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Ligand Binding Sites

Ligand Binding Sites

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...

Ligand Binding Sites

Ligand Binding Sites

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...

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 analyses the...

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 the...

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 polypeptide...

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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Related Experiment Video

Updated: Jun 2, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Network approach for capturing ligand-induced subtle global changes in protein structures.

Anshul Sukhwal¹, Moitrayee Bhattacharyya, Saraswathi Vishveshwara

¹Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

Acta Crystallographica. Section D, Biological Crystallography

|May 6, 2011

Summary

This summary is machine-generated.

Graph theory reveals subtle protein structural changes upon ligand binding. This network analysis method captures global rewiring and aids in rigorous protein structure comparison.

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

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Measuring Interactions of Globular and Filamentous Proteins by Nuclear Magnetic Resonance Spectroscopy (NMR) and Microscale Thermophoresis (MST)

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy

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Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Ligand-induced conformational changes are crucial for protein function.
Elucidating the amino acid networks responsible for these changes globally is challenging.
Subtle side-chain conformational variations upon ligand binding are often missed by conventional methods like root-mean-square deviation (r.m.s.d.).

Purpose of the Study:

To present a network representation and analysis of protein structures for capturing conformational variations.
To apply graph theory metrics for rigorous comparison of protein structures.
To quantify ligand-induced global rewiring in protein structures.

Main Methods:

Representing protein structures as networks.
Utilizing generalized graph theoretical metrics (e.g., cliques, communities) for structural analysis.
Applying the method to high-resolution crystal structures of serine proteases (S1A family).

Main Results:

The network approach effectively captures both drastic and subtle conformational variations in atomistic detail.
Graph theory metrics provide a rigorous way to compare protein structures and quantify structural differences.
Ligand-induced global rewiring in protein structures was successfully quantified using network parameters.

Conclusions:

Network representation and graph theory offer an efficient tool for analyzing protein structures.
This approach provides meaningful insights into global structural reorganizations upon perturbation.
The method is valuable for rigorous structural comparison and understanding subtle ligand-induced changes.