Analysis of sequence repeats of proteins in the PDB

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• 作者：David Mary Rajathei ; Samuel Selvaraj
• 关键词：Sequence repeats ; PDB ; Structure ; Function ; Domain
• 刊名：Computational Biology and Chemistry
• 出版年：December, 2013
• 年：2013
• 卷：47
• 期：Complete
• 页码：156-166
• 全文大小：1932 K

文摘

Internal repeats in protein sequences play a significant role in the evolution of protein structure and function. Applications of different bioinformatics tools help in the identification and characterization of these repeats. In the present study, we analyzed sequence repeats in a non-redundant set of proteins available in the Protein Data Bank (PDB). We used RADAR for detecting internal repeats in a protein, PDBeFOLD for assessing structural similarity, PDBsum for finding functional involvement and Pfam for domain assignment of the repeats in a protein. Through the analysis of sequence repeats, we found that identity of the sequence repeats falls in the range of 20-40% and, the superimposed structures of the most of the sequence repeats maintain similar overall folding. Analysis sequence repeats at the functional level reveals that most of the sequence repeats are involved in the function of the protein through functionally involved residues in the repeat regions. We also found that sequence repeats in single and two domain proteins often contained conserved sequence motifs for the function of the domain.