Fully Automated Ancestral Sequence Reconstruction using FireProtASR
Jazyk angličtina Země Spojené státy americké Médium print
Typ dokumentu časopisecké články
Grantová podpora
CZ.02.1.01/0.0/0.0/16_026/0008451
Czech Ministry of Education
20-15915Y
Czech Grant Agency
TH02010219
Technology Agency of Czech Republic
FIT-S-20-6293
Brno University of Technology
814418
European Commission
722610
European Commission
PubMed
33524240
DOI
10.1002/cpz1.30
Knihovny.cz E-zdroje
- Klíčová slova
- ancestral sequence reconstruction, automation, protein engineering, protein evolution, thermostability,
- MeSH
- fylogeneze MeSH
- molekulární evoluce * MeSH
- proteiny * genetika MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- proteiny * MeSH
Protein evolution and protein engineering techniques are of great interest in basic science and industrial applications such as pharmacology, medicine, or biotechnology. Ancestral sequence reconstruction (ASR) is a powerful technique for probing evolutionary relationships and engineering robust proteins with good thermostability and broad substrate specificity. The following protocol describes the setting up and execution of an automated FireProtASR workflow using a dedicated web site. The service allows for inference of ancestral proteins automatically, from a single protein sequence. Once a protein sequence is submitted, the server will build a dataset of homology sequences, perform a multiple sequence alignment (MSA), build a phylogenetic tree, and reconstruct ancestral nodes. The protocol is also highly flexible and allows for multiple forms of input, advanced settings, and the ability to start jobs from: (i) a single sequence, (ii) a set of homologous sequences, (iii) an MSA, and (iv) a phylogenetic tree. This approach automates all necessary steps and offers a way for novices with limited exposure to ASR techniques to improve the properties of a protein of interest. The technique can even be used to introduce catalytic promiscuity into an enzyme. A web server for accessing the fully automated workflow is freely accessible at https://loschmidt.chemi.muni.cz/fireprotasr/. © 2021 Wiley Periodicals LLC. Basic Protocol: ASR using the Web Server FireProtASR.
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