Speed, dissipation, and error in kinetic proofreading
Speed, dissipation, and error in kinetic proofreading
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DOI：
10.1073/pnas.1119911109
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发表时间：
2012-07-24
影响因子：
11.1
通讯作者：
Leibler, Stanislas
中科院分区：
文献类型：
--
作者：
Murugan, Arvind;Huse, David A.;Leibler, Stanislas
校正机制通过允许中间复合物的解离来增加生化反应中的特异性。这些机制破坏和重置反应以撤销错误，代价是增加反应时间和自由能消耗。在这里，我们在校对和微管生长之间进行类比，它们具有上述的一些特征。我们的类比与统计的增长和收缩的微管在物理空间中的循环的中间复合物在空间中的化学状态的校对机制。使用这个类比，我们发现一个新的动力学制度的校对，在这个过程中，可以实现指数级的速度加快的成本有点大的错误率。这个政权是类似的过渡区之间的两个已知的增长制度的微管（有界和无界），并明确定义在大型校对网络的限制。我们发现，这种有利的制度的速度错误的权衡可能存在于校对计划研究较早的收费的tRNA合成酶，在RecA丝组装ssDNA，并在蛋白质合成的核糖体。
Proofreading mechanisms increase specificity in biochemical reactions by allowing for the dissociation of intermediate complexes. These mechanisms disrupt and reset the reaction to undo errors at the cost of increased time of reaction and free energy expenditure. Here, we draw an analogy between proofreading and microtubule growth which share some of the features described above. Our analogy relates the statistics of growth and shrinkage of microtubules in physical space to the cycling of intermediate complexes in the space of chemical states in proofreading mechanisms. Using this analogy, we find a new kinetic regime of proofreading in which an exponential speed-up of the process can be achieved at the cost of a somewhat larger error rate. This regime is analogous to the transition region between two known growth regimes of microtubules (bounded and unbounded) and is sharply defined in the limit of large proofreading networks. We find that this advantageous regime of speed-error tradeoff might be present in proofreading schemes studied earlier in the charging of tRNA by tRNA synthetases, in RecA filament assembly on ssDNA, and in protein synthesis by ribosomes.