Related Experiment Video
Updated: Sep 24, 2025
07:08
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
7.4K
DEPCOD: a tool to detect and visualize co-evolution of protein domains
Fei Ji1,2, Gracia Bonilla1,2, Rustem Krykbaev1
1Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
Nucleic Acids Research
|May 10, 2022
Summary
Analyzing protein domain conservation patterns reveals functional links between non-homologous proteins. The new DEPCOD web server (DEtection of Phylogenetically COrrelated Domains) aids in discovering these evolutionary relationships.
Area of Science:
- Evolutionary biology
- Bioinformatics
- Computational biology
Background:
- Proteins with similar evolutionary conservation patterns often share cellular functions or interactions.
- Previous methods analyzed whole proteins, overlooking domain-specific evolutionary pressures.
- Protein domains, rather than whole proteins, may provide a more accurate unit for detecting functional associations.
Purpose of the Study:
- To develop and present a novel web server, DEPCOD (DEtection of Phylogenetically COrrelated Domains), for identifying functional relationships between protein domains.
- To leverage phylogenetic sequence profiling at the domain level for enhanced detection of functional associations.
- To provide an interactive tool for exploring evolutionary conservation patterns of protein domains.
Main Methods:
- Analysis of sequence conservation patterns across the entire tree of life for individual protein domains from various organisms.
- Development of the DEPCOD web server to accept pre-defined domains or user sequences as queries.
- Comparison of conservation patterns on evolutionary scales including the whole tree of life and eukaryotic genomes.
Main Results:
- DEPCOD successfully detects functional relationships between non-homologous protein domains that were missed by whole-protein analysis.
- The web server displays top similarities, known protein interactions, shared complexes, and pathway enrichment for detected domains.
- Detailed visualization of the sources contributing to detected similarities is provided.
Conclusions:
- Analyzing protein domains as units of evolution significantly improves the detection of functional associations.
- DEPCOD offers a powerful, interactive platform for discovering novel functional links between protein domains based on phylogenetic profiles.
- The tool facilitates a deeper understanding of protein function and evolution by focusing on domain-level conservation patterns.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
11.6K
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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.6K
02:26Conservation of Protein Domains
3.2K
3.2K
01:57Protein Complexes with Interchangeable Parts
2.6K
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...
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...
2.6K
02:54Evolutionary Relationships through Genome Comparisons
6.2K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.2K
02:04Protein-protein Interfaces
13.8K
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...
13.8K
02:15Protein and Protein Structures
11.1K
11.1K