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

Overview

Journal Membranes (Basel)

Date 2022 Jan 21

PMID 35054576

Authors

Irena Roterman

Katarzyna Stapor

Krzysztof Gadek

Tomasz Gubala

Piotr Nowakowski

Piotr Fabian

Leszek Konieczny

Affiliations

Soon will be listed here.

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.

Citing Articles

External Force Field for Protein Folding in Chaperonins-Potential Application in Protein Folding.

Roterman I, Stapor K, Dulak D, Konieczny L ACS Omega. 2024; 9(16):18412-18428.

PMID: 38680295 PMC: 11044213. DOI: 10.1021/acsomega.4c00409.

Model of the external force field for the protein folding process-the role of prefoldin.

Roterman I, Stapor K, Konieczny L Front Chem. 2024; 12:1342434.

PMID: 38595701 PMC: 11002104. DOI: 10.3389/fchem.2024.1342434.

Hydrophobicity-Based Force Field In Enzymes.

Roterman I, Konieczny L, Stapor K, Slupina M ACS Omega. 2024; 9(7):8188-8203.

PMID: 38405467 PMC: 10882594. DOI: 10.1021/acsomega.3c08728.

Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone.

Roterman I, Stapor K, Konieczny L BMC Bioinformatics. 2023; 24(1):418.

PMID: 37932669 PMC: 10629080. DOI: 10.1186/s12859-023-05545-0.

Engagement of intrinsic disordered proteins in protein-protein interaction.

Roterman I, Stapor K, Konieczny L Front Mol Biosci. 2023; 10:1230922.

PMID: 37583961 PMC: 10423874. DOI: 10.3389/fmolb.2023.1230922.

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