The Structure of Amyloid Versus the Structure of Globular Proteins
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 th...
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MDPI AG
2020-06-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/13/4683 |
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| author | Piotr Fabian Mateusz Banach Katarzyna Stapor Leszek Konieczny Magdalena Ptak-Kaczor Irena Roterman |
| author_facet | Piotr Fabian Mateusz Banach Katarzyna Stapor Leszek Konieczny Magdalena Ptak-Kaczor Irena Roterman |
| author_sort | Piotr Fabian |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T18:46:16Z |
| format | Article |
| id | doaj.art-3d09fbc79f24445b9b5993e757b75d08 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T18:46:16Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-3d09fbc79f24445b9b5993e757b75d082023-11-20T05:29:51ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-06-012113468310.3390/ijms21134683The Structure of Amyloid Versus the Structure of Globular ProteinsPiotr Fabian0Mateusz Banach1Katarzyna Stapor2Leszek Konieczny3Magdalena Ptak-Kaczor4Irena Roterman5Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, PolandDepartment of Bioinformatics and Telemedicine, Jagiellonian University – Medical College, Lazarza 16, 31-533 Kraków, PolandInstitute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, PolandChair of Medical Biochemistry – Jagiellonian University – Medical College, Kopernika 7, 31-034 Kraków, PolandDepartment of Bioinformatics and Telemedicine, Jagiellonian University – Medical College, Lazarza 16, 31-533 Kraków, PolandDepartment of Bioinformatics and Telemedicine, Jagiellonian University – Medical College, Lazarza 16, 31-533 Kraków, PolandThe 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.https://www.mdpi.com/1422-0067/21/13/4683amyloidshydrophobic coresynergyexternal force fieldentropy |
| spellingShingle | Piotr Fabian Mateusz Banach Katarzyna Stapor Leszek Konieczny Magdalena Ptak-Kaczor Irena Roterman The Structure of Amyloid Versus the Structure of Globular Proteins International Journal of Molecular Sciences amyloids hydrophobic core synergy external force field entropy |
| title | The Structure of Amyloid Versus the Structure of Globular Proteins |
| title_full | The Structure of Amyloid Versus the Structure of Globular Proteins |
| title_fullStr | The Structure of Amyloid Versus the Structure of Globular Proteins |
| title_full_unstemmed | The Structure of Amyloid Versus the Structure of Globular Proteins |
| title_short | The Structure of Amyloid Versus the Structure of Globular Proteins |
| title_sort | structure of amyloid versus the structure of globular proteins |
| topic | amyloids hydrophobic core synergy external force field entropy |
| url | https://www.mdpi.com/1422-0067/21/13/4683 |
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