Model of Environmental Membrane Field for Transmembrane Proteins.

Irena Roterman,Piotr Fabian,Mateusz Banach,Katarzyna Stapor,Leszek Konieczny

doi:10.3390/ijms22073619

Abstract

The water environment determines the activity of biological processes. The role of such an environment interpreted in the form of an external field expressed by the 3D Gaussian distribution in the fuzzy oil drop model directs the folding process towards the generation of a centrally located hydrophobic core with the simultaneous exposure of polar residues on the surface. In addition to proteins soluble in the water environment, there is a significant group of membrane proteins that act as receptors or channels, including ion channels in particular. The change of the polar (water) environment into a highly hydrophobic (membrane) environment is quite radical, resulting in a different hydrophobicity distribution within the membrane protein. Modification of the notation of the force field expressing the presence of the hydrophobic environment has been proposed in this work. A modified fuzzy oil drop model with its adaptation to membrane proteins was used to interpret the structure of membrane proteins–mechanosensitive channel. The modified model was also used to describe the so-called negative cases—i.e., for water-soluble proteins with a clear distribution consistent with the fuzzy oil drop model.

Highlights

The purpose of the analysis presented here is to assess the diversity of hydrophobicity distributions in proteins consisting of two parts: anchored in the membrane and exposed to the cytoplasmic space
The small-conductance mechanosensitive channel protein—MscS (PDB ID 2VV5) is the subject of a thorough analysis focused on the application of the FOD-M model to describe the structure of the membrane ion channel as an example of “reverse” hydrophobicity distribution versus micelle-like degradation
The modifications to the fuzzy oil drop model have been positively verified by introducing a supplement that takes into account the presence of a non-polar environment

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. The level of protein solubility depends on the exposure of polar residues to the protein surface. The concept of a hydrophobic core is associated with the central concentration of hydrophobic residues with the simultaneous exposure of polar residues on the surface [1]. Even a single mutation—especially changing the local level of hydrophobicity/polarity—

Methods

Results

Discussion

Conclusion