Jove
Visualize
联系我们
JoVE
x logofacebook logolinkedin logoyoutube logo
关于 JoVE
概览领导团队博客JoVE 帮助中心
作者
出版流程编辑委员会范围与政策同行评审常见问题投稿
图书馆员
用户评价订阅访问资源图书馆顾问委员会常见问题
研究
JoVE JournalMethods CollectionsJoVE Encyclopedia of Experiments存档
教育
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab Manual教师资源中心教师网站
使用条款与条件
隐私政策
政策

相关概念视频

Protein-protein Interfaces02:04

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 Networks02:26

Protein Networks

4.0K
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,...
4.0K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
Antibody Structure01:10

Antibody Structure

60.2K
Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
60.2K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

13.0K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
13.0K

您也可能阅读

相关文章

通过共同作者、期刊和引用图与本文相关的文章。

排序
Same author

A Paired Database of Predicted and Experimental Protein Peptide Binding Information.

Scientific data·2025
Same author

Extracellular Peptide-Ligand Dimerization Actuator Receptor Design for Reversible and Spatially Dosed 3D Cell-Material Communication.

ACS synthetic biology·2024
Same author

Analysis of how antigen mutations disrupt antibody binding interactions toward enabling rapid and reliable antibody repurposing.

mAbs·2024
Same author

Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody-Protein Complexes.

Proteins·2024
Same author

An Orthogonal Workflow of Electrochemical, Computational, and Thermodynamic Methods Reveals Limitations of Using a Literature-Reported Insulin Binding Peptide in Biosensors.

ACS omega·2024
Same author

Analysis of conformational stability of interacting residues in protein binding interfaces.

Protein engineering, design & selection : PEDS·2023

相关实验视频

Updated: Jul 12, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

1.9K

开发抗体与蛋白质结合相互作用的相似性矩阵.

Sumaiya Islam1, Robert J Pantazes1

  • 1Department of Chemical Engineering, Auburn University, Auburn, Alabama, United States of America.

PloS one
|October 26, 2023
PubMed
概括

研究人员通过分析抗体-抗原复合物的突变开发了新的蛋白质-蛋白质相互作用相似性矩阵. 这些矩阵对于计算蛋白质科学至关重要,为结合接口提供了洞察力,并指导了未来的蛋白质工程工作.

科学领域:

  • 计算型蛋白质科学 计算型蛋白质科学
  • 结构生物学是结构生物学.
  • 生物信息学是一种生物信息学.

背景情况:

  • 使用像AlphaFold和RoseTTAFold这样的工具来预测蛋白质结构,已经推进了计算蛋白质科学.
  • 蛋白质序列相似性信息是这些成功的关键,它依赖于已建立的相似性矩阵.
  • 预测蛋白质-蛋白质相互作用是自然的延伸,但目前缺乏相互作用相似度矩阵.

研究的目的:

  • 为抗体与蛋白质相互作用开发新的相似性矩阵.
  • 为预测和分析蛋白质-蛋白质结合接口提供基础.

主要方法:

  • 对384个抗体-蛋白质抗原复合体进行突变分析.
  • 对所有其他氨基酸的抗体和抗原中的突变关键残留物.
  • 使用CHARMM,珀和罗塞塔力场计算相互作用能量的变化.

主要成果:

  • 构建了六个相互作用相似性矩阵 (抗体和抗原的三个力场).
  • 确定了共同点 (芳香/充电残留突变是有害的) 和跨力场的差异 (例如,罗塞塔对血清突变的耐受性).
  • 新的相互作用矩阵彼此的相似性比现有的蛋白质序列相似性矩阵更高.

更多相关视频

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.7K
Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

5.0K

相关实验视频

Last Updated: Jul 12, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

1.9K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.7K
Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
08:31

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

5.0K

结论:

  • 开发的相互作用相似度矩阵是特定于力场的.
  • 这些矩阵可以指导蛋白质工程和计算蛋白质设计中的决策.
  • 它们代表了理解和预测蛋白质与蛋白质相互作用的重要一步.