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通过搜索受限结构域预测β-桶状膜蛋白

Prediction of beta-barrel membrane proteins by searching for restricted domains.

作者信息

Mirus Oliver, Schleiff Enrico

机构信息

Botanisches Institut der Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany.

出版信息

BMC Bioinformatics. 2005 Oct 14;6:254. doi: 10.1186/1471-2105-6-254.

DOI:10.1186/1471-2105-6-254
PMID:16225682
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1280923/
Abstract

BACKGROUND

The identification of beta-barrel membrane proteins out of a genomic/proteomic background is one of the rapidly developing fields in bioinformatics. Our main goal is the prediction of such proteins in genome/proteome wide analyses.

RESULTS

For the prediction of beta-barrel membrane proteins within prokaryotic proteomes a set of parameters was developed. We have focused on a procedure with a low false positive rate beside a procedure with lowest false prediction rate to obtain a high certainty for the predicted sequences. We demonstrate that the discrimination between beta-barrel membrane proteins and other proteins is improved by analyzing a length limited region. The developed set of parameters is applied to the proteome of E. coli and the results are compared to four other described procedures.

CONCLUSION

Analyzing the beta-barrel membrane proteins revealed the presence of a defined membrane inserted beta-barrel region. This information can now be used to refine other prediction programs as well. So far, all tested programs fail to predict outer membrane proteins in the proteome of the prokaryote E. coli with high reliability. However, the reliability of the prediction is improved significantly by a combinatory approach of several programs. The consequences and usability of the developed scores are discussed.

摘要

背景

从基因组/蛋白质组背景中识别β-桶状膜蛋白是生物信息学中快速发展的领域之一。我们的主要目标是在全基因组/蛋白质组分析中预测此类蛋白。

结果

针对原核生物蛋白质组中β-桶状膜蛋白的预测，开发了一组参数。我们重点关注了一个假阳性率低的程序以及一个预测错误率最低的程序，以确保预测序列具有高确定性。我们证明，通过分析长度受限区域，可以提高β-桶状膜蛋白与其他蛋白之间的区分度。将开发的参数集应用于大肠杆菌的蛋白质组，并将结果与其他四种已描述的程序进行比较。

结论

对β-桶状膜蛋白的分析揭示了存在一个确定的插入膜的β-桶状区域。该信息现在也可用于改进其他预测程序。到目前为止，所有测试程序都无法高度可靠地预测原核生物大肠杆菌蛋白质组中的外膜蛋白。然而，通过几个程序的组合方法，预测的可靠性得到了显著提高。讨论了所开发分数的影响和可用性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/b7b6611af1a3/1471-2105-6-254-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/0074e6dfc66f/1471-2105-6-254-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/9508c21e2140/1471-2105-6-254-2.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/6bf78d5663ba/1471-2105-6-254-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/d97d4298e0d0/1471-2105-6-254-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/b7b6611af1a3/1471-2105-6-254-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/0074e6dfc66f/1471-2105-6-254-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/9508c21e2140/1471-2105-6-254-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/8b239099c1d8/1471-2105-6-254-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/6bf78d5663ba/1471-2105-6-254-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/d97d4298e0d0/1471-2105-6-254-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ed88/1280923/b7b6611af1a3/1471-2105-6-254-6.jpg

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