Misprediction of Structural Disorder in Halophiles.

TitleMisprediction of Structural Disorder in Halophiles.
Publication TypeJournal Article
Year of Publication2019
AuthorsPancsa, R., D. Kovacs, and P. Tompa
JournalMolecules
Volume24
Issue3
Date Published2019 Jan 29
ISSN1420-3049
KeywordsComputational Biology, Databases, Protein, Models, Molecular, Protein Conformation, Proteins, Proteome
Abstract

Whereas the concept of intrinsic disorder derives from biophysical observations of the lack of structure of proteins or protein regions under native conditions, many of our respective concepts rest on proteome-scale bioinformatics predictions. It is established that most predictors work reliably on proteins commonly encountered, but it is often neglected that we know very little about their performance on proteins of microorganisms that thrive in environments of extreme temperature, pH, or salt concentration, which may cause adaptive sequence composition bias. To address this issue, we predicted structural disorder for the complete proteomes of different extremophile groups by popular prediction methods and compared them to those of the reference mesophilic group. While significant deviations from mesophiles could be explained by a lack or gain of disordered regions in hyperthermophiles and radiotolerants, respectively, we found systematic overprediction in the case of halophiles. Additionally, examples were collected from the Protein Data Bank (PDB) to demonstrate misprediction and to help understand the underlying biophysical principles, i.e., halophilic proteins maintain a highly acidic and hydrophilic surface to avoid aggregation in high salt conditions. Although sparseness of data on disordered proteins from extremophiles precludes the development of dedicated general predictors, we do formulate recommendations for how to address their disorder with current bioinformatics tools.

DOI10.3390/molecules24030479
Alternate JournalMolecules
PubMed ID30699990
PubMed Central IDPMC6384707
Grant ListG.0029.12 / / Fonds Wetenschappelijk Onderzoek /
PREMIUM-2017-48 / / Magyar Tudományos Akadémia /
K124670 / / Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal /
FK128133 / / Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal /
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