Model of Environmental Membrane Field for Transmembrane Proteins

Roterman, Irena; Stąpor, Katarzyna; Fabian, Piotr; Konieczny, Leszek; Banach, Mateusz

doi:10.3390/ijms22073619

Cited by 21 publications

(39 citation statements)

References 40 publications

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“…The simulation of the protein-folding process should be performed in an environment expressed by the distribution of 3DG and in an environment that gradually changes through an increase in the K value. As shown in [ 37 , 49 ], the K value turns out to be specific for a given protein. Further analysis of proteins for the corresponding K parameter value is performed on a large database.…”

Section: Discussionmentioning

confidence: 99%

“…It expresses the inverse distribution to the system observed in soluble proteins. This is the case with membrane proteins which additionally play the role of ion channels, where apart from the exposure of the hydrophobic surface (directed towards the environment of the membrane), polar residues forming the surface of the channel are located in the center [ 37 ].…”

Section: Introductionmentioning

confidence: 99%

“…The degree of mismatch in the hydrophobicity distribution in the protein may suggest the participation of factors involved in the process of shaping the structure of a given protein. Such a consensus, expressed in the quantitative contribution of the polar environment and the opposite to polar environment, was applied to the exemplary membrane proteins serving as the ion channel and to proteins of different status [ 37 ]. Generally speaking, such a quantitative assessment of the differences between the idealized (3DG) distribution and that observed in the protein (the result of inter-amino-acid interactions) allows speculation about the participation of a factor other than water in the process of shaping the structure.…”

Section: Introductionmentioning

confidence: 99%

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In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model

Roterman

Stąpor

Fabian

et al. 2021

IJMS

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The role of the environment in amyloid formation based on the fuzzy oil drop model (FOD) is discussed here. This model assumes that the hydrophobicity distribution within a globular protein is consistent with a 3D Gaussian (3DG) distribution. Such a distribution is interpreted as the idealized effect of the presence of a polar solvent—water. A chain with a sequence of amino acids (which are bipolar molecules) determined by evolution recreates a micelle-like structure with varying accuracy. The membrane, which is a specific environment with opposite characteristics to the polar aquatic environment, directs the hydrophobic residues towards the surface. The modification of the FOD model to the FOD-M form takes into account the specificity of the cell membrane. It consists in “inverting” the 3DG distribution (complementing the Gaussian distribution), which expresses the exposure of hydrophobic residues on the surface. It turns out that the influence of the environment for any protein (soluble or membrane-anchored) is the result of a consensus factor expressing the participation of the polar environment and the “inverted” environment. The ratio between the proportion of the aqueous and the “reversed” environment turns out to be a characteristic property of a given protein, including amyloid protein in particular. The structure of amyloid proteins has been characterized in the context of prion, intrinsically disordered, and other non-complexing proteins to cover a wider spectrum of molecules with the given characteristics based on the FOD-M model.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model

Roterman

Stąpor

Fabian

et al. 2021

IJMS

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“…Both the fuzzy oil drop model (FOD) and its modified form (FOD-M), which takes into account the influence of the nonpolar environment on the membrane protein structure, have been presented in numerous papers [ 26 , 39 , 40 , 41 ]. The short model description provided here is intended to facilitate the interpretation of the presented results.…”

Section: Methodsmentioning

confidence: 99%

“…The aim of the study is to demonstrate the applicability of the fuzzy oil drop model as a tool for analyzing transmembrane proteins that act as transport channels not only for the various compounds necessary for the life of bacteria but also for potential drugs in the form of antibiotics. The set of proteins in question include examples of various structures, structural forms, and the role of bacteria, although proteins with the helical transmembrane part are discussed in reference [ 26 ]. Here, only one representative of this group is discussed.…”

Section: Introductionmentioning

confidence: 99%

The Functional Significance of Hydrophobic Residue Distribution in Bacterial Beta-Barrel Transmembrane Proteins

et al. 2021

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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.

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New insights on the catalytic center of proteins from peptidylprolyl isomerase group based on the FOD‐M model

Roterman

Stąpor

Konieczny

2023

J of Cellular Biochemistry

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Generating the structure of the hydrophobic core is based on the orientation of hydrophobic residues towards the central part of the protein molecule with the simultaneous exposure of polar residues. Such a course of the protein folding process takes place with the active participation of the polar water environment. While the self‐assembly process leading to the formation of micelles concerns freely moving bi‐polar molecules, bipolar amino acids in polypeptide chain have limited mobility due to the covalent bonds. Therefore, proteins form a more or less perfect micelle‐like structure. The criterion is the hydrophobicity distribution, which to a greater or lesser extent reproduces the distribution expressed by the 3D Gaussian function on the protein body. The vast majority of proteins must ensure solubility, so a certain part of it—as it is expected—should reproduce the structuring of micelles. The biological activity of proteins is encoded in the part that does not reproduce the micelle‐like system. The location and quantitative assessment of the contribution of orderliness to disorder is of critical importance for the determination of biological activity. The form of maladjustment to the 3D Gauss function may be varied—hence the obtained high diversity of specific interactions with strictly defined molecules: ligands or substrates. The correctness of this interpretation was verified on the basis of the group of enzymes Peptidylprolyl isomerase—E.C.5.2.1.8. In proteins representing this class of enzymes, zones responsible for solubility—micelle‐like hydrophobicity system—the location and specificity of the incompatible part in which the specific activity of the enzyme is located and coded were identified. The present study showed that the enzymes of the discussed group show two different schemes of the structure of catalytic center (taking into account the status as defined by the fuzzy oil drop model).

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Model of Environmental Membrane Field for Transmembrane Proteins

Cited by 21 publications

References 40 publications

In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model

In Silico Modeling of the Influence of Environment on Amyloid Folding Using FOD-M Model

The Functional Significance of Hydrophobic Residue Distribution in Bacterial Beta-Barrel Transmembrane Proteins

New insights on the catalytic center of proteins from peptidylprolyl isomerase group based on the FOD‐M model

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