PolarProtPred: predicting apical and basolateral localization of transmembrane proteins using putative short linear motifs and deep learning

Author:

Dobson Laszlo12,Zeke András1,Tusnády Gábor E1ORCID

Affiliation:

1. Institute of Enzymology, Research Centre for Natural Sciences, Budapest 1117, Hungary

2. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany

Abstract

Abstract Motivation Cell polarity refers to the asymmetric organization of cellular components in various cells. Epithelial cells are the best-known examples of polarized cells, featuring apical and basolateral membrane domains. Mounting evidence suggests that short linear motifs play a major role in protein trafficking to these domains, although the exact rules governing them are still elusive. Results In this study we prepared neural networks that capture recurrent patterns to classify transmembrane proteins localizing into apical and basolateral membranes. Asymmetric expression of drug transporters results in vectorial drug transport, governing the pharmacokinetics of numerous substances, yet the data on how proteins are sorted in epithelial cells is very scattered. The provided method may offer help to experimentalists to identify or better characterize molecular networks regulating the distribution of transporters or surface receptors (including viral entry receptors like that of COVID-19). Availability and implementation The prediction server PolarProtPred is available at http://polarprotpred.ttk.hu. Supplementary information Supplementary data are available at Bioinformatics online.

Funder

Hungarian Research and Developments Fund

EMBO

Momentum Grant of the Hungarian Academy of Sciences

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Reference46 articles.

1. DeepLoc: prediction of protein subcellular localization using deep learning;Almagro Armenteros;Bioinformatics,2017

2. SignalP 5.0 improves signal peptide predictions using deep neural networks;Armenteros;Nat. Biotechnol,2019

3. From cells to organs: building polarized tissue;Bryant;Nat. Rev. Mol. Cell Biol,2008

4. Quantitative proteomics of MDCK cells identify unrecognized roles of clathrin adaptor AP-1 in polarized distribution of surface proteins;Caceres;Proc. Natl. Acad. Sci. USA,2019

5. Coronavirus entry and release in polarized epithelial cells: a review;Cong;Rev. Med. Virol,2014

Cited by 1 articles. 订阅此论文施引文献 订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3