N个滑动蛋白在DNA上的靶点搜索
Target search of N sliding proteins on a DNA.
作者信息
Sokolov Igor M, Metzler Ralf, Pant Kiran, Williams Mark C
机构信息
Institut für Physik, Humboldt Universität zu Berlin, Germany.
出版信息
Biophys J. 2005 Aug;89(2):895-902. doi: 10.1529/biophysj.104.057612. Epub 2005 May 20.
Abstract
At low to moderate ambient salt concentrations, DNA-binding proteins bind relatively tightly to DNA, and only very rarely detach. Intersegmental transfer due to DNA-looping can be excluded by applying an external pulling force to the DNA molecule. Under such conditions, we explore the targeting dynamics of N proteins sliding diffusively along DNA in search of their specific target sequence. At lower densities of binding proteins, we find a reduction of the characteristic search time proportional to N(-2), with corrections at higher concentrations. Rates for detachment and attachment of binding proteins are incorporated in the model. Our findings are in agreement with recent single molecule studies in the presence of bacteriophage T4 gene 32 protein for which the unbinding rate is much lower than the specific binding rate.
摘要
在低至中等环境盐浓度下，DNA结合蛋白与DNA结合相对紧密，且极少分离。通过对DNA分子施加外部拉力，可以排除由于DNA环化导致的片段间转移。在这种条件下，我们探究了N蛋白沿DNA进行扩散滑动以寻找其特定靶序列的靶向动力学。在结合蛋白密度较低时，我们发现特征搜索时间的减少与N的-2次方成正比，在较高浓度时有修正。结合蛋白的分离和附着速率被纳入模型。我们的发现与最近在噬菌体T4基因32蛋白存在下的单分子研究一致，其解离速率远低于特异性结合速率。
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本文引用的文献
1
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J Mol Biol. 2005 Jun 3;349(2):317-30. doi: 10.1016/j.jmb.2005.03.065. Epub 2005 Apr 9.
2
Nonspecific binding of the OR repressors CI and Cro of bacteriophage lambda.噬菌体λ的OR阻遏蛋白CI和Cro的非特异性结合。
J Theor Biol. 2004 Dec 21;231(4):525-33. doi: 10.1016/j.jtbi.2004.07.007.
3
Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.蛋白质 - DNA 相互作用的动力学：在序列依赖性势场中促进靶点定位
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4
Kinetics of target site localization of a protein on DNA: a stochastic approach.蛋白质在DNA上靶位点定位的动力学：一种随机方法。
Biophys J. 2004 Sep;87(3):1640-9. doi: 10.1529/biophysj.104.045773.
5
Diffusion in correlated random potentials, with applications to DNA.关联随机势场中的扩散及其在DNA中的应用。
Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Jun;69(6 Pt 1):061903. doi: 10.1103/PhysRevE.69.061903. Epub 2004 Jun 1.
6
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7
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J Mol Biol. 2004 Feb 27;336(4):851-70. doi: 10.1016/j.jmb.2003.12.025.
8
In vivo non-specific binding of lambda CI and Cro repressors is significant.λCI和Cro阻遏物在体内的非特异性结合很显著。
FEBS Lett. 2004 Apr 9;563(1-3):66-8. doi: 10.1016/S0014-5793(04)00249-2.
9
Sensitivity of OR in phage lambda.λ噬菌体中OR的敏感性。
Biophys J. 2004 Jan;86(1 Pt 1):58-66. doi: 10.1016/S0006-3495(04)74083-7.
10
Entropy loss in long-distance DNA looping.远距离DNA环化中的熵损失
Biophys J. 2003 Jul;85(1):167-73. doi: 10.1016/S0006-3495(03)74463-4.
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