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Updated: May 28, 2026
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Algorithms to detect multiprotein modularity conserved during evolution
Luqman Hodgkinson1, Richard M Karp
1Division of Computer Science and the Center for Computational Biology, University of California, Berkeley, CA 94720, USA. luqman@icsi.berkeley.edu
Summary
We developed Produles, a fast algorithm to find conserved protein modules in cells, crucial for understanding evolution and cell biology. This method identifies essential, stable protein groups across species.
Area of Science:
- Computational biology
- Evolutionary biology
- Systems biology
Background:
- Understanding protein interactions is key to cell function and evolution.
- Identifying stable, conserved multiprotein modules is algorithmically challenging.
- Existing methods for detecting conserved protein modules have limitations.
Purpose of the Study:
- To define a novel measure of modularity for biological networks (interactomes).
- To present Produles, a linear-time algorithm for detecting evolutionarily conserved multiprotein modules.
- To introduce new evaluation metrics and analyze algorithm performance on interactomics data.
Main Methods:
- Defined a new measure of modularity for protein-protein interaction networks.
- Developed Produles, a linear-time algorithm for identifying conserved modules.
- Introduced graph-theoretic evaluation measures and analyzed algorithm performance.
- Conducted randomization experiments and computational experiments on human and fly interactomes.
Main Results:
- Produles offers improved running time and theoretical guarantees compared to previous algorithms.
- The new evaluation measures revealed anomalies in prior algorithm performance.
- Conserved modularity is a fundamental characteristic of biological interactomes.
- Approximately 10% of proteins in human and fly interactomes participate in conserved modules.
Conclusions:
- Produles is an efficient and effective tool for detecting conserved multiprotein modules.
- The study provides new insights into interactomics data and module detection.
- Conserved protein modules play a significant role in the evolution of cellular organization.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:26Conservation of Protein Domains
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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,...
01:57Protein Complexes with Interchangeable Parts
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
01:57Protein Complexes with Interchangeable Parts
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...