Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength.
Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength.
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DOI：
10.1093/nar/gku418
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发表时间：
2014-06
影响因子：
14.9
通讯作者：
Iwahara J
中科院分区：
文献类型：
--
作者：
Esadze A;Kemme CA;Kolomeisky AB;Iwahara J
诱导型转录因子Egr-1通过三个锌指结构域识别9-bp的靶DNA序列，在细胞刺激如神经元信号和血管应激时快速激活特定基因。在这里，使用停流荧光方法，我们测量了Egr-1锌指蛋白在40和400 mM KCl之间的各种离子强度下的目标搜索动力学，并发现在150 mM KCl下最有效的搜索。我们进一步研究了在不同浓度的KCl下，这种蛋白质在DNA上的片段间转移、解离和滑动的动力学。我们的数据表明，Egr-1的动力学特性非常适合在体内有效扫描染色体DNA。基于一种新的理论，我们分析了生理离子强度下最佳搜索效率的来源。通过与附近位点的非特异性结合和随后的向靶的滑动以及通过片段间转移来加速靶缔合。虽然这些作用在较低的离子强度下更强，但这样的条件也有利于将蛋白质捕获在远处的非特异性位点，从而减缓靶向缔合。我们的数据表明，Egr-1通过与DNA非特异性相互作用的正面和负面影响之间的妥协，实现了在生理离子强度的最佳搜索。
The inducible transcription factor Egr-1, which recognizes a 9-bp target DNA sequence via three zinc-finger domains, rapidly activates particular genes upon cellular stimuli such as neuronal signals and vascular stresses. Here, using the stopped-flow fluorescence method, we measured the target search kinetics of the Egr-1 zinc-finger protein at various ionic strengths between 40 and 400 mM KCl and found the most efficient search at 150 mM KCl. We further investigated the kinetics of intersegment transfer, dissociation, and sliding of this protein on DNA at distinct concentrations of KCl. Our data suggest that Egr-1's kinetic properties are well suited for efficient scanning of chromosomal DNA in vivo. Based on a newly developed theory, we analyzed the origin of the optimal search efficiency at physiological ionic strength. Target association is accelerated by nonspecific binding to nearby sites and subsequent sliding to the target as well as by intersegment transfer. Although these effects are stronger at lower ionic strengths, such conditions also favor trapping of the protein at distant nonspecific sites, decelerating the target association. Our data demonstrate that Egr-1 achieves the optimal search at physiological ionic strength through a compromise between the positive and negative impacts of nonspecific interactions with DNA.
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影响因子：
15
作者：
Anderson, Kurtis M.;Esadze, Alexandre;Manoharan, Mariappan;Brueschweiler, Rafael;Gorenstein, David G.;Iwahara, Junji
通讯作者：
Iwahara, Junji
影响因子：
5.6
作者：
Esadze A;Iwahara J
通讯作者：
Iwahara J
影响因子：
5.6
作者：
BRESLOFF, JL;CROTHERS, DM
通讯作者：
CROTHERS, DM
影响因子：
3.6
作者：
Iwahara, Junji;Levy, Yaakov
通讯作者：
Levy, Yaakov
影响因子：
16.2
作者：
Bozon, B;Davis, S;Laroche, S
通讯作者：
Laroche, S