基质的结合和转移均促进了AlkB-AlkG电子转移复合体内的功能相互作用
Karolina Mikulska-Ruminska1, Matthew Licht2, Mehmed Z Ertem3
1Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, PL 87100 Torun, Poland.
Journal of molecular biology
|November 16, 2025
概括
阿尔干单氧化酶AlkB-AlkG复合物氧化了阿尔干. 多尺度计算揭示了多德干基质通过疏水通道的转移,影响了酶功能,并为改进的基转化提供了目标.
科学领域:
- 生物化学 生化学
- 结构生物学 结构生物学
- 计算化学的计算化学
背景情况:
- 单氧化酶 (AlkB) 和毒素 (AlkG) 复合物催化的氧化.
- 最近的一项冷EM研究详细介绍了Fontimonas热AlkB-AlkG复合结构与多德干 (D12) 基质.
- 这种复杂的精确分子机制在很大程度上仍未被阐明.
研究的目的:
- 研究Fontimonas热AlkB-AlkG复合体内的动态和相互作用.
- 阐明烯氧化和基质转位的分子机制.
- 为了确定AlkB变体的潜在工程的关键站点和相互作用.
主要方法:
- 多尺度计算,包括分子动力学 (MD) 模拟.
- 弹性网络模型 (ENM) 用于全效应分析.
- 量子力学/分子力学 (QM/MM) 用于氧气激活机制.
主要成果:
- 在MD模拟过程中,多德干 (D12) 基质在活性部位表现出稳定的相互作用.
- 鉴定了一条由I54封闭的疏水通道,允许D12通过中间点IS1和IS2转移到通过膜暴露的部位.
- 基质转位影响铁中心和AlkB-AlkG接口之间的合,与通道连接到O2通道站点.
- ENM分析证实了基质进入,催化部位和AlkB-AlkG接口之间的全效应.
结论:
- 这项研究揭示了AlkB-AlkG复合体中基质转位的动态机制.
- 确定了参与基质结合,转位和全调节的关键残留物和途径.
- 为工程AlkB变体提供了机械洞察力,这些变体具有增强的基转换能力.
相关概念视频
Cooperative Allosteric Transitions
8.6K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
8.6K
Cooperative Allosteric Transitions
2.6K
2.6K
Cooperative Allosteric Transitions
3.0K
3.0K
Allosteric Regulation
62.9K
Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
62.9K
Allosteric Proteins-ATCase
6.4K
Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
6.4K
Ligand Binding and Linkage
5.4K
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...
5.4K


