New insights into disordered proteins and regions according to the FOD-M model

Irena Roterman; Katarzyna Stapor; Piotr Fabian; Leszek Konieczny

doi:10.1371/journal.pone.0275300

New insights into disordered proteins and regions according to the FOD-M model

PLoS One. 2022 Oct 10;17(10):e0275300. doi: 10.1371/journal.pone.0275300. eCollection 2022.

Authors

Irena Roterman¹, Katarzyna Stapor², Piotr Fabian³, Leszek Konieczny⁴

Affiliations

¹ Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Kraków, Poland.
² Faculty of Automatic, Department of Applied Informatics, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.
³ Faculty of Automatic, Electronics and Computer Science, Department of Algorithmics and Software, Silesian University of Technology, Gliwice, Poland.
⁴ Chair of Medical Biochemistry, Jagiellonian University, Medical College, Kraków, Poland.

Abstract

A collection of intrinsically disordered proteins (IDPs) having regions with the status of intrinsically disordered (IDR) according to the Disprot database was analyzed from the point of view of the structure of hydrophobic core in the structural unit (chain / domain). The analysis includes all the Homo Sapiens as well as Mus Musculus proteins present in the DisProt database for which the structure is available. In the analysis, the fuzzy oil drop modified model (FOD-M) was used, taking into account the external force field, modified by the presence of other factors apart from polar water, influencing protein structuring. The paper presents an alternative to secondary-structure-based classification of intrinsically disordered regions (IDR). The basis of our classification is the ordering of hydrophobic core as calculated by the FOD-M model resulting in FOD-ordered or FOD-unordered IDRs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Humans
Hydrophobic and Hydrophilic Interactions
Intrinsically Disordered Proteins* / chemistry
Mice
Protein Conformation
Protein Structure, Secondary
Water

Substances

Intrinsically Disordered Proteins
Water

Grants and funding

This research was funded by Jagiellonian University Medical College grant number N41/DBS/000722. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.