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

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

doi:10.3390/membranes12010050

Leszek Konieczny, Piotr Fabian + Show 5 more

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https://doi.org/10.3390/membranes12010050

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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.

Highlights

The aquatic environment is a natural environment for proteins and one that conditions biological activity
A distinction is made between small conductance mechanosensitive channels (MscS) and large ones (MscL) [6,7,8]
The characteristics of the HpMscS and EcMscS proteins are presented in Table 2, wherein the values of the RD and K parameters are given

Summary

Introduction

The aquatic environment is a natural environment for proteins and one that conditions biological activity. The vast majority of proteins are water-soluble proteins. Another important environment is that of the cell membrane, the characteristics of which (high hydrophobicity) are radically different to those of polar water. An increased transport of water towards environments with higher osmotic pressure can be observed. Such increased transport can result in cell rupture. This process is controlled by proteins called Conductance Mechanosensitive Ion Channels (Msc) [1,2,3,4,5]. A distinction is made between small conductance mechanosensitive channels (MscS) and large ones (MscL) [6,7,8]

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