Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA
Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA
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DOI：
10.1021/jp077568f
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发表时间：
2008-05-15
影响因子：
3.3
通讯作者：
Xie, X. Sunney
中科院分区：
文献类型：
--
作者：
Bagchi, Biman;Blainey, Paul C.;Xie, X. Sunney
蛋白质沿着DNA片段扩散的机制是当前非常感兴趣的主题，因为这种扩散涉及许多生物过程，包括DNA序列的识别和DNA的化学修饰。在这项工作中，我们提出了一个非特异性结合蛋白质的扩散系数的理论推导，假设蛋白质遵循螺旋轨道沿着DNA。结果表明，对于蛋白质大小的分子，总的平移摩擦力的主要贡献来自于沿着螺旋的曲线运动，其贡献为6 π η 7 RR（α）（2）+ 8 π η R-3，其中R为蛋白质半径，R-α为蛋白质质心与DNA螺旋轴之间的距离，η是介质的粘度。因此，蛋白质沿着DNA螺旋轨道的平移扩散被预测为具有接近R-3的尺寸依赖性，而不是表征简单平移扩散的R-1依赖性。结果表明，该表达式给出了相当好的估计的平移扩散系数在单分子实验中测量。
The mechanism of a protein's diffusion along a DNA segment is a subject of much current interest because of the involvement of this diffusion in numerous biological processes, including the recognition of DNA sequences and chemical modifications of DNA. In this work we present a theoretical derivation of the diffusion coefficient of a nonspecifically bound protein, assuming that the protein follows a helical track along the DNA. It is shown that, for protein-sized molecules, the principal contribution to the total translational friction comes from the curvilinear motion along the helix, and this contribution is given by 6 pi eta 7RR(oc)(2) + 8 pi eta R-3, where R is the protein radius, R-oc is the distance of separation between the center of mass of the protein and the helical axis of DNA, and eta is the viscosity of the medium. The translational diffusion of the protein along the helical track of DNA is thus predicted to have a nearly R-3 size dependence, not the R-1 dependence characterizing simple translational diffusion. It is shown that this expression gives rather good estimates of the translational diffusion coefficient measured in single molecule experiments.