MESPEUS:是蛋白质中的金属协调组的数据库
Geng-Yu Lin1, Yu-Cheng Su1, Yen Lin Huang1
1Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan.
Nucleic acids research
|November 9, 2023
概括
MESPEUS是一个新的数据库,详细介绍金属蛋白中的金属协调几何学. 它提供了一个用户友好的界面,用于探索金属部位,帮助研究结构生物学和金属蛋白功能.
科学领域:
- 结构生物学 结构生物学
- 生物有机化学 生物有机化学
- 生物信息学是一种生物信息学.
背景情况:
- 金属蛋白在生物系统中起着至关重要的作用.
- 了解金属协调几何学对于阐明蛋白质功能至关重要.
- 现有的数据库可能缺乏金属现场的全面几何细节.
研究的目的:
- 开发MESPEUS,一个自由访问的金属协调组在金属蛋白结构的数据库.
- 为了提供详细的几何信息,金属网站,包括40种金属类型.
- 通过一个用户友好的界面来促进金属现场特征的探索.
主要方法:
- 从蛋白质数据库 (PDB) 结构中提取金属协调组.
- 包含使用空间组操作的对称性相关单元,以提供完整的协调描述.
- 开发一个用于搜索和可视化金属现场数据的Web界面.
- 每月同步与PDB数据库以获得最新信息.
主要成果:
- MESPEUS包含各种金属蛋白中的金属位点的几何数据.
- 该数据库支持基于金属类型,协调号,供体残留物和结构分辨率的搜索.
- 交互式可视化工具允许详细检查金属部位及其结构上下文.
- 一个案例研究证明了MESPEUS在分析Mg-ATP相互作用中的实用性.
结论:
- 对于研究金属蛋白和金属协调的研究人员来说,MESPEUS提供了一个宝贵的资源.
- 该数据库增强了对金属位点几何及其对蛋白质功能的影响的理解.
- 它的全面数据和直观的界面简化了金属蛋白相互作用的调查.
更多相关视频
11:38Quantifying the Binding Interactions Between CuII and Peptide Residues in the Presence and Absence of Chromophores
Published on: April 5, 2022
2.5K
11:04Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides
Published on: September 7, 2019
9.2K
相关概念视频
02:51Metal-Ligand Bonds
20.8K
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...
20.8K
03:02Colors and Magnetism
11.7K
Color in Coordination Complexes
When atoms or molecules absorb light at the proper frequency, their electrons are excited to higher-energy orbitals. For many main group atoms and molecules, the absorbed photons are in the ultraviolet range of the electromagnetic spectrum, which cannot be detected by the human eye. For coordination compounds, the energy difference between the d orbitals often allows photons in the visible range to be absorbed and emitted, which is seen as colors by the human...
When atoms or molecules absorb light at the proper frequency, their electrons are excited to higher-energy orbitals. For many main group atoms and molecules, the absorbed photons are in the ultraviolet range of the electromagnetic spectrum, which cannot be detected by the human eye. For coordination compounds, the energy difference between the d orbitals often allows photons in the visible range to be absorbed and emitted, which is seen as colors by the human...
11.7K
02:54Coordination Compounds and Nomenclature
21.4K
In most main group element compounds, the valence electrons of the isolated atoms combine to form chemical bonds that satisfy the octet rule. For instance, the four valence electrons of carbon overlap with electrons from four hydrogen atoms to form CH4. The one valence electron leaves sodium and adds to the seven valence electrons of chlorine to form the ionic formula unit NaCl (Figure 1a). Transition metals do not normally bond in this fashion. They primarily form coordinate covalent bonds, a...
21.4K
02:57Coordination Number and Geometry
15.9K
For transition metal complexes, the coordination number determines the geometry around the central metal ion. Table 1 compares coordination numbers to molecular geometry. The most common structures of the complexes in coordination compounds are octahedral, tetrahedral, and square planar.
15.9K
02:26Protein Networks
4.0K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.0K
02:47Protein Families
15.4K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
15.4K