Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy

Fabian, Piotr; Stąpor, Katarzyna; Banach, Mateusz; Ptak-Kaczor, Magdalena; Konieczny, Leszek; Roterman, Irena

doi:10.3390/sym12020273

Cited by 8 publications

(7 citation statements)

References 67 publications

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“…The early stage model was described in detail in [33,[36][37][38][39]. To make the interpretation of results easier the basic elements of this model is given.…”

Section: Early Stage Model-structural Codesmentioning

confidence: 99%

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Structure of the Hydrophobic Core Determines the 3D Protein Structure—Verification by Single Mutation Proteins

et al. 2020

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Four de novo proteins differing in single mutation positions, with a chain length of 56 amino acids, represent diverse 3D structures: monomeric 3α and 4β + α folds. The reason for this diversity is seen in the different structure of the hydrophobic core as a result of synergy leading to the generation of a system in which the polypeptide chain as a whole participates. On the basis of the fuzzy oil drop model, where the structure of the hydrophobic core is expressed by means of the hydrophobic distribution function in the form of a 3D Gaussian distribution, it has been shown that the composition of the hydrophobic core in these two structural forms is different. In addition, the use of a model to determine the structure of the early intermediate in the folding process allows to indicate differences in the polypeptide chain geometry, which, combined with the construction of a common hydrophobic nucleus as an effect of specific synergy, may indicate the reason for the diversity of the folding process of the polypeptide chain. The results indicate the need to take into account the presence of an external force field originating from the water environment and that its active impact on the formation of a hydrophobic core whose participation in the stabilization of the tertiary structure is fundamental.

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“…The early stage model was described in detail in [33,[36][37][38][39]. To make the interpretation of results easier the basic elements of this model is given.…”

Section: Early Stage Model-structural Codesmentioning

confidence: 99%

“…Analysis of these proteins based on the characteristics of the hydrophobic core form reveals the possibility of alternative organization of the central core [33].…”

Section: Introductionmentioning

confidence: 99%

Structure of the Hydrophobic Core Determines the 3D Protein Structure—Verification by Single Mutation Proteins

et al. 2020

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“…After normalizing both these distributions, it becomes possible to compare them to determine the differences between them. For this purpose, Kullback-Leibler divergence entropy was used [28].…”

Section: Introductionmentioning

confidence: 99%

The Structure of Amyloid Versus the Structure of Globular Proteins

Fabian

Banach

Stąpor

et al. 2020

IJMS

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The issue of changing the structure of globular proteins into an amyloid form is in the focus of researchers' attention. Numerous experimental studies are carried out, and mathematical models to define the essence of amyloid transformation are sought. The present work focuses on the issue of the hydrophobic core structure in amyloids. The form of ordering the hydrophobic core in globular proteins is described by a 3D Gaussian distribution analog to the distribution of hydrophobicity in a spherical micelle. Amyloid fibril is a ribbon-like micelle made up of numerous individual chains, each representing a flat structure. The distribution of hydrophobicity within a single chain included in the fibril describes the 2D Gaussian distribution. Such a description expresses the location of polar residues on a circle with a center with a high level of hydrophobicity. The presence of this type of order in the amyloid forms available in Preotin Data Bank (PDB) (both in proto- and superfibrils) is demonstrated in the present work. In this system, it can be assumed that the amyloid transformation is a chain transition from 3D Gauss ordering to 2D Gauss ordering. This means changing the globular structure to a ribbon-like structure. This observation can provide a simple mathematical model for simulating the amyloid transformation of proteins.

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“…The structural analysis described below is based on the fuzzy oil drop model. As the model itself has been thoroughly described in numerous publications [ 6 , 7 ], we will restrict ourselves to a recapitulation of its core concepts, enabling interpretation of the presented results.…”

Section: Methodsmentioning

confidence: 99%

Structure and Location of Protein Sites Binding Self-Associated Congo Red Molecules with Intercalated Drugs as Compact Ligands—Theoretical Studies

et al. 2021

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In the search for new carriers capable of transporting toxic drugs to a target, particular attention has been devoted to supramolecular systems with a ribbon-like micellar structure of which Congo red is an example. A special promise of the possible use of such systems for directing drugs to a target emerges from their particular affinity to immune complexes and as an independent property, binding many organic compounds including drugs by intercalation. Serum albumin also appeared able to bind micellar particles of such systems. It may protect them against dilution in transport. The mathematical tool, which relies on analysis of the distribution of polarity and hydrophobicity in protein molecules (fuzzy oil drop model), has been used to find the location of binding area in albumin as well as anchorage site for Congo red in heated IgG light chain used as a model presenting immunoglobulin-like structures. Results confirm the suggested formerly binding site of Congo red in V domain of IgG light chain and indicated the cleft between pseudo-symmetric domains of albumin as the area of attachment for the dye.

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Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy

Cited by 8 publications

References 67 publications

Structure of the Hydrophobic Core Determines the 3D Protein Structure—Verification by Single Mutation Proteins

Structure of the Hydrophobic Core Determines the 3D Protein Structure—Verification by Single Mutation Proteins

The Structure of Amyloid Versus the Structure of Globular Proteins

Structure and Location of Protein Sites Binding Self-Associated Congo Red Molecules with Intercalated Drugs as Compact Ligands—Theoretical Studies

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