Active site identification through geometry-based and sequence profile-based calculations: Burial of catalytic clefts
Active site identification through geometry-based and sequence profile-based calculations: Burial of catalytic clefts
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DOI：
10.1016/j.jmb.2005.04.018
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发表时间：
2005-06-10
影响因子：
5.6
通讯作者：
Warwicker, J
中科院分区：
文献类型：
--
作者：
Greaves, R;Warwicker, J
对在体积上均匀带电的蛋白质进行静电学计算有助于区分酶和非酶。对于已知的酶，此类方法在77%的测试集中能将活性位点定位在酶表面的5%范围内。我们现在报告，去除介电边界可将活性位点定位提高到80%，酶与非酶之间的最佳区分度约为80%的特异性和80%的敏感性。这种计算可量化溶剂可及区域的掩埋程度。许多被错误归类为非酶的真正的酶，其活性位点位于亚基边界。在基于单体的计算中会遗漏这些位点。在此活性/结合位点掩埋的背景下研究了催化性和非催化性抗体。虽然催化性抗体平均而言其活性位点掩埋程度略高于非催化性抗体，但这些值通常比非抗体酶的要小，这可能是它们相对较低的周转率的原因。当基于序列谱的权重取代均匀电荷分布时，活性位点定位的预测进一步提高，从而可以评估掩埋程度和氨基酸保守性的组合。在测试集中，对于最佳的谱权重方案，93%的活性位点能定位在5%范围内。在一个单独的验证集中，等效值是89%在5%范围内。对结构基因组学蛋白质进行了酶/非酶和酶功能位点预测，结果表明这些蛋白质中绝大多数是非酶。(c) 2005 Elsevier Ltd.保留所有权利。
Electrostatics calculations with proteins that are uniformly charged over volume can aid enzyme/non-enzyme discrimination. For known enzymes, such methods locate active sites to within 5% on the enzyme surface, in 77% of a test set. We now report that removing the dielectric boundary improves active site location to 80%, with optimal discrimination between enzymes and non-enzymes of around 80% specificity and 80% sensitivity. This calculation quantifies burial of solvent-accessible regions. Many of the true enzymes incorrectly assigned as non-enzymes have active sites at subunit boundaries. These are missed in monomer-based calculations. Catalytic and non-catalytic antibodies are studied in this context of active/binding site burial. Whilst catalytic antibodies, on average, have marginally higher active site burial than non-catalytic antibodies, these values are generally smaller than for non-antibody enzymes, possibly contributing to their relatively low turnover. Prediction of active site location improves further when sequence profile-based weights replace the uniform charge distribution, so that a combination of burial and amino acid conservation is assessed. Accuracy rises to 93% of active sites to within 5%, in the test set, for the optimal profile weights scheme. The equivalent value in a separate validation set is 89% to within 5%. Enzyme/non-enzyme and enzyme functional site predictions are made for structural genomics proteins, suggesting that a substantial majority of these are non-enzymes. (c) 2005 Elsevier Ltd. All rights reserved.