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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >Motif discovery with data mining in 3D protein structure databases: Discovery, validation and prediction of the u-shape zinc binding (HUF-ZINC) motif
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Motif discovery with data mining in 3D protein structure databases: Discovery, validation and prediction of the u-shape zinc binding (HUF-ZINC) motif

机译：通过3D蛋白质结构数据库中的数据挖掘进行母题发现：u形锌结合（ HUF-ZINC）主题的发现，验证和预测

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摘要

Data mining in protein databases, derivatives from more fundamental protein 3D structure and sequence databases, has considerable unearthed potential for the discovery of sequence motif-structural motif-function relationships as the finding of the U-shape (Huf-Zinc) motif, originally a small student's project, exemplifies. The metal ion zinc is critically involved in universal biological processes, ranging from protein-DNA complexes and transcription regulation to enzymatic catalysis and metabolic pathways. Proteins have evolved a series of motifs to specifically recognize and bind zinc ions. Many of these, so called zinc fingers, are structurally independent globular domains with discontinuous binding motifs made up of residues mostly far apart in sequence. Through a systematic approach starting from the BRIX structure fragment database, we discovered that there exists another predictable subset of zinc-binding motifs that not only have a conserved continuous sequence pattern but also share a characteristic local conformation, despite being included in totally different overall folds. While this does not allow general prediction of all Zn binding motifs, a HMM-based web server, Huf-Zinc, is available for prediction of these novel, as well as conventional, zinc finger motifs in protein sequences. The Huf-Zinc webserver can be freely accessed through this URL.
机译：蛋白质数据库中的数据挖掘（来自更基本的蛋白质3D结构和序列数据库的派生）具有巨大的挖掘潜力，可发现序列基序-结构基序-功能关系，如发现U型（Huf-Zinc）基序，最初是小学生的项目，就是一个例证。金属离子锌至关重要地参与了普遍的生物过程，从蛋白质-DNA复合物和转录调控到酶催化和代谢途径。蛋白质已经进化出一系列基序，可以特异性识别并结合锌离子。这些中的许多，所谓的锌指，是结构上独立的球状结构域，具有不连续的结合基序，由不连续的残基组成，残基在序列上相距甚远。通过从BRIX结构片段数据库开始的系统方法，我们发现存在锌结合基序的另一个可预测子集，尽管其包含在完全不同的总折叠中，它们不仅具有保守的连续序列模式，而且还具有特征性的局部构象。 。虽然这不能全面预测所有Zn结合基序，但是基于HMM的Web服务器Huf-Zinc可用于预测这些新的以及常规的蛋白质序列中的锌指基序。可以通过此URL自由访问Huf-Zinc网络服务器。

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