Dps蛋白保护大肠杆菌的DNA以三元体的形式
Vladislav Kovalenko1, Ksenia Tereshkina1, Andrey Moiseenko2
1Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia.
International journal of molecular sciences
|January 25, 2025
概括
在DNA-Dps晶体形成过程中,DNA结合蛋白Dps (DNA结合蛋白) 从十二体转变为三体,解释了观察到的尺寸变化并揭示了细胞内DNA保护机制.
科学领域:
- 结构生物学是结构生物学.
- 微生物学 微生物学
- 生物物理学的生物物理.
背景情况:
- Dps蛋白是一种主要的 prokaryotic DNA 结合蛋白.
- 在饥饿期间,Dps通过形成晶体复合体来保护DNA.
- 在此之前,DNA-Dps复合体的细胞内结构和复合体形成期间的Dps尺寸变化是无法解释的.
研究的目的:
- 为了阐明Dps蛋白在细胞内DNA-Dps晶体形成过程中的结构转变.
- 为了解释在DNA复杂化过程中观察到的Dps蛋白大小的减少.
- 为了确定细胞内DNA-Dps复合物的晶体结构.
主要方法:
- 分子动态建模,以生成一个dps的trimer模型.
- 整合DPS三元体模型到体外DNA-DPS晶体电子密度.
- 来自大肠杆菌细胞的小角度X射线散射 (SAXS) 数据的分析.
主要成果:
- 在DNA-Dps晶体形成过程中,Dps蛋白从90 Å的十二分体转变为70 Å的圆柱状三分体.
- 确定了一个晶体结构模型,显示DPS剪切器形成的通道内的DNA.
- 该模型与来自细胞内晶体的SAXS数据有很好的一致性.
结论:
- Dps的寡合转变解释了观察到的尺寸缩小,并为DNA保护提供了结构基础.
- 细胞内DNA-Dps晶体结构揭示了位于Dps三元管道内的DNA.
- 代谢物调节的寡合转换提供了一个灵活的机制来适应 prokaryotic 的代谢状态.
相关概念视频
Single-Strand DNA Binding Proteins
13.9K
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
13.9K
Translesion DNA Polymerases
9.8K
Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
9.8K
The Replisome
32.9K
DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
32.9K
Molecular Chaperones and Protein Folding
17.7K
The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
The...
17.7K
Restarting Stalled Replication Forks
5.7K
DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
5.7K
Mismatch Repair
4.8K
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
4.8K


