通过使用AlphaFold和NMR化学转移扰乱数据的贝叶斯模型选择对蛋白质聚化合物的综合建模
Tiburon L Benavides1, Gaetano T Montelione2
1Department of Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.
bioRxiv : the preprint server for biology
|September 30, 2024
概括
我们开发了CSP-Rank,这是一种使用增强采样和NMR数据来建模蛋白质-化合物的新计算方法. 这种方法提炼结构以更好地与实验观测相一致,有助于生物学功能研究.
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:
- 蛋白质-的相互作用对于生物过程至关重要.
- 实验确定蛋白质-质复杂结构是具有挑战性的.
- 计算方法需要实验验证.
研究的目的:
- 介绍CSP-Rank,一种针对蛋白质-化合物的综合建模方法.
- 将AlphaFold2 (AF2) 增强采样与使用NMR CSP数据的贝叶斯形状选择结合起来.
- 为了提高蛋白质-相互作用的计算模型的准确性.
主要方法:
- 使用AlphaFold2 (AF2) 进行增强采样.
- 基于核磁共振 (NMR) 化学转移扰乱 (CSP) 数据的应用贝叶斯形态选择.
- 纳入AF2信心指标和实验性NMR数据 (CSP和NOE) 进行模型改进.
主要成果:
- 仅AF2就与CSP实验数据有很好的一致性.
- CSP-Rank 始终在生产结构组合,并且与NMR可观测值有更好的一致性.
- 用两个系统的独立NOE NMR数据验证了CSP选择的模型.
结论:
- CSP-Rank是一种用于蛋白质-化合物的新型整合建模方法.
- 该方法通过将计算预测与实验性NMR数据相结合来提高结构准确性.
- CSP-Rank对于理解蛋白质-相互作用和生物功能具有广泛的影响.
相关概念视频
Protein Organization
6.3K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
The primary structure of a protein is its amino acid sequence....
6.3K
Protein Networks
3.9K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K
Protein-protein Interfaces
12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
Protein Folding
7.8K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
7.8K


