A new method to model membrane protein structure based on silent amino acid substitutions
A new method to model membrane protein structure based on silent amino acid substitutions
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DOI：
10.1002/prot.1102
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发表时间：
2001-08-15
影响因子：
2.9
通讯作者：
Arkin, IT
中科院分区：
文献类型：
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作者：
Briggs, JAG;Torres, J;Arkin, IT
准确建模膜蛋白的重要性不能被夸大，而不是通过实验解决其结构的困难。然而，通常，建模过程（例如，全局搜索分子动力学）产生几个可能的候选者，而不是指向一个单一的模型。在此，我们提出了一种基于一般假设的新方法来选择候选模型，即从进化保护数据或诱变分析中确定的变异中存在的沉默氨基酸取代不会影响天然结构的稳定性，但可能会破坏也发现的非天然结构的稳定性。这一假设的证据已经在两种同型二聚体，人糖蛋白A和人CD3-zeta （t细胞受体的一种成分）的α -螺旋跨膜结构域上进行了测试。对于这两种蛋白质，使用所有变体只鉴定出一种结构。对于糖蛋白A，这种结构实际上与NAM实验确定的结构相同。我们提出了CD3-zeta跨膜结构域的模型，该模型与基于诱变、同源建模和二硫键存在的预测一致。我们的实验表明，这种方法可以仅基于广泛可用的进化守恒数据来预测跨膜结构域结构。(C) 2001 Wiley-Liss, Inc。
The importance of accurately modeling membrane proteins cannot be overstated, in lieu of the difficulties in solving their structures experimentally. Often, however, modeling procedures (e.g., global searching molecular dynamics) generate several possible candidates rather then pointing to a single model. Herein we present a new approach to select among candidate models based on the general hypothesis that silent amino acid substitutions, present in variants identified from evolutionary conservation data or mutagenesis analysis, do not affect the stability of a native structure but may destabilize the non-native structures also found. The proof of this hypothesis has been tested on the alpha -helical transmembrane domains of two homodimers, human glycophorin A and human CD3-zeta, a component of the T-cell receptor. For both proteins, only one structure was identified using all the variants. For glycophorin A, this structure is virtually identical to the structure determined experimentally by NAM. We present a model for the transmembrane domain of CD3-zeta that is consistent with predictions based on mutagenesis, homology modeling, and the presence of a disulfide bond. Our experiments suggest that this method allows the prediction of transmembrane domain structure based only on widely available evolutionary conservation data. (C) 2001 Wiley-Liss, Inc.