使用P450Atlas探索P450超级家族的多样性 - - 在线工具用于自动化分家族分配
Dominik Gront1, Khajamohiddin Syed2, David R Nelson3
1Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
Protein science : a publication of the Protein Society
|February 19, 2025
概括
P450Atlas网站提供了关于细胞染色体P450命名的统一资源. 它的新隐藏马尔科夫模型算法准确地将P450序列分配给子家族,改进了现有的方法.
科学领域:
- 生物化学 生物化学
- 生物信息学是一种生物信息学.
- 酶学 是一种酶学.
背景情况:
- 细胞染色体P450单氧化酶 (CYPs/P450s) 是具有含量的关键酶,具有不同的生物学作用.
- 庞大的P450超级家族包括近1万个已知的家族,需要强大的分类系统.
- 以前用于P450序列分配的方法缺乏最佳的灵敏度和准确性.
研究的目的:
- 介绍P450Atlas网站,作为一个关于细胞染色体P450命名的全面资源.
- 介绍一种新的,自动化的算法,用于将P450序列分配给各自的子家族.
- 为研究人员提供一种有效的工具来探索和分类P450多样性.
主要方法:
- 开发和实施基于隐藏马尔科夫模型 (HMM) 的算法来分配P450亚家族.
- 将HMM方法与传统的BLAST程序进行对序列分配精度和灵敏度的比较.
- 创建了P450Atlas网站 (https://p450atlas.org),用于浏览,搜索和序列分配.
主要成果:
- 与BLAST相比,基于HMM的算法在将P450序列分配到子家族时表现出更高的灵敏度和准确性.
- P450Atlas网站提供自动序列分配,促进有效的P450分类.
- 该网站提供了一个可浏览和搜索的P450家族和子家族的在线数据库.
结论:
- 由先进的HMM算法驱动的P450Atlas网站提供了P450序列分类的卓越方法.
- 这种资源显著增强了对细胞染色体P450命名和多样性的研究.
- P450Atlas准备成为P450信息的最终来源.
相关概念视频
02:47Protein Families
15.2K
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...
15.2K
01:57Gene Families
8.7K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
8.7K
01:19Allosteric Proteins-ATCase
5.6K
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...
5.6K
00:49Ligand Binding and Linkage
4.7K
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...
4.7K