Combining protein evolution and secondary structure
Combining protein evolution and secondary structure
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DOI：
10.1093/oxfordjournals.molbev.a025627
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发表时间：
1996-05-01
影响因子：
10.7
通讯作者：
Jones, DT
中科院分区：
文献类型：
--
作者：
Thorne, JL;Goldman, N;Jones, DT
引入了结合蛋白质二级结构和氨基酸替代的进化模型。它允许对排列蛋白序列进行可能分析，并且不需要这些序列的基本二级（或第三级）结构。该模型的一个组成部分描述了沿蛋白质序列的二级结构的组织，另一个指定了每个类别的二级结构的进化过程。具有已知二级结构的蛋白质数据库用于估计代表这两个组件的模型参数。系统发育是模型的第三个组成部分，可以从感兴趣的数据集中估算。例如，我们采用我们的模型来分析一组蔗糖合酶序列。对于蔗糖合酶的进化，参数引导方法表明我们的模型在统计上比忽略二级结构的模型更可取。
An evolutionary model that combines protein secondary structure and amino acid replacement is introduced. It allows likelihood analysis of aligned protein sequences and does not require the underlying secondary (or tertiary) structures of these sequences to be known. One component of the model describes the organization of secondary structure along a protein sequence and another specifies the evolutionary process for each category of secondary structure. A database of proteins with known secondary structures is used to estimate model parameters representing these two components. Phylogeny, the third component of the model, can be estimated from the data set of interest. As an example, we employ our model to analyze a set of sucrose synthase sequences. For the evolution of sucrose synthase, a parametric bootstrap approach indicates that our model is statistically preferable to one that ignores secondary structure.