Publication Details

EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities

HON Jiří, BORKO Simeon, ŠTOURAČ Jan, PROKOP Zbyněk, BEDNÁŘ David, ZENDULKA Jaroslav, MARTÍNEK Tomáš and DAMBORSKÝ Jiří. EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. Nucleic Acids Research, vol. 48, no. 1, 2020, pp. 104-109. ISSN 1362-4962.
Czech title
EnzymeMiner: automatické dolování rozpustných enzymů s různorodými strukturami, katalytickými vlastnostmi a stabilitou
Type
journal article
Language
english
Authors
Hon Jiří, Ing., Ph.D. (DIFS FIT BUT)
Borko Simeon, Ing. (FIT BUT)
Štourač Jan (LL)
Prokop Zbyněk, doc. RnDr., Ph.D. (LL)
Bednář David, Mgr. (LL)
Zendulka Jaroslav, doc. Ing., CSc. (DIFS FIT BUT)
Martínek Tomáš, doc. Ing., Ph.D. (DCSY FIT BUT)
Damborský Jiří, prof. Mgr., Dr. (LL)
Keywords

computational characterization, enzyme mining, enzyme diversity, novel biocatalysts

Abstract

Millions of protein sequences are being discovered at an incredible pace, representing an inexhaustible source of biocatalysts. Despite genomic databases growing exponentially, classical biochemical characterization techniques are time-demanding, cost-ineffective and low-throughput. Therefore, computational methods are being developed to explore the unmapped sequence space efficiently. Selection of putative enzymes for biochemical characterization based on rational and robust analysis of all available sequences remains an unsolved problem. To address this challenge, we have developed EnzymeMiner - a web server for automated screening and annotation of diverse family members that enables selection of hits for wet-lab experiments. EnzymeMiner prioritizes sequences that are more likely to preserve the catalytic activity and are heterologously expressible in a soluble form in Escherichia coli. The solubility prediction employs the in-house SoluProt predictor developed using machine learning. EnzymeMiner reduces the time devoted to data gathering, multi-step analysis, sequence prioritization and selection from days to hours. The successful use case for the haloalkane dehalogenase family is described in a comprehensive tutorial available on the EnzymeMiner web page. EnzymeMiner is a universal tool applicable to any enzyme family that provides an interactive and easy-to-use web interface freely available at https://loschmidt.chemi.muni.cz/enzymeminer/.

Published
2020
Pages
104-109
Journal
Nucleic Acids Research, vol. 48, no. 1, ISSN 1362-4962
Publisher
Oxford University Press
DOI
10.1093/nar/gkaa372
UT WoS
000562474100017
EID Scopus
2-s2.0-85085984246
BibTeX 
@ARTICLE{FITPUB12197,
   author = "Ji\v{r}\'{i} Hon and Simeon Borko and Jan \v{S}toura\v{c} and Zbyn\v{e}k Prokop and David Bedn\'{a}\v{r} and Jaroslav Zendulka and Tom\'{a}\v{s} Mart\'{i}nek and Ji\v{r}\'{i} Damborsk\'{y}",
   title = "EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities",
   pages = "104--109",
   journal = "Nucleic Acids Research",
   volume = 48,
   number = 1,
   year = 2020,
   ISSN = "1362-4962",
   doi = "10.1093/nar/gkaa372",
   language = "english",
   url = "https://www.fit.vut.cz/research/publication/12197"
}
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