基于序列结构的预测,对与原发性免疫缺陷相关的蛋白质中氨基酸替代的病原性
Ekaterina S Porfireva1, Anton D Zadorozhny1, Anastasia V Rudik2
1Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia.
Frontiers in immunology
|February 20, 2025
概括
这项研究开发了序列结构属性关系 (SSPR) 模型,以预测初级免疫缺陷 (PID) 中氨基酸替代的致病性. 这些模型实现了高精度,性能优于现有工具,并通过SAV-Pred网络应用程序提供.
科学领域:
- 遗传学 遗传学 是一个
- 免疫学 免疫学 免疫学
- 生物信息学是一种生物信息学.
背景情况:
- 初级免疫缺陷 (PID) 是一种罕见的遗传疾病,影响免疫系统功能.
- 早期诊断对于预防严重并发症至关重要,但不同的临床症状带来了诊断挑战.
- 确定特定的氨基酸替代物 (AAS) 是PID诊断的关键.
研究的目的:
- 开发序列结构属性关系 (SSPR) 模型,用于预测25个PID相关基因中AAS的致病性.
- 为临床医生和遗传学家创建一个用户友好的工具,以帮助PID诊断.
主要方法:
- 从ClinVar和gnomAD.AD提取了4825种致病和良性AAS的数据.
- 利用MultiPASS软件和贝叶斯算法与多层次原子邻近 (MNA) 描述符来构建SSPR模型.
- 使用5倍交叉验证验证模型准确性,并与其他生物信息学工具比较性能.
主要成果:
- 开发了准确的SSPR模型,用于预测PID相关蛋白质中的AAS病原性.
- 实现了高预测准确度,平均ROC AUC为0.831.
- SSPR模型的性能优于流行生物信息学工具,如SIFT4G,Polyphen2 HDIV和FATHMM.
结论:
- 开发的SSPR模型提供了一种可靠的方法来预测PID中AAS的病原性.
- 在免费可用的网络应用程序SAV-Pred (http://www.way2drug.com/SAV-Pred/) 中实现了最好的SSPR模型.
- 在诊断PID时,SAV-Pred是医学遗传学家和临床医生的宝贵工具.
相关概念视频
Signal Sequences and Sorting Receptors
5.2K
Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...
5.2K
Protein 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
Conserved Binding Sites
4.1K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.1K
Mutations
78.5K
Overview
78.5K
Translation
14.4K
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
Translation Produces the Building Blocks of Life
Proteins are...
Translation Produces the Building Blocks of Life
Proteins are...
14.4K
Protein Folding
117.1K
Overview
117.1K


