相关实验视频

Updated: Jun 5, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

无处不在的DNA/RNA结合Alba域的序列,结构和功能多样性的演变

Jaiganesh Jagadeesh¹, Shruthi Sridhar Vembar²

¹Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka, India.

Scientific reports

|December 5, 2024

概括

在所有生命中的DNA/RNA结合蛋白中发现的Alba域显示出多样化的进化. 这项研究确定了15161种Alba蛋白,揭示了这些关键领域的进化关系和结构变异.

科学领域:

分子生物学分子生物学
进化生物学进化生物学
生物信息学是一种生物信息学.

背景情况:

阿尔巴域是参与DNA/RNA结合的保存蛋白质基因,存在于古生物,细菌和真核生物中.
其从RNA结合到DNA结合的进化轨迹及其功能多样化尚未完全理解.
研究Alba域多样性对于理解它在各种细胞过程中的作用至关重要.

研究的目的:

在各种生物体中全面识别和表征含有Alba域的蛋白质.
探索阿尔巴域的序列,结构和功能多样性.
阐明阿尔巴蛋白的进化历史和关系.

主要方法:

利用代的PSI-BLAST搜索,从NCBI非冗余蛋白质数据库中识别Alba域蛋白.
用于集群和子组识别的雇佣序列相似性网络 (SSN) 分析.
进行了序列和结构保护分析,并进行了植物遗传学分析.

主要成果:

确定了15,161种独特的含有Alba域的蛋白质.
聚合蛋白质分为13个不同的子组,包括已知的古生物和真核生物组,以及新型真菌和Plasmodium特异性的Albas.
在单细胞真核生物中揭示了保存的二极体接口和结构偏差,植物遗传学分析指出了从古人类祖先中出现的真核细胞群.

结论:

这项研究为含有Alba域的蛋白质提供了一个全面的进化框架.
突出显著的序列和结构多样性,特别是在真核细胞系.
增强对阿尔巴域进化及其对整个生命的功能影响的理解.

更多相关视频

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

相关概念视频

Conserved Binding Sites

Conserved Binding Sites

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...

Bacterial RNA Polymerase

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

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...

Bacterial Transcription

Bacterial Transcription

RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:

Single-Strand DNA Binding Proteins

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...

Allosteric Proteins-ATCase

Allosteric Proteins-ATCase

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...