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Ligand Binding Sites

Ligand Binding Sites

Ligand Binding and Linkage

Ligand Binding and Linkage

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...

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-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...

Ligand-gated Ion Channels

Ligand-gated Ion Channels

Ligand-gated ion channels are transmembrane proteins with a channel for ions to pass through and a binding site for a ligand. The channel opens only when a ligand attaches to the binding site.
Three Subfamilies of Ligand-gated Ion Channels
Ligand-gated ion channels fall into three subfamilies. The 'Cys-loop' includes the nicotinic acetylcholine receptors, γ-aminobutyric acid (GABA), glycine, and 5-hydroxytryptamine receptors. The second one is the 'Pore-loop' channels that...

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,...

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ProCogGraph: a graph-based mapping of cognate ligand domain interactions.

Matthew Crown¹, Matthew Bashton¹

¹Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom.

Bioinformatics Advances

|November 15, 2024

Summary

ProCogGraph is a new graph database mapping protein domain-cognate ligand interactions in the Protein Data Bank (PDB). It enhances understanding of evolution, protein design, and systematically annotates enzyme functions.

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Area of Science:

Biochemistry
Structural Biology
Bioinformatics

Background:

Understanding protein domain-cognate ligand interactions is crucial for evolutionary studies and protein design.
Existing databases for these interactions have not kept pace with the significant growth of the Protein Data Bank (PDB).
New computational tools for analyzing structural similarity and contacts have become available.

Purpose of the Study:

To present ProCogGraph, a novel graph database of domain-cognate ligand mappings derived from PDB structures.
To build upon previous work (PROCOGNATE) using data-driven methods to define interaction thresholds and modes.
To explore novel aspects of these interactions, including ligand chemical similarity and the impact of domain combinations on binding.

Main Methods:

Developed a graph database (ProCogGraph) to store and analyze domain-cognate ligand interactions from PDB data.
Employed data-driven approaches to establish thresholds for interaction modes.
Investigated chemical properties of bound ligands and the influence of domain pairings on binding specificity.

Main Results:

ProCogGraph systematically maps domain-cognate ligand interactions within the PDB.
The database reveals insights into the chemical similarity of cognate ligands and the role of domain combinations in binding.
ProCogGraph successfully enhances specificity for partial Enzyme Commission (EC) IDs by leveraging cognate ligand information.

Conclusions:

ProCogGraph provides a valuable resource for studying protein-ligand interactions and their evolutionary implications.
The database facilitates advancements in protein design and functional annotation.
ProCogGraph offers a systematic method for annotating enzyme functions using cognate ligand data.