, 2009]. To obtain an atomistic picture of the water dynamics and its DNA sequence dependence, we further calculated lifetimes of DNA-water hydrogen bonds. The results showed that the lifetime t varies from 1 ps to 300 ps, depending on the kind of basepair step. We found that the variation follows t = 1/kPm, where Pm is the probability of formation of multiple hydrogen bonds, which were often observed during the simulation. Based on this relation, we were able to explain the sequence dependence of lifetime in atomic view. Another topic we will present concerns DNA sequence recognition by DNA regulatory proteins. We are now performing molecular dynamics calculations to obtain free energy profiles for DNA-protein interactions. We will discuss how a DNA binding proteins pass over the non-target DNA and eventually recognize the target DNA.