Anashkina Anastasia A
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
Biophys Rev. 2023 Sep 7;15(5):1007-1014. doi: 10.1007/s12551-023-01137-7. eCollection 2023 Oct.
The accumulated knowledge about the structure of protein-DNA complexes allowed us to understand the mechanisms of protein-DNA recognition and searching for a specific site on DNA. Obviously, the mechanism of specific DNA recognition by a protein must satisfy two requirements. First, the probability of incorrect binding should be very small. Second, the time to find the "correct" binding site should not be too long. If we assume that protein recognition of a precise site on DNA occurs at some distance from DNA and calculate global minima, we can avoid local minima at short distances. The only long-range interaction is the interaction of charges. The location of charges on DNA in three-dimensional space depends on the local conformation of DNA and thus reflects the DNA sequence and sets the spatial pattern for recognition. Various factors such as counter ion concentration, ionic strength, and pH can affect protein recognition of DNA. Nowadays, the theory of long-range interactions makes it possible to calculate the best mutual spatial arrangement of protein and DNA molecules by charged groups and avoid misplaced binding.
关于蛋白质 - DNA 复合物结构的累积知识使我们能够理解蛋白质 - DNA 识别机制以及在 DNA 上寻找特定位点的过程。显然，蛋白质对特定 DNA 的识别机制必须满足两个要求。第一，错误结合的概率应该非常小。第二，找到“正确”结合位点的时间不应过长。如果我们假设蛋白质在距 DNA 一定距离处识别 DNA 上的精确位点并计算全局最小值，就可以避免短距离处的局部最小值。唯一的长程相互作用是电荷相互作用。DNA 上电荷在三维空间中的位置取决于 DNA 的局部构象，从而反映 DNA 序列并为识别设定空间模式。诸如抗衡离子浓度、离子强度和 pH 等各种因素会影响蛋白质对 DNA 的识别。如今，长程相互作用理论使得通过带电基团计算蛋白质和 DNA 分子的最佳相互空间排列成为可能，并避免错误的结合。
