Zhai Yufeng, Saier Milton H
Department of Biology, University of California at San Diego, La Jolla, California 92093-0116, USA.
Protein Sci. 2002 Sep;11(9):2196-207. doi: 10.1110/ps.0209002.
Many outer membrane proteins (OMPs) in Gram-negative bacteria possess known beta-barrel three-dimensional (3D) structures. These proteins, including channel-forming transmembrane porins, are diverse in sequence but exhibit common structural features. We here report computational analyses of six outer membrane proteins of known 3D structures with respect to (1) secondary structure, (2) hydropathy, and (3) amphipathicity. Using these characteristics, as well as the presence of an N-terminal targeting sequence, a program was developed allowing prediction of integral membrane beta-barrel proteins encoded within any completely sequenced prokaryotic genome. This program, termed the beta-barrel finder (BBF) program, was used to analyze the proteins encoded within the Escherichia coli genome. Out of 4290 sequences examined, 118 (2.8%) were retrieved. Of these, almost all known outer membrane proteins with established beta-barrel structures as well as many probable outer membrane proteins were identified. This program should be useful for predicting the occurrence of outer membrane proteins in bacteria with completely sequenced genomes.
革兰氏阴性菌中的许多外膜蛋白（OMPs）都具有已知的β-桶状三维（3D）结构。这些蛋白质，包括形成通道的跨膜孔蛋白，在序列上各不相同，但呈现出共同的结构特征。我们在此报告对六种已知3D结构的外膜蛋白进行的关于（1）二级结构、（2）亲水性和（3）两亲性的计算分析。利用这些特征以及N端靶向序列的存在，开发了一个程序，可用于预测任何完全测序的原核基因组中编码的整合膜β-桶状蛋白。这个程序被称为β-桶状蛋白查找器（BBF）程序，用于分析大肠杆菌基因组中编码的蛋白质。在所检查的4290个序列中，检索到了118个（2.8%）。其中，几乎所有已知具有确定β-桶状结构的外膜蛋白以及许多可能的外膜蛋白都被识别出来。该程序对于预测具有完全测序基因组的细菌中外膜蛋白的存在应该是有用的。
