Related Experiment Video
Updated: Nov 23, 2025
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
69.4K
Assessing the low complexity of protein sequences via the low complexity triangle
Pablo Mier1, Miguel A Andrade-Navarro1
1Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany.
Plos One
|December 30, 2020
Summary
This study introduces the low complexity triangle, a novel method to characterize proteins with low complexity regions (LCRs). This tool helps analyze sequence composition and identify repeat patterns in proteomes.
Area of Science:
- Proteomics
- Bioinformatics
- Structural Biology
Background:
- Proteins with low complexity regions (LCRs) exhibit unusual sequence and structural properties.
- LCRs deviate from typical amino acid composition and folding rules of globular regions.
- Characterizing LCRs involves assessing sequence repeatability and local compositional bias.
Purpose of the Study:
- To develop and validate a method for quantifying and representing protein low complexity.
- To analyze proteome-wide low complexity signatures.
- To provide a user-friendly tool for LCR analysis.
Main Methods:
- Combined local measures of sequence repeatability (RES algorithm) and amino acid fraction.
- Utilized a 'low complexity triangle' representation for visualizing low complexity data.
- Applied the method to diverse proteomes, protein datasets, and individual proteins.
Main Results:
- Proteomes display unique signatures within the low complexity triangle, correlating with sequence complexity.
- The low complexity triangle effectively represents compositional bias and sequence features.
- Homorepeats, direpeats, and globular regions occupy distinct positions in the triangle.
Conclusions:
- The low complexity triangle is a suitable method for representing protein and dataset low complexity.
- This approach aids in characterizing LCRs and quantifying degenerate tandem repeats.
- The developed web tool (LCT) facilitates LCR analysis for researchers.
Related Concept Videos
02:26Protein Networks
4.3K
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,...
4.3K
01:57Protein Complexes with Interchangeable Parts
2.0K
2.0K
01:57Protein Complexes with Interchangeable Parts
2.7K
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...
2.7K
02:26Conservation of Protein Domains Over Different Proteins
13.7K
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...
13.7K
01:22Protein Folding
124.7K
Overview
124.7K
02:04Protein-protein Interfaces
14.2K
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...
14.2K