Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins

Roterman, Irena; Stapor, Katarzyna; Gądek, Krzysztof; Gubała, Tomasz; Nowakowski, Piotr; Fabian, Piotr; Konieczny, Leszek

doi:10.3390/membranes12010050

Open AccessArticle

Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins

by

Irena Roterman

^1,*

,

Katarzyna Stapor

²

,

Krzysztof Gądek

³,

Tomasz Gubała

³,

Piotr Nowakowski

³,

Piotr Fabian

⁴

and

Leszek Konieczny

⁵

¹

Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Medyczna 7, 30-688 Krakow, Poland

²

Department of Applied Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland

³

Sano Centre for Computation Medicine, Czarnowiejska 36, 30-054 Kraków, Poland

⁴

Department of Algorithmics and Software, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland

⁵

Chair of Medical biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland

^*

Author to whom correspondence should be addressed.

Membranes 2022, 12(1), 50; https://doi.org/10.3390/membranes12010050

Submission received: 16 November 2021 / Revised: 13 December 2021 / Accepted: 28 December 2021 / Published: 30 December 2021

(This article belongs to the Special Issue Membrane Biological Function in Health and Disease)

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Abstract

The natural environment of proteins is the polar aquatic environment and the hydrophobic (amphipathic) environment of the membrane. The fuzzy oil drop model (FOD) used to characterize water-soluble proteins, as well as its modified version FOD-M, enables a mathematical description of the presence and influence of diverse environments on protein structure. The present work characterized the structures of membrane proteins, including those that act as channels, and a water-soluble protein for contrast. The purpose of the analysis was to verify the possibility that an external force field can be used in the simulation of the protein-folding process, taking into account the diverse nature of the environment that guarantees a structure showing biological activity.

Keywords: membrane proteins; hydrophobicity; hydrophobic core; MscS; mechanosensitive channels; efflux in bacteria; MsbA

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MDPI and ACS Style

Roterman, I.; Stapor, K.; Gądek, K.; Gubała, T.; Nowakowski, P.; Fabian, P.; Konieczny, L. Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins. Membranes 2022, 12, 50. https://doi.org/10.3390/membranes12010050

AMA Style

Roterman I, Stapor K, Gądek K, Gubała T, Nowakowski P, Fabian P, Konieczny L. Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins. Membranes. 2022; 12(1):50. https://doi.org/10.3390/membranes12010050

Chicago/Turabian Style

Roterman, Irena, Katarzyna Stapor, Krzysztof Gądek, Tomasz Gubała, Piotr Nowakowski, Piotr Fabian, and Leszek Konieczny. 2022. "Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins" Membranes 12, no. 1: 50. https://doi.org/10.3390/membranes12010050

APA Style

Roterman, I., Stapor, K., Gądek, K., Gubała, T., Nowakowski, P., Fabian, P., & Konieczny, L. (2022). Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins. Membranes, 12(1), 50. https://doi.org/10.3390/membranes12010050

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

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Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins

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