在HhaI蛋白结合位点的基动力学
Kari Pederson1, Gary A Meints2, Gary P Drobny3
1Department of Chemistry & Biochemistry, California State University at Dominguez Hills, Carson, California 90747, United States.
The journal of physical chemistry. B
|August 10, 2023
概括
HhaI甲基转移酶系统扭曲了DNA,但固态NMR显示目标细胞蛋白并没有从螺旋体中翻转出来. 甲基化也不会影响基动力学,从而澄清了蛋白质-DNA相互作用机制.
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:
- 蛋白质-DNA相互作用对于细胞功能至关重要,通常涉及显著的DNA螺旋扭曲.
- HhaI限制-修改系统就是一个例子,其中DNA甲基化涉及基翻转.
- 在HHAI中基点翻转的精确机制仍然不完全理解.
研究的目的:
- 为了研究特定DNA寡合体内HhaI甲基转移酶和内核酶结合部位的动态.
- 阐明基翻转的机制以及DNA灵活性在蛋白质-DNA相互作用中的作用.
主要方法:
- 使用了固态核磁共振 (SSNMR) 光谱学.
- 分析了在 [5'-GCGC-3']2 序列内和旁边含有基的DNA寡合体.
主要成果:
- SSNMR光谱表明,在DNA寡合体内的所有分析的核酸位上,具有显著的结构灵活性.
- 与先前的假设相反,目标细胞蛋白在毫秒-皮秒时间尺度上不会被动地从双螺旋中翻转出来.
- 基因的甲基化并没有改变基本身的动态,尽管脊柱和 furanose 环的动态受到了影响.
结论:
- HhaI系统的DNA扭曲机制不依赖于目标细胞因子的被动基翻转.
- 虽然DNA骨干和 furanose 环在甲基化时表现出动态变化,但基体动态仍然不受影响.
- 这些发现为通过甲基转移酶识别和修改DNA的分子机制提供了关键的见解.
更多相关视频
11:17Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin
Published on: March 10, 2021
6.4K
09:49Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
Published on: April 2, 2015
10.7K
相关概念视频
02:40Ligand Binding Sites
12.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.9K
01:49Conserved Binding Sites
4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
02:35Noncovalent Attractions in Biomolecules
51.9K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
51.9K
02:04Protein-protein Interfaces
12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
02:18The Equilibrium Binding Constant and Binding Strength
13.0K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
13.0K
00:49Ligand Binding and Linkage
4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K