聚甲基结合蛋白与多甲基RNA复合的合规性质
Arun Chakrabortty1, Sandip Mondal2, Sanjoy Bandyopadhyay2
1Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur - 721302, India.
The journal of physical chemistry. B
|June 28, 2024
概括
分子动力学模拟揭示了人类多A结合蛋白 (PABPs) 如何与多ARNA结合. 蛋白质 蛋白质是蛋白质的组成部分.
科学领域:
- 分子生物学分子生物学
- 生物物理学的生物物理.
- 结构生物学是结构生物学.
背景情况:
- 蛋白质-RNA相互作用对于细胞过程如翻译和RNA运输至关重要.
- 多A结合蛋白 (PABPs) 保护mRNA多A尾从降解.
- 了解PABP-多分子的A) RNA复合体形成是解读基因调节的关键.
研究的目的:
- 用分子动力学模拟来研究复杂化过程中人类PABP和多A) RNA的构造变化.
- 阐明PABP-多元的结构基础 (A) RNA的识别和结合.
- 确定驱动该复合体热力学稳定的关键相互作用.
主要方法:
- 用分子动力学 (MD) 模拟来建模人类PABP与多ARNA之间的相互作用.
- 在复杂化之前和之后对蛋白质和RNA结构的构造分析.
- 具有约束力的自由能量计算,以确定相互作用的热力学驱动力.
主要成果:
- PABP的中间链接域在结合时从无序的线圈过渡到螺旋结构.
- 当与PABP复杂化时,多A) RNA从崩的线圈转变为硬的,延伸的形状.
- 鉴定出疏水性相互作用是结合自由能量和复合稳定性的主要贡献者.
结论:
- 这项研究揭示了复杂形成后PABP和多A) RNA的明显的构造变化.
- 在PABP中过渡到螺旋结构和在RNA中扩展的构造促进了稳定的复合物形成.
- 有利的疏水相互作用对PABP-poly (A) RNA复合体的热力学稳定性至关重要,为RNA结合蛋白机制提供了洞察力.
相关概念视频
RNA Structure
4.8K
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
4.8K
Cooperative Binding of Transcription Regulators
6.4K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.4K
Conjugated Proteins
18.3K
Simple proteins and protein complexes contain only amino acids. In contrast, many other proteins, called conjugated proteins, covalently bond with non-protein moieties.
Nucleoproteins are protein complexes that contain nucleic acids, categorized as deoxyribonucleoproteins (DNPs) or ribonucleoproteins (RNPs) respectively. The nucleosome is a typical example of a DNP where nuclear DNA is associated with histone proteins. The major antigen for the Covid-19 virus SARS-CoV is an RNP that is critical...
Nucleoproteins are protein complexes that contain nucleic acids, categorized as deoxyribonucleoproteins (DNPs) or ribonucleoproteins (RNPs) respectively. The nucleosome is a typical example of a DNP where nuclear DNA is associated with histone proteins. The major antigen for the Covid-19 virus SARS-CoV is an RNP that is critical...
18.3K
Eukaryotic RNA Polymerases
24.1K
RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
All three eukaryotic RNAPs require specific transcription factors, of which the...
24.1K
Ligand Binding and Linkage
4.8K
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...
4.8K
Cooperative Allosteric Transitions
7.9K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
7.9K


