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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
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Comparison of protein repeat classifications based on structure and sequence families
Lisanna Paladin1, Silvio C E Tosatto2
1Department of Biomedical Sciences, University of Padua, viale G. Colombo 3, 35121 Padova, Italy.
Biochemical Society Transactions
|October 31, 2015
Summary
Protein tandem repeats (TRs) have diverse structures, often challenging to identify. This study compares structural classifications in RepeatsDB with sequence-based Pfam families, finding mostly one-to-one mappings for these common protein motifs.
Area of Science:
- Structural biology
- Bioinformatics
- Protein science
Background:
- Tandem repeats (TRs) are prevalent in proteins, exhibiting diverse structures and functions.
- Recognizing TRs from sequence data alone can be challenging.
- The RepeatsDB database offers a structural classification of TRs, complementing sequence-based classifications like Pfam.
Purpose of the Study:
- To compare the structural classification of tandem repeats in RepeatsDB with sequence-based families in Pfam.
- To identify consistencies and discrepancies between structural and sequence-based repeat classifications.
- To highlight specific examples of tandem repeat types with differing classifications.
Main Methods:
- Comparative analysis of tandem repeat classifications between RepeatsDB and Pfam.
- Mapping structural classes from RepeatsDB to corresponding Pfam families and clans.
- Detailed examination of exceptions, including leucine-rich repeats (LRRs) and α-solenoids.
Main Results:
- A predominantly one-to-one correspondence was observed between RepeatsDB structural classes and Pfam repeat families/clans.
- Identified specific tandem repeat types, such as LRRs and α-solenoids, that do not map straightforwardly.
- The study provides insights into the relationship between protein structure and sequence-based evolutionary relationships for tandem repeats.
Conclusions:
- Structural and sequence-based classifications of tandem repeats largely agree.
- Discrepancies highlight the complexity of classifying protein repeats and the need for integrated approaches.
- Understanding these relationships is crucial for functional and evolutionary studies of tandem repeats.
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