Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design.
evolution
protein design
protein fragments
protein recombination
Journal
Journal of molecular biology
ISSN: 1089-8638
Titre abrégé: J Mol Biol
Pays: Netherlands
ID NLM: 2985088R
Informations de publication
Date de publication:
12 06 2020
12 06 2020
Historique:
received:
23
12
2019
revised:
12
04
2020
accepted:
13
04
2020
pubmed:
25
4
2020
medline:
29
12
2020
entrez:
25
4
2020
Statut:
ppublish
Résumé
Natural evolution has generated an impressively diverse protein universe via duplication and recombination from a set of protein fragments that served as building blocks. The application of these concepts to the design of new proteins using subdomain-sized fragments from different folds has proven to be experimentally successful. To better understand how evolution has shaped our protein universe, we performed an all-against-all comparison of protein domains representing all naturally existing folds and identified conserved homologous protein fragments. Overall, we found more than 1000 protein fragments of various lengths among different folds through similarity network analysis. These fragments are present in very different protein environments and represent versatile building blocks for protein design. These data are available in our web server called F(old P)uzzle (fuzzle.uni-bayreuth.de), which allows to individually filter the dataset and create customized networks for folds of interest. We believe that our results serve as an invaluable resource for structural and evolutionary biologists and as raw material for the design of custom-made proteins.
Identifiants
pubmed: 32330481
pii: S0022-2836(20)30300-4
doi: 10.1016/j.jmb.2020.04.013
pmc: PMC7322520
pii:
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3898-3914Informations de copyright
Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.
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