Internal force field in selected proteins

2019
journal article
article
2
cris.lastimport.wos2024-04-10T02:09:31Z
dc.abstract.enThe fuzzy oil drop model suggests that the tertiary conformation of a protein – particularly a globular one - can be likened to a spherical micelle. During the folding process, hydrophilic residues are exposed on the surface, while hydrophobic residues are retained inside the protein. The resulting hydrophobicity distribution can be mathematically modeled as a 3D Gaussian. The fuzzy oil drop model is strikingly effective in explaining the properties of type II antifreeze proteins and fast-folding proteins, as well as a vast majority of autonomous protein domains. This work aims to determine whether similar mechanisms apply to other types of nonbonding interactions. Our analysis indicates that electrostatic and van der Waals forces do not conform to the Gaussian pattern. The study involves a reference protein (titin) which shows a high agreement between the observed distribution of hydrophobicity and the theoretical (Gaussian) distribution, a selection of amyloid structures derived from the Protein Data Bank, as well as transthyretin - a protein known for its susceptibility to amyloid transformation.pl
dc.affiliationWydział Lekarski : Zakład Bioinformatyki i Telemedycynypl
dc.cm.date2020-12-02
dc.cm.id96935
dc.contributor.authorPtak-Kaczor, Magdalena - 222421 pl
dc.contributor.authorBanach, Mateusz - 103003 pl
dc.contributor.authorKonieczny, Leszekpl
dc.contributor.authorRoterman-Konieczna, Irena - 133298 pl
dc.date.accession2020-06-18pl
dc.date.accessioned2020-12-02T10:22:41Zpl
dc.date.available2020-12-02T10:22:41Zpl
dc.date.issued2019pl
dc.date.openaccess0
dc.description.accesstimew momencie opublikowania
dc.description.number4pl
dc.description.physical451-458pl
dc.description.points40pl
dc.description.versionostateczna wersja wydawcy
dc.description.volume66pl
dc.identifier.doi10.18388/abp.2019_2865pl
dc.identifier.eissn1734-154Xpl
dc.identifier.issn0001-527Xpl
dc.identifier.projectROD UJ / OPpl
dc.identifier.urihttps://ruj.uj.edu.pl/xmlui/handle/item/256515
dc.identifier.weblinkhttps://ojs.ptbioch.edu.pl/index.php/abp/article/view/2865pl
dc.languageengpl
dc.language.containerengpl
dc.rightsUdzielam licencji. Uznanie autorstwa - Na tych samych warunkach 4.0 Międzynarodowa*
dc.rights.licenceCC-BY-SA
dc.rights.urihttp://creativecommons.org/licenses/by-sa/4.0/legalcode.pl*
dc.share.typeotwarte czasopismo
dc.subject.enhydrophobicitypl
dc.subject.enamyloidpl
dc.subject.eninternal force fieldpl
dc.subject.enexternal force fieldpl
dc.subtypeArticlepl
dc.titleInternal force field in selected proteinspl
dc.title.journalActa Biochimica Polonicapl
dc.typeJournalArticlepl
dspace.entity.typePublication
cris.lastimport.wos
2024-04-10T02:09:31Z
dc.abstract.enpl
The fuzzy oil drop model suggests that the tertiary conformation of a protein – particularly a globular one - can be likened to a spherical micelle. During the folding process, hydrophilic residues are exposed on the surface, while hydrophobic residues are retained inside the protein. The resulting hydrophobicity distribution can be mathematically modeled as a 3D Gaussian. The fuzzy oil drop model is strikingly effective in explaining the properties of type II antifreeze proteins and fast-folding proteins, as well as a vast majority of autonomous protein domains. This work aims to determine whether similar mechanisms apply to other types of nonbonding interactions. Our analysis indicates that electrostatic and van der Waals forces do not conform to the Gaussian pattern. The study involves a reference protein (titin) which shows a high agreement between the observed distribution of hydrophobicity and the theoretical (Gaussian) distribution, a selection of amyloid structures derived from the Protein Data Bank, as well as transthyretin - a protein known for its susceptibility to amyloid transformation.
dc.affiliationpl
Wydział Lekarski : Zakład Bioinformatyki i Telemedycyny
dc.cm.date
2020-12-02
dc.cm.id
96935
dc.contributor.authorpl
Ptak-Kaczor, Magdalena - 222421
dc.contributor.authorpl
Banach, Mateusz - 103003
dc.contributor.authorpl
Konieczny, Leszek
dc.contributor.authorpl
Roterman-Konieczna, Irena - 133298
dc.date.accessionpl
2020-06-18
dc.date.accessionedpl
2020-12-02T10:22:41Z
dc.date.availablepl
2020-12-02T10:22:41Z
dc.date.issuedpl
2019
dc.date.openaccess
0
dc.description.accesstime
w momencie opublikowania
dc.description.numberpl
4
dc.description.physicalpl
451-458
dc.description.pointspl
40
dc.description.version
ostateczna wersja wydawcy
dc.description.volumepl
66
dc.identifier.doipl
10.18388/abp.2019_2865
dc.identifier.eissnpl
1734-154X
dc.identifier.issnpl
0001-527X
dc.identifier.projectpl
ROD UJ / OP
dc.identifier.uri
https://ruj.uj.edu.pl/xmlui/handle/item/256515
dc.identifier.weblinkpl
https://ojs.ptbioch.edu.pl/index.php/abp/article/view/2865
dc.languagepl
eng
dc.language.containerpl
eng
dc.rights*
Udzielam licencji. Uznanie autorstwa - Na tych samych warunkach 4.0 Międzynarodowa
dc.rights.licence
CC-BY-SA
dc.rights.uri*
http://creativecommons.org/licenses/by-sa/4.0/legalcode.pl
dc.share.type
otwarte czasopismo
dc.subject.enpl
hydrophobicity
dc.subject.enpl
amyloid
dc.subject.enpl
internal force field
dc.subject.enpl
external force field
dc.subtypepl
Article
dc.titlepl
Internal force field in selected proteins
dc.title.journalpl
Acta Biochimica Polonica
dc.typepl
JournalArticle
dspace.entity.type
Publication

* The migration of download and view statistics prior to the date of April 8, 2024 is in progress.

Views
21
Views per month
Views per city
Chandler
4
Dublin
3
Wroclaw
3
Ashburn
2
Cambridge
1
Kolkata
1
Krakow
1
Osaka
1
Downloads
ptak-kaczor_banach_roterman-konieczna_et-al_internal_force_field_in_selected_proteins_2019.pdf
1