Related Experiment Video
Updated: Mar 10, 2026
06:50
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
2.7K
Specificity of broad protein interaction surfaces for proteins with multiple binding partners
Nobuyuki Uchikoga1, Yuri Matsuzaki2, Masahito Ohue3
1Department of Physics, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo 112-8551, Japan.
Biophysics and Physicobiology
|December 8, 2016
Summary
Understanding protein-protein interactions (PPIs) is crucial. This study reveals that the composition of interacting amino acid residue pairs, analyzed via broad interaction profiles (BIPs), is key to determining specific protein interaction surfaces.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Protein-protein interactions (PPIs) are fundamental to cellular processes.
- Hub proteins interact with multiple ligands, complicating PPI prediction.
- Existing methods often fail to capture the specificity of interactions due to varying protein surfaces.
Purpose of the Study:
- To understand protein-protein interaction (PPI) mechanisms by focusing on distinct interaction surfaces.
- To investigate the specificity of protein interactions for proteins with multiple binding partners.
- To develop a method for differentiating true binding partners based on interaction surface characteristics.
Main Methods:
- Rigid-body docking was used to generate decoy structures representing potential interaction interfaces.
- Broad Interaction Profiles (BIPs) were created by aggregating interaction profiles from decoys.
- Cluster analysis was applied to assess the specificity of BIPs for true binding partners.
- Two types of BIPs were analyzed: sequence-based (BIP-seqs) and amino acid pair composition-based (BIP-AAs).
Main Results:
- Broad Interaction Profiles (BIPs) were introduced to characterize differences in protein interaction surfaces.
- Specificity of BIPs was evaluated for alpha-chymotrypsin, actin, and cyclin-dependent kinase 2.
- BIPs derived from the composition of interacting amino acid residue pairs (BIP-AAs) demonstrated higher specificity than sequence-based BIPs (BIP-seqs).
Conclusions:
- The composition of interacting amino acid residue pairs is sufficient for determining the properties of protein interaction surfaces.
- BIP-AAs offer a more specific approach to understanding and predicting protein-protein interactions.
- This work provides insights into the specificity of PPIs, particularly for proteins with multiple interaction partners.
Keywords:
hub proteininteraction profilepostdocking processprotein-protein interactionrigid-body docking processMore Related Videos
06:01Extracellular Protein Microarray Technology for High Throughput Detection of Low Affinity Receptor-Ligand Interactions
Published on: January 7, 2019
7.7K
12:53Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics
Published on: July 6, 2014
32.1K
Related Concept Videos
02:04Protein-protein Interfaces
14.9K
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...
14.9K
02:04Protein-Protein Interfaces
4.6K
4.6K
02:26Protein Networks
4.6K
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,...
4.6K
01:49Conserved Binding Sites
5.3K
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...
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...
5.3K
02:40Ligand Binding Sites
15.6K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
15.6K
00:49Ligand Binding and Linkage
5.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
5.8K