SOSUIsignal: Software System for Prediction of Signal Peptide and Membrane Protein
SOSUIsignal: Software System for Prediction of Signal Peptide and Membrane Protein
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SOSUIsignal：信号肽和膜蛋白预测软件系统
DOI：
10.11234/gi1990.11.414
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发表时间：
2000
期刊：
影响因子：
--
通讯作者：
S. Mitaku
中科院分区：
文献类型：
--
作者：
M. Gomi;F. Akazawa;S. Mitaku
膜蛋白占整个基因组的20%~35%，在生物体中发挥着受体和通道等多种不可缺少的作用。由于膜蛋白的实验结构分析在实验上是非常困难的，因此迫切需要计算工具来从氨基酸序列中提取膜蛋白的结构信息。在此之前，我们开发了一个膜蛋白预测系统SOSUI[1]，它提供了关于跨膜螺旋的存在、数量和序列区域的信息。然而，这个系统不能预测跨膜片段的拓扑结构，也不能预测信号肽的存在。信号肽位于分泌蛋白或分泌蛋白的氨基酸序列的氨基端。信号肽通常和大多数跨膜螺旋一样疏水。它们的主要功能是将氨基酸序列的羧基传递到细胞的外部介质。在羧基部分转移后，信号肽从剩余的多肽中去掉。然而，一些被称为信号锚的疏水片段并没有被切断。因此，对于信号肽的预测，我们必须预测信号序列，这些信号序列具有足够的疏水性，足以穿透细胞膜，还需要区分信号肽和信号锚。在这项工作中，我们开发了一个系统，它结合了一个新的信号肽预测系统和以前的SOSUI系统。建立了两种氨基酸指数，用于信号序列预测和信号肽与信号锚的区分。该系统的输入数据仅为氨基酸序列，输出为信号肽的存在、膜蛋白的识别以及信号肽和跨膜螺旋区域的预测。信号肽的预测准确率在80%以上。
Membrane proteins, which occupies the proportion between 20 and 35% of whole genomes, play various roles indispensable for organisms such as receptor and channels. Since experimental structural analysis of membrane proteins is experimentally very difficult, computational tools are strongly required for extracting the information about the structure of membrane proteins from amino acid sequences. Previously, we developed a membrane protein prediction system SOSUI [1], which provides the information about the existence, the number and the sequence regions of transmembrane helices. However, this system cannot predict the topology of transmembrane segments nor the existence of signal peptides. A signal peptide is located at the amino terminal of an amino acid sequence of a secretion protein or a secretion protein. Signal peptides are usually as hydrophobic as most transmembrane helices. Their main function is to transmit the carboxyl side of an amino acid sequence to the external media of a cell. Signal peptides are cut off from the rest polypeptide after the transfer of the carboxyl part. However, some of hydrophobic segments, which are called signal anchors, are not cut off. Therefore, for the prediction of signal peptides, we have to predict the signal sequences, which are hydrophobic enough to be penetrated into membrane, and also to discriminate signal peptides from signal anchors. In this work, we develop a system, which combines a novel system for the signal peptide prediction with the previous system SOSUI. Two kinds of amino acid indices were developed for the signal sequence prediction and the discrimination between signal peptides and signal anchors. The input data of the system is amino acid sequences alone and the output is the existence of a signal peptide, the discrimination of membrane proteins and the prediction of the region of a signal peptide as well as transmembrane helices. The accuracy of signal peptide prediction was better than 80%.