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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation
Alan L Kwan1, Susan K Dutcher, Gary D Stormo
1Dept. Computer Science & Engineering, Washington University in St. Louis, St. Louis, Missouri, alan@ural.wustl.edu.
Proceedings. IEEE International Symposium on Bioinformatics and Bioengineering
|June 10, 2011
Summary
Automated Protein Annotation by Coordinate Evolution (APACE) enhances protein function prediction by analyzing co-evolution patterns. This novel phylogenetic profile comparison method improves accuracy and scalability for large-scale comparative genomics.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Automated protein characterization is crucial but limited by homology-based methods when protein family functions are unknown.
- Existing methods struggle with characterizing proteins beyond sequence similarity and analyzing large datasets.
Purpose of the Study:
- To introduce a novel phylogenetic profile comparison (PPC) method, Automated Protein Annotation by Coordinate Evolution (APACE), for automated protein characterization.
- To improve the detection of functionally related proteins and enable analysis of larger comparative genomic datasets.
Main Methods:
- Developed APACE, a novel PPC method incorporating a new approach for normalizing similarity scores across multiple species.
- Automated protein characterization based on co-evolution patterns with proteins lacking sequence similarity.
Main Results:
- APACE successfully recapitulated the deep eukaryotic phylogeny and quantified branch lengths.
- Demonstrated superior detection of functionally related proteins compared to existing methods.
- Showcased successful application to large-scale comparative genomic problems where other methods fail.
Conclusions:
- APACE offers a powerful new approach for automated protein annotation beyond sequence homology.
- The method enhances functional inference and is scalable for complex genomic analyses.
- APACE advances the field of comparative genomics and protein function prediction.
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...
02:26Protein 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,...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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...
02:26Conservation 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...