在微秒时间尺度上B-DNA的动态
Alberto Pérez1, F Javier Luque, Modesto Orozco
1Institut de Recerca Biomèdica and Instituto Nacional de BioinformAtica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.
Journal of the American Chemical Society
|November 8, 2007
概括
这项研究揭示了DNA的DNA.
科学领域:
- 结构生物学 结构生物学
- 计算生物物理学的计算生物物理学
背景情况:
- 虽然DNA的B型结构已经很成熟,但它的动态灵活性和局部转换仍然不完全理解.
- 了解DNA动态对于理解其在遗传信息存储和蛋白质相互作用中的作用至关重要.
研究的目的:
- 通过分子动力学 (MD) 模拟来研究B-DNA的微秒动力学.
- 描述DNA内部的局部形态转换,基对开放和阴离结合.
主要方法:
- 进行了第一个微秒分子动力学 (MD) 模拟B-DNA.
- 分析轨迹数据以识别糖过渡,二核酸构造和基对打开事件.
主要成果:
- 观察到许多本地转变,包括S到N的糖回收和稳定的BII形式.
- 记录了依赖序列的α/gamma转换和部分/总基数对开放,A.T和GC对有不同的机制.
- 在小槽中确定了一个高亲和度的Na+结合位,影响DNA构造.
结论:
- B-DNA表现出显著的内在灵活性,使得与蛋白质结合相关的不常见形状的采样.
- DNA的动态特性是微调的,既具有结构稳定性,也具有功能适应性.
- MD模拟为DNA的基本动态和功能相关性提供了关键的见解.
相关概念视频
Lagging Strand Synthesis
During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
Chromatin Packaging
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
Chromatin Packaging
Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter?
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
Replication in Prokaryotes
DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
Many Proteins Work Together to Replicate the Chromosome
Replication is coordinated and carried out by a host of specialized...
Many Proteins Work Together to Replicate the Chromosome
Replication is coordinated and carried out by a host of specialized...
Replication in Prokaryotes
Overview
The Nucleosome
Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...


