Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes
Michail Yu Lobanov1, Oxana V Galzitskaya
1Group of Bioinformatics, Institute of Protein Research Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
Plos One
|November 11, 2011
Summary
This study compiles the largest database of 141 intrinsically disordered protein patterns. These patterns occur more frequently in eukaryotic proteomes than bacterial ones, offering insights into molecular recognition.
Area of Science:
- Biochemistry and Structural Biology
- Bioinformatics and Computational Biology
- Genomics and Proteomics
Background:
- Intrinsically disordered regions (IDRs) are crucial for molecular recognition but their determinants are not fully understood.
- A comprehensive database of disordered patterns is needed to analyze their occurrence and distribution.
Purpose of the Study:
- To construct the largest database of intrinsically disordered protein patterns.
- To analyze the occurrence and distribution of these patterns in eukaryotic and bacterial proteomes.
- To understand the physicochemical and structural determinants of intrinsically disordered regions.
Main Methods:
- Construction of a clustered Protein Data Bank (PDB) with high chain identity (≥75%).
- Compilation of a database of 141 disordered patterns using simple selection rules.
- Analysis of pattern occurrence in 97 eukaryotic and 26 bacterial proteomes.
- Calculation of correlation coefficients between pattern occurrences across different kingdoms and phyla.
Main Results:
- The largest database of 141 intrinsically disordered protein patterns was compiled.
- Disordered patterns were found to be more prevalent in eukaryotic proteomes compared to bacterial proteomes.
- Frequently occurring patterns exhibited low complexity (e.g., PPPPP, GGGGG).
- Correlation coefficients were generally higher within kingdoms than between them.
Conclusions:
- The compiled database provides a valuable resource for studying intrinsically disordered protein patterns.
- Disordered patterns show differential distribution across eukaryotic and bacterial proteomes, suggesting distinct functional roles.
- Low-complexity sequences are common among frequently occurring disordered patterns, highlighting their structural significance.
Related Concept Videos
02:18Intrinsically Disordered Proteins
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
02:18Intrinsically Disordered Proteins
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
02:26Protein Networks
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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,...
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02:26Conservation of Protein Domains Over Different Proteins
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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.
01:22Protein Folding
Overview