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Open AccessArticle

The Structure of Amyloid Versus the Structure of Globular Proteins

1
Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
2
Department of Bioinformatics and Telemedicine, Jagiellonian University – Medical College, Lazarza 16, 31-533 Kraków, Poland
3
Chair of Medical Biochemistry – Jagiellonian University – Medical College, Kopernika 7, 31-034 Kraków, Poland
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(13), 4683; https://doi.org/10.3390/ijms21134683
Received: 15 May 2020 / Revised: 21 June 2020 / Accepted: 27 June 2020 / Published: 30 June 2020
(This article belongs to the Special Issue Structural Biology of Proteins and Peptides)
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. View Full-Text
Keywords: amyloids; hydrophobic core; synergy; external force field; entropy amyloids; hydrophobic core; synergy; external force field; entropy
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Fabian, P.; Banach, M.; Stapor, K.; Konieczny, L.; Ptak-Kaczor, M.; Roterman, I. The Structure of Amyloid Versus the Structure of Globular Proteins. Int. J. Mol. Sci. 2020, 21, 4683.

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