Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
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DOI：
10.1093/nar/gkg922
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发表时间：
2003-12-15
影响因子：
14.9
通讯作者：
Thornton, JM
中科院分区：
文献类型：
--
作者：
Jones, S;Shanahan, HP;Thornton, JM
检测蛋白质结构表面 DNA 结合位点的方法对于功能注释非常重要。这项工作描述了对 DNA 结合蛋白表面残留斑块的分析，以及开发一种利用这些表面斑块的单一特征来预测 DNA 结合位点的方法。最初分析表面斑块和 DNA 结合位点的可及性、静电势、残留倾向、疏水性和残留保守性。由此可见，DNA 结合位点总体上属于具有最大正静电分数的前 10% 的斑块。这一知识导致了一种预测方法的发展，其中选择表面残基斑块，以排除具有负静电分数的残基。该方法用于对 56 个非同源 DNA 结合蛋白的数据集进行预测。对 68% 的数据集做出了正确的预测。
A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set.