Gromiha M Michael
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.
Biophys Chem. 2005 Aug 22;117(1):65-71. doi: 10.1016/j.bpc.2005.04.005.
Discriminating outer membrane proteins (OMPs) from other folding types of globular and membrane proteins is an important problem for predicting their secondary and tertiary structures and detecting outer membrane proteins from genomic sequences as well. In this work, we have systematically analyzed the distribution of amino acid residues in the sequences of globular and outer membrane proteins with several motifs, such as AB, A**B, etc. We observed that the motifs EL, AK and LE occur frequently in globular proteins while SS, NS and RD predominantly occur in OMPs. We have devised a statistical method based on frequently occurring motifs in globular and OMPs and obtained an accuracy of 96% and 82% for correctly identifying OMPs and excluding globular proteins, respectively. Further, we noticed that the motifs of transmembrane helical (TMH) proteins are different from that of OMPs. While IA, IL and LI prefer in TMH proteins SS, NS and NN predominantly occur in OMPs. The information about the occurrence of AB motifs in TMH and OMPs could discriminate them with an accuracy of 80% for excluding OMPs and 100% for identifying OMPs. The influence of protein size and structural class for discrimination is discussed.
区分外膜蛋白（OMP）与其他折叠类型的球状蛋白和膜蛋白是预测其二级和三级结构以及从基因组序列中检测外膜蛋白的一个重要问题。在这项工作中，我们系统地分析了球状蛋白和外膜蛋白序列中氨基酸残基的分布，并使用了几种基序，如AB、A**B等。我们观察到，基序EL、AK和LE在球状蛋白中频繁出现，而SS、NS和RD主要出现在外膜蛋白中。我们基于球状蛋白和外膜蛋白中频繁出现的基序设计了一种统计方法，对于正确识别外膜蛋白和排除球状蛋白，分别获得了96%和82%的准确率。此外，我们注意到跨膜螺旋（TMH）蛋白的基序与外膜蛋白的不同。虽然IA、IL和LI在TMH蛋白中更常见，但SS、NS和NN主要出现在外膜蛋白中。关于TMH和外膜蛋白中AB基序出现情况的信息可以区分它们，排除外膜蛋白的准确率为80%，识别外膜蛋白的准确率为100%。本文还讨论了蛋白质大小和结构类别对区分的影响。
