在外膜β-桶中计数线程
Samuel Lim1, Tejaswi Nimmagadda1, Alaa Khamis2
1Computational Biology Program, The University of Kansas, 2030 Becker Dr., Lawrence, KS USA 66047.
Biophysical journal
|March 11, 2026
概括
一个新的算法准确地计算了细菌外膜中的β-桶蛋白链. 该工具增强了对蛋白质结构和功能的理解,有助于未来的预测和设计研究.
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.
- 生物化学 生化学
背景情况:
- 贝塔桶蛋白在细菌外膜中是必不可少的,它调解了运输和结构完整性.
- 准确确定β-桶链数对于理解蛋白质功能至关重要,但由于结构复杂性而具有挑战性.
研究的目的:
- 改进PolarBearal工具,以准确,大规模识别β-桶链号.
- 创建一个全面的数据集的外膜β-桶结构与标记的链数.
主要方法:
- 开发了一个更新的算法,集成了余量之间的向量角度,键距离和链连接.
- 应用了算法来分析来自AlphaFold2数据库的571,760个预测的外膜β-桶结构.
主要成果:
- 实现了97%的准确性在分配链数的β-桶结构.
- 创建了一个大型数据集,可以评估不同外膜蛋白类型的链数同质性.
结论:
- 精致的PolarBearal算法为大型数据集提供了准确的β-桶链标签.
- 由此产生的数据提供了对β桶分布和进化模式的见解,支持蛋白质结构预测和设计.
相关概念视频
Multi-pass Transmembrane Proteins and β-barrels
6.8K
In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...
6.8K
Structure of Porins
4.1K
Mitochondria, chloroplasts, and gram-negative bacteria have transmembrane, beta-barrel proteins called porins to mediate the free diffusion of ions and metabolites across the membrane. Mitochondrial porin precursors contain conserved amino acid sequences called beta signals at their C-terminal. Beta signals have a motif of PoXGXXHyXHy (Po-Polar, X-Any amino acid, G-Glycine, Hy-LargeHydrophobic), which are crucial for precursor recognition to initiate precursor assembly. Beta-barrel...
4.1K
Porin Insertion in the Outer Mitochondrial Membrane
5.1K
Porins are beta-barrel proteins translocated to the mitochondrial outer membrane through the TOM complex into the intermembrane space. Porin precursors bind TIM chaperones within the intermembrane space and are guided to the Sorting and Assembly Machinery complex or SAM complex on the outer mitochondrial membrane.
Three models describe the assembly of porins by the SAM complex and their insertion into the outer membrane. Model 1 suggests that porins are assembled outside the SAM channel as the...
Three models describe the assembly of porins by the SAM complex and their insertion into the outer membrane. Model 1 suggests that porins are assembled outside the SAM channel as the...
5.1K
Assembly of the Lipid Bilayer in the ER
4.4K
Biological membranes are more than just a barrier separating cell cytoplasm from the outside environment. They are highly dynamic and help maintain the integrity and physiological stability of the cells as well as membrane-bound organelles. Membranes also play vital roles in cell-to-cell and intracellular communication.
A large chunk of any biological membrane is composed of phospholipids. These lipids have a heterogeneous distribution across different subcellular organelles and even between...
A large chunk of any biological membrane is composed of phospholipids. These lipids have a heterogeneous distribution across different subcellular organelles and even between...
4.4K
Single-Strand DNA Binding Proteins
17.0K
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...
17.0K
Tail-anchoring of Proteins in the ER Membrane
4.0K
Tail-anchored, or TA, proteins are estimated to make up to 3-5% of membrane proteins found in the eukaryotic cell. Such proteins have a single transmembrane domain located approximately 30 amino acid residues upstream from the C-terminal end. As a result, the signal recognition particle (SRP) cannot guide a TA protein to the ER membrane for cotranslational insertion. Hence, they are integrated into the ER membrane post-translationally using their C-terminal end as the anchor. TA proteins...
4.0K


