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Protein-protein Interfaces

Protein-protein Interfaces

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Networks

Protein Networks

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,...

Conserved Binding Sites

Conserved Binding Sites

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...

Protein Organization

Protein Organization

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....

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

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Related Experiment Video

Updated: Jan 6, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Towards a phylogenetically informed approach to solving protein-protein interactions.

Chun Shen Lim^1,2,3, Peter Mace¹, Peter C Fineran^2,3,4,5

¹Department of Biochemistry, Faculty of Biomedical Sciences, University of Otago, Dunedin, 9016, New Zealand.

Biochemical Society Transactions

|December 5, 2025

Summary

Protein-protein interactions (PPIs) are vital for cellular functions but current databases lack diversity. A phylogenetically informed approach can improve PPI discovery and accuracy for researchers.

Keywords:

artificial intelligence evolutionary conserved protein–protein interactions machine learning protein complex prediction

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Last Updated: Jan 6, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Published on: July 14, 2015

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A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Published on: July 18, 2013

Area of Science:

Molecular Biology
Bioinformatics
Systems Biology

Background:

Protein-protein interactions (PPIs) regulate all cellular activities.
Cells precisely control PPIs spatially and temporally to prevent pathway dysregulation.
Extensive research focuses on discovering and curating PPIs into databases for scientific use.

Purpose of the Study:

To evaluate the heterogeneity and species bias in current PPI databases.
To identify limitations in existing PPI data for research applications.
To propose a novel approach for comprehensive PPI landscape analysis.

Main Methods:

Analysis of existing protein-protein interaction databases.
Assessment of data heterogeneity and species distribution within PPI datasets.
Development of a phylogenetically informed strategy for PPI investigation.

Main Results:

PPI databases exhibit significant heterogeneity and are heavily concentrated on a limited number of species.
This bias restricts the comprehensive understanding of reliable PPIs.
Existing data limitations negatively impact machine-learning model accuracy and experimental design.

Conclusions:

Current PPI databases present challenges for researchers due to data bias and heterogeneity.
Computational and experimental methods can address these data gaps.
A phylogenetically informed approach is recommended for robust PPI discovery and validation.