在大肠杆菌的金属结合特异性的物理基础NikRR
Christine M Phillips1, Paul S Nerenberg, Catherine L Drennan
1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Journal of the American Chemical Society
|July 23, 2009
概括
结合转录因子NikR (EcNikR) 在高亲和度位点使用Ni(2+) 来获得稳定性. 当K(+) 占据第二个金属位点,而不是Ni(2+) 时,DNA结合是有利的.
科学领域:
- 生物化学 生物化学
- 分子生物学分子生物学
- 结构生物学 结构生物学
背景情况:
- 大肠杆菌等细菌的吸收受转录因子NikR的调节.
- 尼克R与尼克操作子结合,抑制尼克运输基因 (NikABCDE).
- 除了高亲密性Ni2+) 站点外,NikR上还提出了第二个金属结合站点.
研究的目的:
- 为了确定EcNikR的第二个金属结合点的首选离子 (K(+) 或Ni(2+)) .
- 阐明离子偏好在高亲和和第二金属结合点的物理基础.
- 了解第二个位点的离子占用如何影响EcNikR-DNA复合体的稳定性.
主要方法:
- 详细的分子动力学模拟EcNikR结构的不同离子 (Ni(2+),K(+)) 在不同的位置.
- 静电绑定自由能量计算.
- 包含静电和非静电效应的自由能量模拟.
主要成果:
- 模拟显示了稳定的EcNikR轨迹与Ni(2+) 在高亲和位点,但与K(+).
- 在第二个金属地点,K(+) 和Ni(2+) 均产生了稳定的几何形状.
- 由于Ni2+的溶解处罚,EcNikR-DNA结合在第二个位点的K(+) 更有利,因为Ni(2+).
结论:
- 当Ni(2+) 占据其高亲和位点时,EcNikR是最稳定的.
- 当第二个金属结合部位被单价离子所占据时,例如K(+).
- 这些发现澄清了不同离子在NikR调节功能中的作用.
相关概念视频
01:03Single-Strand DNA Binding Proteins
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...
02:51Metal-Ligand Bonds
The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
01:09Complexation Equilibria: Factors Influencing Stability of Complexes
In complexation reactions, metal cations are the electron pair acceptors, and the ligands are the electron pair donors. The stability of the metal complexes depends primarily on the complexing ability of the central metal ion and the nature of the ligands. Generally, the complexing ability of the metal ion depends on the size and charge of the ion. As the metal ion size increases, the stability of the metal complexes decreases, provided that the valency of the metal ion and the ligands remain...
03:45Formation of Complex Ions
A type of Lewis acid-base chemistry involves the formation of a complex ion (or a coordination complex) comprising a central atom, typically a transition metal cation, surrounded by ions or molecules called ligands. These ligands can be neutral molecules like H2O or NH3, or ions such as CN− or OH−. Often, the ligands act as Lewis bases, donating a pair of electrons to the central atom. These types of Lewis acid-base reactions are examples of a broad subdiscipline called coordination...
01:23Stringent Response in E. coli
Bacterial growth is closely tied to nutrient availability, with cells proliferating exponentially under favorable conditions and entering a stationary phase when resources become scarce. This transition is mediated by a regulatory mechanism known as the stringent response, which allows bacteria to adapt to nutrient deprivation by modulating gene expression and metabolic activity.During nutrient scarcity, intracellular amino acid levels decline. It results in the accumulation of uncharged tRNAs...
01:27Chemotaxis in E. coli
Chemotaxis in Escherichia coli is a sensory-driven motility mechanism that enables bacteria to navigate chemical gradients, moving toward beneficial environments while avoiding harmful conditions. This process relies on a signal transduction system integrating external chemical cues with flagellar motor control.Chemoreceptors and Signal DetectionE. coli detects chemical gradients through methyl-accepting chemotaxis proteins (MCPs), which are membrane-bound chemoreceptors that sense attractants...