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首页> 外文期刊>Journal of physics, A. Mathematical and theoretical >How conformational dynamics influences the protein search for targets on DNA
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How conformational dynamics influences the protein search for targets on DNA

机译：构象动力学如何影响蛋白质对DNA靶标的搜索

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摘要

Protein search and association to specific sequences on DNA is a starting point for all fundamental biological processes. It has been intensively studied in recent years by a variety of experimental and theoretical methods. However, many features of these complex biological phenomena are still not resolved at the molecular level. Experiments indicate that proteins can be bound non-specifically to DNA in multiple configurations. But the role of conformational fluctuations in the protein search dynamics remains not well understood. Here we develop a theoretical method to analyze how the conformational transitions affect the process of finding the specific targets on DNA. Our approach is based on discrete-state stochastic calculations that take into account the most relevant physical-chemical processes. This allows us to explicitly evaluate the protein search for the targets on DNA at different conditions. Our calculations suggest that conformational fluctuations might strongly affect the protein search dynamics. We explain how the shift in the conformational equilibrium influences the target search kinetics. Theoretical predictions are supported by Monte Carlo computer simulations.
机译：蛋白质搜索以及与DNA上特定序列的关联是所有基本生物学过程的起点。近年来，已经通过各种实验和理论方法对其进行了深入研究。但是，这些复杂的生物学现象的许多特征仍未在分子水平上得到解决。实验表明，蛋白质可以多种结构非特异性地与DNA结合。但是，构象性波动在蛋白质搜索动力学中的作用仍未得到很好的理解。在这里，我们开发了一种理论方法来分析构象转变如何影响在DNA上寻找特定靶标的过程。我们的方法基于离散状态随机计算，其中考虑了最相关的物理化学过程。这使我们能够明确评估蛋白质在不同条件下对DNA靶标的搜索。我们的计算表明构象波动可能强烈影响蛋白质搜索动力学。我们解释了构象平衡的变化如何影响目标搜索动力学。蒙特卡洛计算机模拟支持理论预测。

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