Integrative analysis workflow for the structural and functional classification of C-type lectins

• Published in: BMC bioinformatics Vol. 12 Suppl 14; no. Suppl 14; p. S5
• Main Authors: Koh, Geoffrey, Low, Ariana, Poh, Daren, Yao, Yujian, Ng, Say Kong, Wong, Victor Vai Tak, Vagenende, Vincent, Lam, Kong-Peng, Lee, Dong-Yup
• Format: Journal Article
• Language: English
• Published: England BioMed Central 14.12.2011; BioMed Central Ltd; BMC
• Subjects: Algorithms; Amino acid sequence; Animals; Automation; Binding sites; Bioinformatics; Carbohydrates; Colleges & universities; Computer programs; Conferences; Filters; Genomes; Humans; Immune system; Informatics; Lectins; Lectins, C-Type - chemistry; Ligands; Models, Molecular; Polysaccharides; Polysaccharides - chemistry; Proceedings; Proteins; Rural development; Sequence Analysis, Protein; Software; Structure-function relationships; Technological change; Workflow
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-12-S14-S5

It is important to understand the roles of C-type lectins in the immune system due to their ubiquity and diverse range of functions in animal cells. It has been observed that currently confirmed C-type lectins share a highly conserved domain known as the C-type carbohydrate recognition domain (CRD). Using the sequence profile of the CRD, an increasing number of putative C-type lectins have been identified. Hence, it is highly needed to develop a systematic framework that enables us to elucidate their carbohydrate (glycan) recognition function, and discover their physiological and pathological roles. Presented herein is an integrated workflow for characterizing the sequence and structural features of novel C-type lectins. Our workflow utilizes web-based queries and available software suites to annotate features that can be found on the C-type lectin, given its amino acid sequence. At the same time, it incorporates modeling and analysis of glycans - a major class of ligands that interact with C-type lectins. Thereafter, the results are analyzed together with context-specific knowledge to filter off unlikely predictions. This allows researchers to design their subsequent experiments to confirm the functions of the C-type lectins in a systematic manner. The efficacy and usefulness of our proposed immunoinformatics workflow was demonstrated by applying our integrated workflow to a novel C-type lectin -CLEC17A - and we report some of its possible functions that warrants further validation through wet-lab experiments.