DNA
高分子
化学物理
生物物理学
蒙特卡罗方法
违反直觉
航程(航空)
物理
分子物理学
化学
生物
材料科学
量子力学
生物化学
统计
数学
复合材料
作者
Vincent Dahirel,Fabien Paillusson,Marie Jardat,Maria Barbi,Jean–Marc Victor
标识
DOI:10.1103/physrevlett.102.228101
摘要
Recent single molecule experiments have reported that DNA binding proteins (DNA-BPs) can diffuse along DNA. This suggests that interactions between proteins and DNA play a role during the target search even far from their specific site on DNA. Here we show by means of Monte Carlo simulations and analytical calculations that there is a counterintuitive repulsion between the two oppositely charged macromolecules at a nanometer range. For the concave shape of DNA-BPs, and for realistic protein charge densities, we find that the DNA-protein interaction free energy has a minimum at a finite surface-to-surface separation, in which proteins can easily slide. When a protein encounters its target, the free energy barrier is completely counterbalanced by the H-bond interaction, thus enabling the sequence recognition.
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