从AlphaFold结构数据库使用DPAM2对48个完整蛋白质的ECOD域分类
R Dustin Schaeffer1, Jing Zhang1,2, Kirill E Medvedev1
1Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.
PLoS computational biology
|February 28, 2024
概括
这项研究对AlphaFold数据库中的48个蛋白质组的蛋白质域进行了目录,对超过746,000个域进行了分类. 这些发现揭示了真核生物和细菌蛋白质域种群的差异,有助于未来的蛋白质分类.
科学领域:
- 结构生物学是结构生物学.
- 生物信息学是一种生物信息学.
- 计算生物学是一种计算生物学.
背景情况:
- 像AlphaFold这样的蛋白质结构预测模型产生了庞大的数据集.
- 大规模的域注释对于从这些预测中提取生物学见解至关重要.
- 蛋白质域的进化分类 (ECOD) 为域分类提供了一个框架.
研究的目的:
- 在AlphaFold数据库中检测和目录48个完整蛋白质组中的蛋白质域.
- 分析不同生物体 (真核生物和细菌) 中蛋白质域的分布和特征.
- 将结构预测中的域群与现有数据库进行比较,并识别丰富的组.
主要方法:
- 使用了蛋白质域的进化分类 (ECOD) 分类系统.
- 从AlphaFold数据库中应用域检测和分类到48个完整的蛋白质组.
- 分析了残留物覆盖范围,域群和同源组分布.
主要成果:
- 在所有蛋白质组中成功分类了90%的残留物域或可识别区域.
- 从536,808种蛋白质中编制了746,349个域名,总计超过2.26亿个氨基酸残留物.
- 在真核生物 (更高无序区域,重复) 与细菌中确定了不同的域模式,并列举了像罗斯曼和TIM桶这样的共享域.
结论:
- 预测的蛋白质结构的大规模域注释是可行的,并产生了重要的生物学见解.
- 对比分析揭示了真核生物和细菌之间的蛋白质域组成的进化差异.
- 这些发现为未来蛋白质分类和针对大型蛋白质集的目标选择策略提供了信息.
更多相关视频
相关概念视频
Conservation of Protein Domains Over Different Proteins
10.9K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.9K
Conservation of Protein Domains
3.1K
3.1K
Proteomics
7.3K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
7.3K
Protein Families
15.3K
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...
15.3K
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
12.5K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
12.5K
Genomic DNA in Eukaryotes
46.9K
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
46.9K


