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Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins
Shunsuke Teraguchi1, Ashwini Patil, Daron M Standley
1Laboratory of Host Defense, WPI Immunology Frontier Research Center (IFReC), Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan. teraguch@ifrec.osaka-u.ac.jp
Mammalian intrinsically disordered domains (IDDs) exhibit unique sequence patterns distinct from random sequences, suggesting biophysical constraints shape their evolution. These findings highlight specific sequence preferences within IDDs, particularly in immune response proteins.
Area of Science:
- Biochemistry
- Genomics
- Bioinformatics
Background:
- Mammalian intrinsically disordered domains (IDDs) play crucial roles in biological processes.
- Understanding the sequence characteristics of IDDs is essential for deciphering their function.
- This study investigates IDDs from mouse innate immune proteins and generic human genes.
Purpose of the Study:
- To characterize the amino acid abundance and local sequence motifs of mammalian IDDs.
- To compare IDD sequences with randomly generated sequences and ordered domains.
- To identify significant co-occurrences between IDD clusters and Pfam domains.
Main Methods:
- Analysis of amino acid abundance and local sequence motifs in IDDs.
- Comparison of IDD sequences against artificially generated random sequences.
- Clustering of IDDs based on amino acid composition.
- Statistical analysis of Pfam domain co-occurrence with IDD clusters.
Main Results:
- IDDs show significant deviation from random sequence distributions, comparable to ordered domains.
- Specific Pfam domains significantly co-occur with distinct IDD clusters (p < 0.01).
- Overrepresented motifs in immune-related IDDs are low-complexity fragments with amino acid repeats, lacking clear function.
Conclusions:
- Mammalian IDDs are restricted to a narrow sequence space, likely due to uncharacterized biophysical constraints.
- Further research into the functional interplay between IDDs and associated Pfam domains is warranted.
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