从基因组序列中建立全面的四级结构蛋白质
bioRxiv : the preprint server for biology
|May 7, 2024
概括
我们开发了QSPACE,这是一个计算平台,可以在基因组中绘制蛋白质结构和突变图. 这种工具有助于理解全细胞功能和预测突变影响.
科学领域:
- 结构生物学是结构生物学.
- 计算生物学是一种计算生物学.
- 基因组学就是基因组学.
背景情况:
- 蛋白质显微镜和计算方法的进步揭示了多个子单元蛋白质结构.
- 需要一个统一的平台来将数据映射到这些结构上进行基因组规模分析.
研究的目的:
- 开发QSPACE,一个用于注释四级结构蛋白质的计算平台.
- 将可操作的数据,如突变,映射到蛋白质结构上,并确定亚细胞局部.
主要方法:
- QSPACE评估资源,以找到最佳的蛋白质结构.
- 它将突变和活跃部位的3D位置映射到结构上.
- 第三方API为所有氨基酸确定亚细胞区.
主要成果:
- 使用QSPACE生成大肠杆菌K-12 MG1655.5的四级结构蛋白质.
- 该平台可以使用随机森林分类器预测突变严重程度.
- 它与基因组规模模型集成,以确定空间蛋白质组分配.
结论:
- QSPACE提供了四级结构蛋白质体的基因组规模注释.
- 这使得我们能够从分子层面了解整个细胞的功能.
- 该平台促进了大规模的突变分析和基因组规模建模.
相关概念视频
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
Genome Annotation and Assembly
18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
Globular Proteins
7.4K
In organisms, proteins are the most abundant macromolecules. They act as the building blocks of life and play various crucial roles in the body. Proteins can be broadly classified into two distinct subtypes based on their shape and solubilities: globular proteins and fibrous proteins.
Globular proteins serve many important physiological functions, such as acting as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be soluble in the aqueous...
Globular proteins serve many important physiological functions, such as acting as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be soluble in the aqueous...
7.4K
Multi-species Conserved Sequences
3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K
Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
Protein Complex Assembly
10.6K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Many viruses self-assemble into a fully functional unit using the infected host cell to...
10.6K


