標題: The fragment transformation method to detect the protein structural motifs
作者: Lu, CH
Lin, YS
Chen, YC
Yu, CS
Chang, SY
Hwang, JK
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
關鍵字: local structure alignment;DNA-binding proteins;structural motif;structural genomics
公開日期: 15-May-2006
摘要: To identify functional structural motifs from protein structures of unknown function becomes increasingly important in recent years due to the progress of the structural genomics initiatives. Although certain structural patterns such as the Asp-His-Ser catalytic triad are easy to detect because of their conserved residues and stringently constrained geometry, it is usually more challenging to detect a general structural motifs like, for example, the beta beta alpha-metal binding motif, which has a much more variable conformation and sequence. At present, the identification of these motifs usually relies on manual procedures based on different structure and sequence analysis tools. In this study, we develop a structural alignment algorithm combining both structural and sequence information to identify the local structure motifs. We applied our method to the following examples: the beta beta alpha-metal binding motif and the treble clef motif. The beta beta alpha-metal binding motif plays an important role in nonspecific DNA interactions and cleavage in host defense and apoptosis. The treble clef motif is a zinc-binding motif adaptable to diverse functions such as the binding of nucleic acid and hydrolysis of phosphodiester bonds. Our results are encouraging, indicating that we can effectively identify these structural motifs in an automatic fashion. Our method may provide a useful means for automatic functional annotation through detecting structural motifs associated with particular functions.
URI: http://dx.doi.org/10.1002/prot.20904
http://hdl.handle.net/11536/12244
ISSN: 0887-3585
DOI: 10.1002/prot.20904
期刊: PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume: 63
Issue: 3
起始頁: 636
結束頁: 643
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