The amyloid as a ribbon-like micelle in contrast to spherical micelles represented by globular proteins

2019
journal article
article
13
dc.abstract.enSelected amyloid structures available in the Protein Data Bank have been subjected to a comparative analysis. Classification is based on the distribution of hydrophobicity in amyloids that differ with respect to sequence, chain length, the distribution of beta folds, protofibril structure, and the arrangement of protofibrils in each superfibril. The study set includes the following amyloids: $A\beta$ (1-42), which is listed as $A\beta$ (15-40) and carries the D23N mutation, and $A\beta$ (11-42) and $A\beta$ (1-40), both of which carry the $E22\Delta$ mutation, tau amyloid, and $\alpha$-synuclein. Based on the fuzzy oil drop model (FOD), we determined that, despite their conformational diversity, all presented amyloids adopt a similar structural pattern that can be described as a ribbon-like micelle. The same model, when applied to globular proteins, results in structures referred to as "globular micelles," emerging as a result of interactions between the proteins' constituent residues and the aqueous solvent. Due to their composition, amyloids are unable to attain entropically favorable globular forms and instead attempt to limit contact between hydrophobic residues and water by producing elongated structures. Such structures typically contain quasi hydrophobic cores that stretch along the fibril’s long axis. Similar properties are commonly found in ribbon-like micelles, with alternating bands of high and low hydrophobicity emerging as the fibrils increase in length. Thus, while globular proteins are generally consistent with a 3D Gaussian distribution of hydrophobicity, the distribution instead conforms to a 2D Gaussian distribution in amyloid fibrils.pl
dc.affiliationWydział Lekarski : Zakład Bioinformatyki i Telemedycynypl
dc.affiliationWydział Lekarski : Zakład Biochemii Ogólnejpl
dc.cm.date2020-12-02
dc.cm.id97215
dc.contributor.authorBanach, Mateusz - 103003 pl
dc.contributor.authorKonieczny, Leszekpl
dc.contributor.authorRoterman-Konieczna, Irena - 133298 pl
dc.date.accession2019-12-30pl
dc.date.accessioned2020-12-02T10:22:47Zpl
dc.date.available2020-12-02T10:22:47Zpl
dc.date.issued2019pl
dc.date.openaccess0
dc.description.accesstimew momencie opublikowania
dc.description.number23pl
dc.description.points100pl
dc.description.versionostateczna wersja wydawcy
dc.description.volume24pl
dc.identifier.articleid4395pl
dc.identifier.doi10.3390/molecules24234395pl
dc.identifier.eissn1420-3049pl
dc.identifier.projectROD UJ / OPpl
dc.identifier.urihttps://ruj.uj.edu.pl/xmlui/handle/item/256639
dc.identifier.weblinkhttps://www.mdpi.com/1420-3049/24/23/4395pl
dc.languageengpl
dc.language.containerengpl
dc.rightsUdzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa*
dc.rights.licenceCC-BY
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/legalcode.pl*
dc.share.typeotwarte czasopismo
dc.subject.enamyloidpl
dc.subject.enfibrilpl
dc.subject.entaupl
dc.subject.ensynucleinpl
dc.subject.enhydrophobicitypl
dc.subject.enhydrophobic corepl
dc.subject.enspherical micellepl
dc.subject.enribbon-like micellepl
dc.subject.ensymmetrypl
dc.subtypeArticlepl
dc.titleThe amyloid as a ribbon-like micelle in contrast to spherical micelles represented by globular proteinspl
dc.title.journalMoleculespl
dc.typeJournalArticlepl
dspace.entity.typePublication
dc.abstract.enpl
Selected amyloid structures available in the Protein Data Bank have been subjected to a comparative analysis. Classification is based on the distribution of hydrophobicity in amyloids that differ with respect to sequence, chain length, the distribution of beta folds, protofibril structure, and the arrangement of protofibrils in each superfibril. The study set includes the following amyloids: $A\beta$ (1-42), which is listed as $A\beta$ (15-40) and carries the D23N mutation, and $A\beta$ (11-42) and $A\beta$ (1-40), both of which carry the $E22\Delta$ mutation, tau amyloid, and $\alpha$-synuclein. Based on the fuzzy oil drop model (FOD), we determined that, despite their conformational diversity, all presented amyloids adopt a similar structural pattern that can be described as a ribbon-like micelle. The same model, when applied to globular proteins, results in structures referred to as "globular micelles," emerging as a result of interactions between the proteins' constituent residues and the aqueous solvent. Due to their composition, amyloids are unable to attain entropically favorable globular forms and instead attempt to limit contact between hydrophobic residues and water by producing elongated structures. Such structures typically contain quasi hydrophobic cores that stretch along the fibril’s long axis. Similar properties are commonly found in ribbon-like micelles, with alternating bands of high and low hydrophobicity emerging as the fibrils increase in length. Thus, while globular proteins are generally consistent with a 3D Gaussian distribution of hydrophobicity, the distribution instead conforms to a 2D Gaussian distribution in amyloid fibrils.
dc.affiliationpl
Wydział Lekarski : Zakład Bioinformatyki i Telemedycyny
dc.affiliationpl
Wydział Lekarski : Zakład Biochemii Ogólnej
dc.cm.date
2020-12-02
dc.cm.id
97215
dc.contributor.authorpl
Banach, Mateusz - 103003
dc.contributor.authorpl
Konieczny, Leszek
dc.contributor.authorpl
Roterman-Konieczna, Irena - 133298
dc.date.accessionpl
2019-12-30
dc.date.accessionedpl
2020-12-02T10:22:47Z
dc.date.availablepl
2020-12-02T10:22:47Z
dc.date.issuedpl
2019
dc.date.openaccess
0
dc.description.accesstime
w momencie opublikowania
dc.description.numberpl
23
dc.description.pointspl
100
dc.description.version
ostateczna wersja wydawcy
dc.description.volumepl
24
dc.identifier.articleidpl
4395
dc.identifier.doipl
10.3390/molecules24234395
dc.identifier.eissnpl
1420-3049
dc.identifier.projectpl
ROD UJ / OP
dc.identifier.uri
https://ruj.uj.edu.pl/xmlui/handle/item/256639
dc.identifier.weblinkpl
https://www.mdpi.com/1420-3049/24/23/4395
dc.languagepl
eng
dc.language.containerpl
eng
dc.rights*
Udzielam licencji. Uznanie autorstwa 4.0 Międzynarodowa
dc.rights.licence
CC-BY
dc.rights.uri*
http://creativecommons.org/licenses/by/4.0/legalcode.pl
dc.share.type
otwarte czasopismo
dc.subject.enpl
amyloid
dc.subject.enpl
fibril
dc.subject.enpl
tau
dc.subject.enpl
synuclein
dc.subject.enpl
hydrophobicity
dc.subject.enpl
hydrophobic core
dc.subject.enpl
spherical micelle
dc.subject.enpl
ribbon-like micelle
dc.subject.enpl
symmetry
dc.subtypepl
Article
dc.titlepl
The amyloid as a ribbon-like micelle in contrast to spherical micelles represented by globular proteins
dc.title.journalpl
Molecules
dc.typepl
JournalArticle
dspace.entity.type
Publication
Affiliations

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