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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...

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 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,...

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,...

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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Related Experiment Video

Updated: Jun 28, 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

Annotating proteins with generalized functional linkages.

Richard Llewellyn¹, David S Eisenberg

¹Department of Energy Institute for Genomics and Proteomics, and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.

Proceedings of the National Academy of Sciences of the United States of America

|November 14, 2008

Summary

A new computational method, Generalized Functional Linkages (GFL), improves protein function annotation by analyzing protein interaction networks. GFL enhances accuracy by integrating diverse data, overcoming limitations of homology-based methods.

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

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Published on: June 17, 2012

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Last Updated: Jun 28, 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

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Area of Science:

Bioinformatics
Computational Biology
Molecular Biology

Background:

Accurate protein function annotation is crucial but lags behind genome sequencing due to experimental limitations.
Current homology-based annotation methods are error-prone for divergent sequences and can corrupt databases.

Purpose of the Study:

To develop a computational method, Generalized Functional Linkages (GFL), for accurate protein function assignment.
To improve biomolecular annotation by integrating non-homology-based data and functional linkages.

Main Methods:

GFL utilizes a Bayesian framework to arbitrate among biological process annotations.
It incorporates protein-protein interaction network data, including indirect and high-throughput interactions, quantified by the zorch algorithm.
The method accounts for varying linkage strengths, annotation quality, and similarity, integrating cellular location and molecular function data.

Main Results:

GFL successfully predicted biological processes for proteins in Saccharomyces cerevisiae.
The method demonstrated a 20% improvement in annotation accuracy compared to majority voting.
GFL effectively utilizes functional linkages derived from protein-protein interaction networks.

Conclusions:

Generalized Functional Linkages (GFL) offers a robust computational approach to enhance protein function annotation.
This method addresses key limitations of homology-based annotation, improving data accuracy in biomolecular databases.
GFL provides a significant advancement in predicting protein functions, particularly when experimental data is scarce.