Lipke P N, Chen M H, de Nobel H, Kurjan J, Kahn P C
Department of Biological Sciences, Hunter College of the City University of New York, New York 10021, USA.
Protein Sci. 1995 Oct;4(10):2168-78. doi: 10.1002/pro.5560041023.
The Saccharomyces cerevisiae adhesion protein alpha-agglutinin is expressed by cells of alpha mating type. On the basis of sequence similarities, alpha-agglutinin has been proposed to contain variable-type immunoglobulin-like (IgV) domains. The low level of sequence similarity to IgV domains of known structure made homology modeling using standard sequence-based alignment algorithms impossible. We have therefore developed a secondary structure-based method that allowed homology modeling of alpha-aggulutinin domain III, the domain most similar to IgV domains. The model was assessed and where necessary refined to accommodate information obtained by biochemical and molecular genetic approaches, including the positions of a disulfide bond, glycosylation sites, and proteolytic sites. The model successfully predicted surface exposure of glycosylation and proteolytic sites, as well as identifying residues essential for binding activity. One side of the domain was predicted to be covered by carbohydrate residues. Surface accessibility and volume packing analyses showed that the regions of the model that have greatest sequence dissimilarity from the IgV consensus sequence are poorly structured in the biophysical sense. Nonetheless, the utility of the model suggests that these alignment and testing techniques should be of general use for building and testing of models of proteins that share limited sequence similarity with known structures.
酿酒酵母黏附蛋白α-凝集素由α交配型细胞表达。基于序列相似性，有人提出α-凝集素含有可变型免疫球蛋白样（IgV）结构域。与已知结构的IgV结构域的序列相似性较低，使得使用基于标准序列比对算法的同源建模变得不可能。因此，我们开发了一种基于二级结构的方法，该方法允许对α-凝集素结构域III进行同源建模，该结构域与IgV结构域最相似。对该模型进行了评估，并在必要时进行了优化，以纳入通过生化和分子遗传学方法获得的信息，包括二硫键、糖基化位点和蛋白水解位点的位置。该模型成功预测了糖基化和蛋白水解位点的表面暴露情况，并确定了结合活性所必需的残基。预测该结构域的一侧被碳水化合物残基覆盖。表面可及性和体积堆积分析表明，该模型中与IgV共有序列序列差异最大的区域在生物物理意义上结构较差。尽管如此，该模型的实用性表明，这些比对和测试技术应普遍用于构建和测试与已知结构序列相似性有限的蛋白质模型。
