蛋白质- dna识别机制和特异性

IF 4.9 Q1 BIOPHYSICS
Biophysical reviews Pub Date : 2023-09-07 eCollection Date: 2023-10-01 DOI:10.1007/s12551-023-01137-7
Anastasia A Anashkina
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引用次数: 0

摘要

关于蛋白质-DNA复合物结构的知识积累使我们能够理解蛋白质-DNA识别和寻找DNA上特定位点的机制。显然,一种蛋白质对特定DNA的识别机制必须满足两个条件。首先,错误绑定的概率应该非常小。其次,寻找“正确”结合位点的时间不宜过长。如果我们假设蛋白质对DNA上一个精确位点的识别发生在距离DNA一定距离的地方,并计算全局最小值,我们就可以在短距离上避免局部最小值。唯一的远距离相互作用是电荷的相互作用。DNA上的电荷在三维空间中的位置取决于DNA的局部构象,从而反映了DNA的序列,并为识别设定了空间模式。反离子浓度、离子强度和pH值等多种因素都会影响DNA对蛋白质的识别。目前,远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,从而避免错位结合。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Protein-DNA recognition mechanisms and specificity.

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.

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来源期刊
Biophysical reviews
Biophysical reviews Biochemistry, Genetics and Molecular Biology-Biophysics
CiteScore
8.90
自引率
0.00%
发文量
93
期刊介绍: Biophysical Reviews aims to publish critical and timely reviews from key figures in the field of biophysics. The bulk of the reviews that are currently published are from invited authors, but the journal is also open for non-solicited reviews. Interested authors are encouraged to discuss the possibility of contributing a review with the Editor-in-Chief prior to submission. Through publishing reviews on biophysics, the editors of the journal hope to illustrate the great power and potential of physical techniques in the biological sciences, they aim to stimulate the discussion and promote further research and would like to educate and enthuse basic researcher scientists and students of biophysics. Biophysical Reviews covers the entire field of biophysics, generally defined as the science of describing and defining biological phenomenon using the concepts and the techniques of physics. This includes but is not limited by such areas as: - Bioinformatics - Biophysical methods and instrumentation - Medical biophysics - Biosystems - Cell biophysics and organization - Macromolecules: dynamics, structures and interactions - Single molecule biophysics - Membrane biophysics, channels and transportation
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