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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,...

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-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...

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...

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.

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Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Published on: July 6, 2014

Literature-curated protein interaction datasets.

Michael E Cusick¹, Haiyuan Yu, Alex Smolyar

¹Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA. michael_cusick@dfci.harvard.edu

|January 1, 2009

Summary

High-quality protein interaction datasets are crucial for understanding biological mechanisms. However, current curation of these interactome networks may contain errors, impacting research reliability.

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Area of Science:

Proteomics
Systems Biology
Bioinformatics

Background:

Understanding protein-protein interactions (PPIs) is vital for elucidating biological mechanisms.
High-quality interactome datasets are essential for network analysis and protein research.
Existing curated PPI data may not meet expected quality standards.

Purpose of the Study:

To evaluate the quality of curated protein interaction data from scientific literature.
To assess the reliability of current interactome network databases.
To identify potential errors in the curation process of PPI experiments.

Main Methods:

Systematic review and evaluation of published protein interaction experiment curation.
Comparative analysis of different curation strategies and their impact on data quality.
Assessment of error rates and consistency in curated PPI datasets.

Main Results:

Curation of protein interaction experiments is prone to errors.
The quality of commonly assumed protein interactome data may be lower than anticipated.
Inconsistencies were identified in the reporting and curation of PPI data.

Conclusions:

Current methods for curating protein-protein interaction data require improvement.
The reliability of existing interactome datasets may be compromised by curation errors.
Further efforts are needed to enhance the accuracy and quality of PPI data for biological research.