The Effect of Nonspecific Binding of Lambda Repressor on DNA Looping Dynamics
The Effect of Nonspecific Binding of Lambda Repressor on DNA Looping Dynamics
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DOI：
10.1016/j.bpj.2012.09.006
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发表时间：
2012-10-17
影响因子：
3.4
通讯作者：
Finzi, Laura
中科院分区：
文献类型：
--
作者：
Manzo, Carlo;Zurla, Chiara;Finzi, Laura
λ阻遏物（Cl）蛋白诱导的DNA环保持稳定的溶原性，但允许有效地切换到裂解。在此，循环的形成和分解的动力学已被表征在不同浓度的蛋白质使用拴系粒子显微镜和一种新的，据我们所知，分析方法。我们的研究结果表明，一个广泛的分布的速率常数和复杂的动力学环路的形成和崩溃。此外，循环在野生型DNA和DNA与突变的O3运营商的动力学的比较表明，这些网站可能会触发成核的非特异性结合在关闭的循环。从速率常数分布计算的平均活化能是一致的模型，其中操作员之间的非特异性结合CI缩短其有效的分离，从而降低环形成的能量势垒和扩大的速率常数分布的循环。类似地，非特异性结合通过增加环-固定蛋白相互作用的数量来影响环分解的动力学，并扩大该反应的速率常数分布。因此，同时增加环形成的速率常数和减少环破裂稳定溶原性。考虑到这些同时发生的变化，循环和非循环状态之间的转换频率几乎保持不变。尽管随着CI浓度的增加，该环在热力学上变得更加稳定，但它仍然周期性地打开，从而对环境变化具有敏感性，这可能需要切换到溶解条件。
The lambda repressor (CI) protein-induced DNA loop maintains stable lysogeny, yet allows efficient switching to lysis. Herein, the kinetics of loop formation and breakdown has been characterized at various concentrations of protein using tethered particle microscopy and a novel, to our knowledge, method of analysis. Our results show that a broad distribution of rate constants and complex kinetics underlie loop formation and breakdown. In addition, comparison of the kinetics of looping in wild-type DNA and DNA with mutated o3 operators showed that these sites may trigger nucleation of nonspecific binding at the closure of the loop. The average activation energy calculated from the rate constant distribution is consistent with a model in which nonspecific binding of CI between the operators shortens their effective separation, thereby lowering the energy barrier for loop formation and broadening the rate constant distribution for looping. Similarly, nonspecific binding affects the kinetics of loop breakdown by increasing the number of loop-securing protein interactions, and broadens the rate constant distribution for this reaction. Therefore, simultaneous increase of the rate constant for loop formation and reduction of that for loop breakdown stabilizes lysogeny. Given these simultaneous changes, the frequency of transitions between the looped and the unlooped state remains nearly constant. Although the loop becomes more stable thermodynamically with increasing CI concentration, it still opens periodically, conferring sensitivity to environmental changes, which may require switching to lytic conditions.