分析蛋白质中的芳香-芳香相互作用:A2ID 2.0
Y Bhargav Kumar1, Nandan Kumar2, S Vaikundamani2
1Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, U. P., India.
International journal of biological macromolecules
|October 5, 2023
概括
更新的芳香-芳香相互作用数据库 (A2ID) 现在列出了超过340万个蛋白质芳香 (π-π) 网络. 大多数网络涉及两到三种芳香残留物,主要是氨酸和氨酸.
科学领域:
- 结构生物学 结构生物学
- 生物信息学是一种生物信息学.
- 计算化学计算化学
背景情况:
- 芳香-芳香 (π-π) 相互作用对蛋白质的结构和功能至关重要.
- 芳香-芳香相互作用数据库 (A2ID) 之前记录了这些相互作用.
- 自2011年以来,已经报告了A2ID的以前版本.
研究的目的:
- 将更新的芳香-芳香相互作用数据库 (A2ID) 提供扩展的数据集和增强的分析能力.
- 在实验确定的蛋白质结构中分析 π-π 网络的特征和普遍性.
- 为研究蛋白质结构动机的研究人员提供全面的资源.
主要方法:
- 用几何参数识别和描述 π-π 网络,例如中心距离 (r) 和平面间角 (φ).
- 从84,500个蛋白质结构中分析了超过340万个π-π网络.
- 将SCOP2和ECOD分类器与现有的SCOP,CATH和EC分类器相结合,以便进行更广泛的分析.
主要成果:
- 目前的A2ID版本包含3,444,619个π-π网络.
- 大约92.50%的实例是2π (77.34%) 或3π (15.23%) 的网络.
- 氨 (PHE) 和氨酸 (TYR) 残留物是2π网络中最常见的相互作用对.
结论:
- 更新的A2ID为研究蛋白质芳香相互作用提供了广泛而详细的资源.
- 较小的π-π网络 (2π和3π) 的普及凸显了它们在蛋白质架构中的重要性.
- 扩展的分类系统可以从多个角度探索 π-π 网络的特性和功能角色.
相关概念视频
NMR Spectroscopy of Aromatic Compounds
4.8K
Aromatic compounds can be identified or analyzed using proton NMR and carbon‐13 NMR. Typically, aromatic hydrogens or hydrogens directly bonded to the aromatic rings are strongly deshielded by the aromatic ring current. Therefore, they absorb in the range of 6.5–8.0 ppm in proton NMR spectra. For instance, aromatic hydrogens directly bonded to the benzene ring absorb at 7.3 ppm. However, aromatic hydrogens of larger rings absorb farther upfield or downfield than the ideal range.
4.8K
Aromatic Hydrocarbon Anions: Structural Overview
2.8K
Neutral hydrocarbons like cyclopentadiene with an odd number of carbon atoms and one intervening CH2 group in the ring are not aromatic. Cyclopentadiene with 4 π electrons does not satisfy the 4n + 2 π electron rule. Additionally, the intervening CH2 group is sp3 hybridized and lacks a vacant p orbital, thereby interrupting the overlap of p orbitals in a continuous manner and preventing the delocalization of π electrons throughout the ring.
Due to the absence of continuous...
Due to the absence of continuous...
2.8K
π Electron Effects on Chemical Shift: Aromatic and Antiaromatic Compounds
1.2K
In aromatic compounds, such as benzene, the circulation of (4n + 2) π-electrons sets up a diamagnetic or diatropic ring current around the perimeter of the molecule. This current induces a magnetic field that opposes the external field inside the ring and reinforces it on the outside. The protons in benzene are deshielded and exhibit high chemical shifts in the range 6.5–8.5 ppm. The shielding effect at the center of the ring is evident in complex aromatic molecules, such as...
1.2K
Aromatic Compounds: Overview
10.7K
In general, the term ‘aromatic’ indicates a pleasant smell or fragrance from fresh flowers, freshly prepared coffee, etc. In the early history of organic chemistry, many benzene derivatives were isolated from the pleasant odor oils of the plants. For example, vanillin was isolated from the oil of vanilla, methyl salicylate from the oil of wintergreen, and cinnamaldehyde from the oil of cinnamon. They all had a pleasant odor; hence the name aromatic was given.
In 1825, Faraday...
In 1825, Faraday...
10.7K
Criteria for Aromaticity and the Hückel 4n + 2 Rule
10.6K
Like benzene, cyclobutadiene and cyclooctatetraene are cyclic compounds with alternate single and double bonds. However, their chemical behavior differs from benzene, as they are unstable and not aromatic. So, what are the structural characteristics of unsaturated compounds categorized as aromatic?
For the first time, Eric Hückel, a German chemical physicist, derived a set of structural features for a compound to be classified as aromatic. This is now known as...
For the first time, Eric Hückel, a German chemical physicist, derived a set of structural features for a compound to be classified as aromatic. This is now known as...
10.6K
Aromatic Hydrocarbon Cations: Structural Overview
2.8K
Cycloheptatriene is a neutral monocyclic unsaturated hydrocarbon that consists of an odd number of carbon atoms and an intervening sp3 carbon in the ring. The three double bonds in the ring correspond to 6 π electrons, which is a Huckel number, and therefore satisfies the criteria of 4n + 2 π electrons. However, the intervening sp3 carbon disrupts the continuous overlap of p orbitals. As a result, cycloheptatriene is not aromatic.
Removing one hydrogen from the intervening CH2 group...
Removing one hydrogen from the intervening CH2 group...
2.8K


