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首页> 外文期刊>Journal of Molecular Biology >Functional Sites in Protein Families Uncovered via an Objective and Automated Graph Theoretic Approach.
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Functional Sites in Protein Families Uncovered via an Objective and Automated Graph Theoretic Approach.

机译：通过客观和自动图论方法发现的蛋白质家族中的功能位点。

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摘要

We report a method for detection of recurring side-chain patterns (DRESPAT) using an unbiased and automated graph theoretic approach. We first list all structural patterns as sub-graphs where the protein is represented as a graph. The patterns from proteins are compared pair-wise to detect patterns common to a protein pair based on content and geometry criteria. The recurring pattern is then detected using an automated search algorithm from the all-against-all pair-wise comparison data of proteins. Intra-protein pattern comparison data are used to enable detection of patterns recurring within a protein. A method has been proposed for empirical calculation of statistical significance of recurring pattern. The method was tested on 17 protein sets of varying size, composed of non-redundant representatives from SCOP superfamilies. Recurring patterns in serine proteases, cysteine proteases, lipases, cupredoxin, ferredoxin, ferritin, cytochrome c, aspartoyl proteases, peroxidases, phospholipase A2, endonuclease, SH3 domain, EF-hand and lectins show additional residues conserved in the vicinity of the known functional sites. On the basis of the recurring patterns in ferritin, EF-hand and lectins, we could separate proteins or domains that are structurally similar yet different in metal ion-binding characteristics. In addition, novel recurring patterns were observed in glutathione-S-transferase, phospholipase A2 and ferredoxin with potential structural/functional roles. The results are discussed in relation to the known functional sites in each family. Between 2000 and 50,000 patterns were enumerated from each protein with between ten and 500 patterns detected as common to an evolutionarily related protein pair. Our results show that unbiased extraction of functional site pattern is not feasible from an evolutionarily related protein pair but is feasible from protein sets comprising five or more proteins. The DRESPAT method does not require a user-defined pattern, size or location of the pattern and therefore, has the potential to uncover new functional sites in protein families.
机译：我们报告了一种使用无偏自动图论方法检测重复侧链模式（DRESPAT）的方法。我们首先将所有结构模式列为子图，其中蛋白质以图表示。成对比较蛋白质的模式，以根据含量和几何标准检测蛋白质对共有的模式。然后使用自动搜索算法从蛋白质的所有相对所有配对比较数据中检测出重复模式。蛋白质内模式比较数据用于检测蛋白质内重复出现的模式。已经提出了一种用于经验计算重复模式的统计显着性的方法。该方法在17种不同大小的蛋白质上进行了测试，这些蛋白质由来自SCOP超家族的非冗余代表组成。丝氨酸蛋白酶，半胱氨酸蛋白酶，脂肪酶，铜氧还蛋白，铁氧还蛋白，铁蛋白，细胞色素c，天冬氨酸蛋白酶，过氧化物酶，磷脂酶A2，核酸内切酶，SH3结构域，EF-手和凝集素的重复模式显示在已知功能位点附近保守的其他残基。根据铁蛋白，EF-手和凝集素的重复模式，我们可以分离出结构相似但金属离子结合特性不同的蛋白质或结构域。另外，在谷胱甘肽-S-转移酶，磷脂酶A2和铁氧还蛋白中观察到新的重复模式，具有潜在的结构/功能作用。讨论了有关每个家族中已知功能位点的结果。从每种蛋白质中列举出2000至50,000种模式，其中10种至500种模式被检测为与进化相关的蛋白质对共有的模式。我们的结果表明，从进化相关的蛋白对中无偏倚地提取功能位点模式是不可行的，但是从包含五个或更多蛋白的蛋白集中是可行的。 DRESPAT方法不需要用户定义的图案，图案的大小或位置，因此具有发现蛋白质家族新功能位点的潜力。

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