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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
The effects of incomplete protein interaction data on structural and evolutionary inferences
Eric de Silva1, Thomas Thorne, Piers Ingram
1Theoretical Genomics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London, UK. e.desilva@imperial.ac.uk <e.desilva@imperial.ac.uk>
BMC Biology
|November 4, 2006
Summary
Protein interaction networks are incomplete, leading to biased analyses. Researchers must account for network sampling properties to accurately understand biological systems and avoid misinterpretations.
Area of Science:
- Systems Biology
- Bioinformatics
- Network Science
Background:
- Current protein interaction network datasets represent only partial coverage of an organism's proteome.
- Previous analyses have often overlooked the potential biases introduced by using incomplete network data.
Purpose of the Study:
- To demonstrate the necessity of explicitly considering network sampling properties in all analyses.
- To evaluate the impact of incomplete network data on network statistics, network motifs, and functional/evolutionary inferences.
Main Methods:
- Analysis of the yeast protein interaction network using various network statistics.
- Simulation of random and non-random sampling schemes to assess data incompleteness.
- Evaluation of effects independent of inherent noise in protein interaction data.
Main Results:
- Incomplete network data significantly affects network properties, particularly network motifs.
- The observed effects are robust and independent of inherent noise in protein interaction data.
- Bias in network analysis is almost unavoidable when using small, partial datasets.
Conclusions:
- Ignoring the incomplete nature of protein interaction network data leads to inevitable bias.
- Previous studies relying on partial network data may require reassessment.
- Accurate understanding of biological systems necessitates addressing network incompleteness from the start.
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02:26Protein 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,...
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,...
02:26Protein 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,...
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,...
01:24Protein 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.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview
02:04Protein-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...
02:04Protein-Protein Interfaces
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