Abstract
β-barrel membrane proteins have several important biological functions, including transporting water and solutes across the membrane. They are active in the highly hydrophobic environment of the lipid membrane, as opposed to soluble proteins, which function in a more polar, aqueous environment. Globular soluble proteins typically have a hydrophobic core and a polar surface that interacts favorably with water. In the fuzzy oil drop (FOD) model, this distribution is represented by the 3D Gauss function (3DG). In contrast, membrane proteins expose hydrophobic residues on the surface, and, in the case of ion channels, the polar residues face inwards towards a central pore. The distribution of hydrophobic residues in membrane proteins can be characterized by means of 1–3DG, a complementary 3D Gauss function. Such an analysis was carried out on the transmembrane proteins of bacteria, which, despite the considerable similarities of their super-secondary structure (β-barrel), have highly differentiated properties in terms of stabilization based on hydrophobic interactions. The biological activity and substrate specificity of these proteins are determined by the distribution of the polar and nonpolar amino acids. The present analysis allowed us to compare the ways in which the different proteins interact with antibiotics and helped us understand their relative importance in the development of the resistance mechanism. We showed that beta barrel membrane proteins with a hydrophobic core interact less strongly with the molecules they transport.
Highlights
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The present analysis indicates that, based on the hydrophobicity distribution characteristics, no barrier exists in the transport of antibiotics through the BamA pore (PDB: 6FSU, 4K3C, and 4N75)
The present analysis aimed to demonstrate the validity of the modifications made to the fuzzy oil drop (FOD) model that take into account the influence of a hydrophobic environmental factor
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Introduction β-barrel transmembrane proteins are expressed in the outer membrane of bacterial cells Since mutations in these proteins have been implicated in conferring antibiotic resistance, knowledge of their structures and functions is important for the development of clinical therapies [1,2,3]. A molecular understanding of how drug molecules pass through the channels in this membrane is essential when endeavoring to develop new therapeutic compounds [21,22,23,24,25] The analysis of this phenomenon at the molecular level focuses on the mechanism involved in the penetration of the designed antibiotic into the transmembrane channels. The subject of the current analysis is a set of bacterial proteins from the OmpX group We focused on their structures, characterized by the presence of regular beta-barrels, analyzing their adaptation to the hydrophobic environment of the membrane and preparation for the transport of various molecules. The fuzzy oil drop model has been proven to be a suitable platform for the evaluation and structural–functional characterization of transmembrane proteins
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