一种沿DNA的序列依赖性蛋白质扩散模型。
A model of sequence-dependent protein diffusion along DNA.
作者信息
Barbi Maria, Place Christophe, Popkov Vladislav, Salerno Mario
机构信息
Dipartimento di Fisica "E.R. Caianiell" and INFM, Università di Salerno, Baronissi (SA), Italy ; Laboratoire de Physique Théorique des Liquides, Université Pierre et Marie Curie, case courrier 121, 4 Place Jussieu, 75252 Paris cedex 05, France.
出版信息
J Biol Phys. 2004 Sep;30(3):203-26. doi: 10.1023/B:JOBP.0000046728.51620.14.
Abstract
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. Hydrogen bonds formed at the target site are used as the main sequence-dependent interaction between protein and DNA. The resulting dynamical properties and the possibility of an experimental verification are discussed in details. We show that, while at large times the process reaches a linear diffusion regime, it initially displays a sub-diffusive behavior. The sub-diffusive regime can last sufficiently long to be of biological interest.
摘要
我们引入了一个概率模型，用于描述蛋白质在搜索目标序列过程中沿DNA的滑动运动。该模型考虑了非特异性DNA与蛋白质之间序列依赖性相互作用可能产生的影响。在目标位点形成的氢键被用作蛋白质与DNA之间主要的序列依赖性相互作用。详细讨论了由此产生的动力学性质以及进行实验验证的可能性。我们表明，虽然在较长时间后该过程会进入线性扩散 regime，但它最初表现出亚扩散行为。亚扩散 regime 可以持续足够长的时间，具有生物学意义。
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