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

BMC Bioinformatics

Proceedings

Ariana Low¹  Victor Vai Tak Wong¹  Say Kong Ng¹  Kong-Peng Lam¹  Geoffrey Koh¹  Daren Poh¹  Vincent Vagenende¹  Yujian Yao¹  Dong-Yup Lee² 

[1] Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, 138668, Centros, Singapore;Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, 138668, Centros, Singapore;Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117576, Singapore;

关键词: Homology Modeling;    Virtual Screening;    Docking Study;    Carbohydrate Recognition Domain;    Surface Binding Site;   

DOI  :  10.1186/1471-2105-12-S14-S5

来源: Springer

【 摘 要 】

BackgroundIt 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.ResultsPresented 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Koh et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.