在SARS-CoV-2 Mpro中剖析单氨基酸替代的效果
Shwetha Sreenivasan1, Joseph D Fontes1, Liskin Swint-Kruse1
1Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas, USA.
Protein science : a publication of the Protein Society
|July 17, 2025
概括
预测蛋白质的变化是很困难的. 这项研究使用SARS-CoV-2 Mpro将蛋白质功能与丰度效应分开,揭示了不同的影响并改进了计算模型.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 蛋白质工程是指蛋白质工程.
背景情况:
- 预测氨基酸替代对蛋白质功能和稳定性的影响是分子生物学中的一个重大挑战.
- 深度突变扫描 (DMS) 产生高通量数据,但将蛋白质功能与体内丰富性混为一谈.
- 区分功能变化与丰度效应对于理解中间结果和改进预测模型至关重要.
研究的目的:
- 研究SARS-CoV-2主要蛋白酶 (Mpro) 中关键位置的替代物的体内丰度变化.
- 识别和描述表现出广泛的中间替代结果的"静脉静止器"位置.
- 区分氨基酸替代对蛋白质功能和蛋白质丰富性的影响.
主要方法:
- 利用先前公布的深度突变扫描 (DMS) 结果来识别SARS-CoV-2 Mpro.的风湿位.
- 在6个选定的Mpro位置中生成了10个不同的氨基酸替代.
- 独立测量了这些替代物对蛋白质功能和体内蛋白质丰度的影响.
主要成果:
- 观察到大约45倍的蛋白质丰度变化范围,表明对DMS结果的实质性贡献.
- 在六个测试位置中表现出对功能和丰度的多样化的替代灵敏度.
- 确定了仅影响功能或丰度的位置,重要的是,位置同时对这两个参数显示静电效应.
结论:
- 蛋白质丰富程度显著影响深度突变扫描 (DMS) 结果,必须独立评估.
- 确定影响功能和丰度的位置凸显了预测替代效应的复杂性.
- 未来的计算模型需要独立测量蛋白质功能和丰度的数据集,以增强机械洞察力和预测准确性.
相关概念视频
01:39Mutations
84.5K
Overview
84.5K
01:05Single Nucleotide Polymorphisms-SNPs
15.9K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.9K
01:30Point and Frameshift Mutations
92
Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
92
02:18The Proteasome
9.1K
Eukaryotic cells can degrade proteins through several pathways. One of the most important amongst these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. A series of enzymes carry out the ubiquitination of the target proteins - E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3...
9.1K
01:28Protein Denaturation
5.6K
The function of proteins depends on their native three-dimensional structure, which is dictated by the amino acid sequence of the specific protein. Folding of the polypeptide chain takes place under specific conditions that energetically favor the folded conformation. In contrast, protein denaturation occurs spontaneously under unfavorable conditions that disrupt the integrity of the folded conformation. Thus, the chemical and physical environment of a protein, such as significant changes in pH...
5.6K
00:36Viral Mutations
33.0K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
33.0K