Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli

CORC > 天津工业生物技术研究所 > 结构生物信息学和整合系统生物学实验室宋江宁 > 期刊论文

	Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli
	Chang, Catherine Ching Han 1,3; Li, Chen 3; Webb, Geoffrey I.4; Tey, BengTi 1,2; Song, Jiangning 3,4,6; Ramanan, Ramakrishnan Nagasundara 1,2,5
刊名	SCIENTIFIC REPORTS
	2016-03-02
卷号	6
英文摘要	Periplasmic expression of soluble proteins in Escherichia coli not only offers a much-simplified downstream purification process, but also enhances the probability of obtaining correctly folded and biologically active proteins. Different combinations of signal peptides and target proteins lead to different soluble protein expression levels, ranging from negligible to several grams per litre. Accurate algorithms for rational selection of promising candidates can serve as a powerful tool to complement with current trial-and-error approaches. Accordingly, proteomics studies can be conducted with greater efficiency and cost-effectiveness. Here, we developed a predictor with a two-stage architecture, to predict the real-valued expression level of target protein in the periplasm. The output of the first-stage support vector machine (SVM) classifier determines which second-stage support vector regression (SVR) classifier to be used. When tested on an independent test dataset, the predictor achieved an overall prediction accuracy of 78% and a Pearson's correlation coefficient (PCC) of 0.77. We further illustrate the relative importance of various features with respect to different models. The results indicate that the occurrence of dipeptide glutamine and aspartic acid is the most important feature for the classification model. Finally, we provide access to the implemented predictor through the Periscope webserver, freely accessible at http://lightning.med.monash.edu/periscope/.
WOS标题词	Science & Technology
类目[WOS]	Multidisciplinary Sciences
研究领域[WOS]	Science & Technology - Other Topics
关键词[WOS]	HIGH-LEVEL EXPRESSION ; TWIN-ARGININE TRANSLOCATION ; SUPPORT VECTOR MACHINE ; HUMAN GROWTH-HORMONE ; AMINO-ACID-SEQUENCE ; FOLDING RATES ; INCLUSION-BODY ; RECOMBINANT PROTEIN ; PENICILLIN ACYLASE ; BINDING PROTEIN
收录类别	SCI
语种	英语
WOS记录号	WOS:000371146600001
内容类型	期刊论文
源URL	[http://124.16.173.210/handle/834782/1538]
专题	天津工业生物技术研究所_结构生物信息学和整合系统生物学实验室宋江宁_期刊论文
作者单位	1.Monash Univ, Sch Engn, Chem Engn Discipline, Jalan Lagoon Selatan, Bandar Sunway 46150, Selangor, Malaysia 2.Monash Univ, Sch Engn, Adv Engn Platform, Jalan Lagoon Selatan, Bandar Sunway 46150, Selangor, Malaysia 3.Monash Univ, Dept Biochem & Mol Biol, Melbourne, Vic 3800, Australia 4.Monash Univ, Fac Informat Technol, Monash Ctr Data Sci, Melbourne, Vic 3800, Australia 5.Monash Univ, Sch Chem, Melbourne, Vic 3800, Australia 6.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Natl Engn Lab Ind Enzymes, Tianjin 300308, Peoples R China
推荐引用方式 GB/T 7714	Chang, Catherine Ching Han,Li, Chen,Webb, Geoffrey I.,et al. Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli[J]. SCIENTIFIC REPORTS,2016,6.
APA	Chang, Catherine Ching Han,Li, Chen,Webb, Geoffrey I.,Tey, BengTi,Song, Jiangning,&Ramanan, Ramakrishnan Nagasundara.(2016).Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli.SCIENTIFIC REPORTS,6.
MLA	Chang, Catherine Ching Han,et al."Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli".SCIENTIFIC REPORTS 6(2016).