膜内和膜上的蛋白质复合体的组合,具有预测的空间布局约束
Charles Christoffer1, Kannan Harini2, Gupta Archit3
1Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA.
Journal of molecular biology
|February 9, 2024
概括
Mem-LZerD 是一种用于模拟膜蛋白复合体的新计算工具. 它准确地预测了细胞膜内和细胞膜上的蛋白质相互作用,有助于结构生物学研究.
科学领域:
- 结构生物学 结构生物学
- 计算生物学 计算生物学
- 生物物理学的生物物理.
背景情况:
- 膜蛋白对细胞功能至关重要,但它们的结构数据有限.
- 了解膜蛋白复杂相互作用对于破译细胞机制至关重要.
- 膜蛋白复合体的实验性结构确定具有挑战性.
研究的目的:
- 介绍Mem-LZerD,一个新的刚体对接算法,用于模拟膜蛋白复合体.
- 为了提高精度,利用先进的膜建模和蛋白质对接技术.
- 为预测膜蛋白相互作用提供计算工具.
主要方法:
- Mem-LZerD是基于LZerD蛋白质对接算法.
- 它使用由预测的膜高度和倾斜角度所限制的几何哈希.
- 模型得分结合了膜插入的能量,以准确预测.
主要成果:
- 在一个基准数据集中,Mem-LZerD成功实现了61.9%的跨膜复合体的无结合对接.
- 它成功地模拟了79.5%的新型跨膜复合体和16.3%的外周膜蛋白质复合体.
- 包括非盲目导向在内的外围目标建模成功率提高到58.7%.
结论:
- Mem-LZerD有效地模拟了多种膜蛋白-蛋白质复合体,性能优于以前的方法.
- 生成的模型适用于下游分子动力学模拟.
- Mem-LZerD是推动膜蛋白结构研究的宝贵工具.
更多相关视频
09:30Analyzing Dynamic Protein Complexes Assembled On and Released From Biolayer Interferometry Biosensor Using Mass Spectrometry and Electron Microscopy
Published on: August 6, 2018
9.4K
10:01Directed Assembly of Elastin-like Proteins into defined Supramolecular Structures and Cargo Encapsulation In Vitro
Published on: April 8, 2020
5.9K
相关概念视频
Assembly of Signaling Complexes
5.8K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
5.8K
Protein Complex Assembly
10.6K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Many viruses self-assemble into a fully functional unit using the infected host cell to...
10.6K
Mechanisms of Membrane Domain Formation
3.0K
Different physical properties of lipids and proteins allow them to localize and form distinct islands or domains in the membrane. Some membrane domains are formed due to protein-protein interactions, whereas others are formed due to the presence of specific lipids such as sphingolipids and sterols—for example, large proteins, such as bacteriorhodopsin, aggregate and create distinct domains.
Another mechanism for membrane domain formation involves membrane proteins interacting with...
Another mechanism for membrane domain formation involves membrane proteins interacting with...
3.0K
Protein Translocation Machinery on the ER Membrane
4.6K
The translocon complex situated on the ER membrane is the main gateway for the protein secretory pathway. It facilitates the transport of nascent peptides into the ER lumen and their insertion into the ER membrane.
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the...
Sec61 protein conducting channel
In eukaryotes, the translocon complex comprises a core heterotrimeric translocator channel called the Sec61 complex. This channel includes three transmembrane proteins, Sec61α, Sec61β, and Sec61γ, and is the largest subunit of the...
4.6K
Coat Assembly and GTPases
3.5K
Vesicles incorporate different coat protein subunits in different cell locations, which changes the properties of the coat, such as the shape and geometry of the transport vesicles. Thus, vesicle coat proteins also play a significant role in cargo selection.
Coat assembly depends on the local availability of phosphatidylinositol phosphates or PIPs and GTP-binding proteins. Adaptor proteins, which link the coat proteins to the membrane, bind to these PIPs and play a crucial role in controlling...
Coat assembly depends on the local availability of phosphatidylinositol phosphates or PIPs and GTP-binding proteins. Adaptor proteins, which link the coat proteins to the membrane, bind to these PIPs and play a crucial role in controlling...
3.5K
Protein Diffusion in the Membrane
4.4K
Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
4.4K
