Helical structure motifs made searchable for functional peptide design

Cheng-Yu Tsai, Emmanuel Oluwatobi Salawu, Hongchun Li, Guan-Yu Lin, Ting-Yu Kuo, Liyin Voon, Adarsh Sharma, Kai-Di Hu, Yi-Yun Cheng, Sobha Sahoo, Lutimba Stuart, Chih-Wei Chen, Yuan-Yu Chang, Yu-Lin Lu, Simai Ke, Christopher Llynard D. Ortiz, Bai-Shan Fang, Chen-Chi Wu, Chung-Yu Lan (), Hua-Wen Fu () and Lee-Wei Yang ()
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Cheng-Yu Tsai: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Emmanuel Oluwatobi Salawu: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Hongchun Li: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Guan-Yu Lin: Institute of Molecular and Cellular Biology, National Tsing Hua University
Ting-Yu Kuo: Institute of Molecular and Cellular Biology, National Tsing Hua University
Liyin Voon: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Adarsh Sharma: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Kai-Di Hu: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Yi-Yun Cheng: Praexisio Taiwan Inc.
Sobha Sahoo: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Lutimba Stuart: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Chih-Wei Chen: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Yuan-Yu Chang: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Yu-Lin Lu: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Simai Ke: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Christopher Llynard D. Ortiz: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
Bai-Shan Fang: Xiamen University
Chen-Chi Wu: National Taiwan University Hospital
Chung-Yu Lan: Institute of Molecular and Cellular Biology, National Tsing Hua University
Hua-Wen Fu: Institute of Molecular and Cellular Biology, National Tsing Hua University
Lee-Wei Yang: Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: Abstract The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/ .

Date: 2022
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DOI: 10.1038/s41467-021-27655-0

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