无序蛋白质的酸化调整了局部和全球的分子内相互作用
Emery T Usher1,2, Martin J Fossat3, Alex S Holehouse1,2
1Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
bioRxiv : the preprint server for biology
|June 25, 2024
概括
固有无序蛋白区域 (IDR) 的酸化改变了它们的结构和功能. 新的模拟方法准确地模拟了这些变化,揭示了酸化如何影响蛋白质构成组合.
科学领域:
- 生物化学和分子生物学
- 计算生物学 计算生物学
- 结构生物学 结构生物学
背景情况:
- 蛋白质的翻译后修改,如酸化,调节细胞功能.
- 内在无序的蛋白质区域 (IDR) 是通过酸化调节的关键调节元素.
- 了解酸化对IDR形态组合的影响是解读功能结果的关键.
研究的目的:
- 开发和验证用于模拟化IDR的计算工具.
- 调查酸化如何影响IDRs的构造组合.
- 探索酸化位点与IDR形状变化之间的关系.
主要方法:
- 在ABSINTH连续溶剂模型中,使用OPLS参数对素 (pSer) 和三 (pThr) 的全原子蒙特卡洛模拟.
- 模拟短 (<20个残留量) 和长 (>80个残留量) 的-IDR.
- 分析形态组合的指标,如旋转半径,短暂的螺旋性和持久长度.
主要成果:
- 模拟表明,对于四种经过充分研究的-IDRs,它们与已发表的实验结果几乎有数量一致.
- 酸化被证明可以改变IDR的形状组合,影响局部和全球特征.
- 对多酸化IDR的探索揭示了多种位组合对形状的影响.
结论:
- 开发的模拟方法准确地模拟了IDR形状集中的酸化诱导的变化.
- 酸化通过改变序列化学,净电荷,电荷模式和分子内部相互作用来调节IDR行为.
- 这些发现为IDR酸化的功能后果提供了宝贵的见解.
相关概念视频
Phosphorylation
50.3K
The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...
50.3K
Protein Kinases and Phosphatases
13.1K
Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
13.1K
Intrinsically Disordered Proteins
17.8K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
17.8K
Covalently Linked Protein Regulators
6.8K
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
These groups modify specific amino acids in a protein....
6.8K
Disassembly of Intermediate Filaments
2.1K
Intermediate filaments (IFs) do not undergo spontaneous disassembly. Enzymes, kinases, and phosphatases add and remove phosphates from specific sites to regulate their disassembly. The IF concentration in the cytoplasm also regulates the disassembly. If the concentration crosses a threshold, it activates the protein kinases in the vicinity, allowing the phosphorylation of IFs.
Keratin proteins, found at the cell periphery near cell junctions, undergo a cycle of assembly and disassembly. In Type...
Keratin proteins, found at the cell periphery near cell junctions, undergo a cycle of assembly and disassembly. In Type...
2.1K
Amplifying Signals via Enzymatic Cascade
8.5K
When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze...
8.5K


